Starting phenix.real_space_refine on Thu May 1 06:17:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xs0_38612/05_2025/8xs0_38612.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xs0_38612/05_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_38612/05_2025/8xs0_38612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xs0_38612/05_2025/8xs0_38612.map" model { file = "/net/cci-nas-00/data/ceres_data/8xs0_38612/05_2025/8xs0_38612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xs0_38612/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 6.33, per 1000 atoms: 0.61 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: 2.37 Conformation dependent library (CDL) restraints added in 1.3 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: 1.13 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: 3.55 Time building geometry restraints manager: 2.86 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: 0.890 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.260 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.400 ------------------------------------------------------------------------------- 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= 0.203 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 Details of bonding type rmsd hydrogen bonds : bond 0.14741 ( 644) hydrogen bonds : angle 5.49981 ( 1845) covalent geometry : bond 0.00434 (10616) covalent geometry : angle 0.83892 (14517) *********************** 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 : 1.301 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: 0.1942 time to fit residues: 57.2729 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 : 1.064 ------------------------------------------------------------------------------- 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 = 0.152500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.110513 restraints weight = 20034.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108583 restraints weight = 16653.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108873 restraints weight = 12852.815| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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= 0.175 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 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 644) hydrogen bonds : angle 4.68115 ( 1845) covalent geometry : bond 0.00386 (10616) covalent geometry : angle 0.76304 (14517) *********************** 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 : 1.178 Fit side-chains REVERT: A 56 ARG cc_start: 0.7596 (ptt180) cc_final: 0.7341 (tmm-80) REVERT: A 248 LYS cc_start: 0.9613 (mmpt) cc_final: 0.9395 (mmmt) REVERT: A 377 TYR cc_start: 0.6351 (p90) cc_final: 0.5094 (p90) REVERT: A 378 MET cc_start: 0.7625 (mmp) cc_final: 0.6848 (mmm) REVERT: B 437 SER cc_start: 0.9144 (t) cc_final: 0.8896 (t) REVERT: B 589 LEU cc_start: 0.8350 (mp) cc_final: 0.8100 (mp) outliers start: 29 outliers final: 17 residues processed: 183 average time/residue: 0.1925 time to fit residues: 52.2702 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 : 1.088 ------------------------------------------------------------------------------- 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: 0.2980 chunk 113 optimal weight: 0.9990 chunk 116 optimal weight: 40.0000 chunk 15 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.155092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114860 restraints weight = 20330.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111224 restraints weight = 16072.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.112199 restraints weight = 14183.666| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1813 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= 0.141 Angle : 0.728 11.163 14517 Z= 0.362 Chirality : 0.044 0.314 1752 Planarity : 0.005 0.067 1794 Dihedral : 5.627 48.192 1475 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.51 % Favored : 88.35 % Rotamer: Outliers : 2.56 % Allowed : 15.47 % Favored : 81.97 % 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: -0.56 (0.24), residues: 1382 helix: 1.08 (0.18), residues: 829 sheet: None (None), residues: 0 loop : -2.79 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 61 HIS 0.005 0.001 HIS A 447 PHE 0.033 0.002 PHE B 224 TYR 0.026 0.001 TYR A 171 ARG 0.002 0.000 ARG B 611 Details of bonding type rmsd hydrogen bonds : bond 0.04217 ( 644) hydrogen bonds : angle 4.48298 ( 1845) covalent geometry : bond 0.00299 (10616) covalent geometry : angle 0.72772 (14517) *********************** 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 201 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 1.146 Fit side-chains REVERT: A 248 LYS cc_start: 0.9599 (mmpt) cc_final: 0.9384 (mmmt) REVERT: A 306 LYS cc_start: 0.8557 (pttp) cc_final: 0.8273 (pttp) REVERT: A 377 TYR cc_start: 0.6381 (p90) cc_final: 0.5319 (p90) REVERT: A 378 MET cc_start: 0.7613 (mmp) cc_final: 0.7064 (mmm) REVERT: A 504 PHE cc_start: 0.7581 (t80) cc_final: 0.7349 (t80) REVERT: B 231 THR cc_start: 0.8271 (p) cc_final: 0.7834 (p) REVERT: B 308 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7438 (pm20) REVERT: B 432 LEU cc_start: 0.9099 (tt) cc_final: 0.8865 (tp) REVERT: B 437 SER cc_start: 0.9056 (t) cc_final: 0.8807 (t) outliers start: 26 outliers final: 14 residues processed: 189 average time/residue: 0.1818 time to fit residues: 51.6758 Evaluate side-chains 172 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 563 MET 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 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: 20.0000 chunk 115 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 68 optimal weight: 30.0000 chunk 110 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.152015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110368 restraints weight = 20294.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.107534 restraints weight = 16550.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.108304 restraints weight = 13194.849| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10616 Z= 0.203 Angle : 0.743 10.045 14517 Z= 0.374 Chirality : 0.045 0.292 1752 Planarity : 0.005 0.066 1794 Dihedral : 5.612 48.997 1475 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.52 % Favored : 87.34 % Rotamer: Outliers : 3.65 % Allowed : 16.95 % Favored : 79.41 % 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: -0.63 (0.24), residues: 1382 helix: 1.03 (0.18), residues: 833 sheet: None (None), residues: 0 loop : -2.86 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 336 HIS 0.003 0.001 HIS A 447 PHE 0.031 0.002 PHE B 513 TYR 0.050 0.002 TYR A 171 ARG 0.005 0.000 ARG B 611 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 644) hydrogen bonds : angle 4.52926 ( 1845) covalent geometry : bond 0.00462 (10616) covalent geometry : angle 0.74294 (14517) *********************** 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 193 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: A 248 LYS cc_start: 0.9615 (mmpt) cc_final: 0.9403 (mmmt) REVERT: A 306 LYS cc_start: 0.8645 (pttp) cc_final: 0.8322 (pttp) REVERT: B 198 ASP cc_start: 0.7848 (m-30) cc_final: 0.7606 (m-30) REVERT: B 437 SER cc_start: 0.9095 (t) cc_final: 0.8801 (t) outliers start: 37 outliers final: 25 residues processed: 175 average time/residue: 0.1875 time to fit residues: 48.8644 Evaluate side-chains 173 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 381 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 574 VAL 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 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 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 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: 7.9990 chunk 135 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 120 optimal weight: 0.0050 chunk 49 optimal weight: 7.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.155467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113980 restraints weight = 19930.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.112684 restraints weight = 16034.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113463 restraints weight = 13619.693| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10616 Z= 0.138 Angle : 0.707 10.421 14517 Z= 0.350 Chirality : 0.043 0.282 1752 Planarity : 0.005 0.066 1794 Dihedral : 5.429 48.565 1475 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.42 % Favored : 89.44 % Rotamer: Outliers : 4.43 % Allowed : 17.83 % Favored : 77.73 % 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: -0.50 (0.24), residues: 1382 helix: 1.13 (0.19), residues: 836 sheet: None (None), residues: 0 loop : -2.81 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 613 HIS 0.005 0.001 HIS A 447 PHE 0.027 0.001 PHE A 513 TYR 0.043 0.001 TYR A 171 ARG 0.003 0.000 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 644) hydrogen bonds : angle 4.39722 ( 1845) covalent geometry : bond 0.00295 (10616) covalent geometry : angle 0.70733 (14517) *********************** 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 209 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 LYS cc_start: 0.8513 (pttp) cc_final: 0.8248 (pttp) REVERT: B 432 LEU cc_start: 0.9059 (tt) cc_final: 0.8833 (tp) REVERT: B 437 SER cc_start: 0.9055 (t) cc_final: 0.8775 (t) outliers start: 45 outliers final: 20 residues processed: 193 average time/residue: 0.1783 time to fit residues: 51.7126 Evaluate side-chains 171 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 71 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 chunk 112 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN A 353 ASN ** B 353 ASN ** 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 = 0.3953 r_free = 0.3953 target = 0.155205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112988 restraints weight = 20376.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.111508 restraints weight = 15488.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.112185 restraints weight = 11993.700| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10616 Z= 0.136 Angle : 0.713 10.174 14517 Z= 0.350 Chirality : 0.043 0.218 1752 Planarity : 0.005 0.065 1794 Dihedral : 5.378 48.106 1475 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.00 % Favored : 88.86 % Rotamer: Outliers : 3.74 % Allowed : 20.89 % Favored : 75.37 % 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: -0.39 (0.24), residues: 1382 helix: 1.26 (0.19), residues: 827 sheet: -0.18 (2.66), residues: 5 loop : -2.79 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 61 HIS 0.004 0.001 HIS A 447 PHE 0.046 0.002 PHE B 505 TYR 0.038 0.001 TYR A 171 ARG 0.003 0.000 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 644) hydrogen bonds : angle 4.37358 ( 1845) covalent geometry : bond 0.00297 (10616) covalent geometry : angle 0.71257 (14517) *********************** 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 200 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 306 LYS cc_start: 0.8633 (pttp) cc_final: 0.8294 (pttp) REVERT: A 351 ASN cc_start: 0.8699 (t0) cc_final: 0.8456 (t0) REVERT: A 377 TYR cc_start: 0.6473 (p90) cc_final: 0.6234 (p90) REVERT: B 437 SER cc_start: 0.9084 (t) cc_final: 0.8801 (t) outliers start: 38 outliers final: 25 residues processed: 184 average time/residue: 0.1749 time to fit residues: 48.6182 Evaluate side-chains 176 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 694 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 134 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 375 LEU 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 584 ILE Chi-restraints excluded: chain B residue 628 GLN 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: 1.9990 chunk 65 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 88 optimal weight: 0.0050 chunk 129 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 67 optimal weight: 0.0070 overall best weight: 0.5614 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.157181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117664 restraints weight = 20058.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.116185 restraints weight = 17607.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.116385 restraints weight = 14551.100| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2789 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= 0.134 Angle : 0.710 10.724 14517 Z= 0.347 Chirality : 0.043 0.291 1752 Planarity : 0.005 0.064 1794 Dihedral : 5.272 48.019 1475 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.93 % Favored : 88.93 % Rotamer: Outliers : 3.55 % Allowed : 20.99 % Favored : 75.47 % 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: -0.31 (0.24), residues: 1382 helix: 1.35 (0.19), residues: 818 sheet: -1.39 (2.95), residues: 5 loop : -2.73 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 61 HIS 0.004 0.000 HIS A 447 PHE 0.026 0.001 PHE A 513 TYR 0.034 0.001 TYR A 171 ARG 0.006 0.000 ARG B 661 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 644) hydrogen bonds : angle 4.32538 ( 1845) covalent geometry : bond 0.00289 (10616) covalent geometry : angle 0.71012 (14517) *********************** 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 198 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 49 TRP cc_start: 0.7121 (m100) cc_final: 0.6883 (m100) REVERT: A 306 LYS cc_start: 0.8528 (pttp) cc_final: 0.8204 (pttp) REVERT: A 351 ASN cc_start: 0.8576 (t0) cc_final: 0.8362 (t0) REVERT: A 377 TYR cc_start: 0.6130 (p90) cc_final: 0.5736 (p90) REVERT: A 513 PHE cc_start: 0.7010 (m-80) cc_final: 0.6532 (m-80) REVERT: B 437 SER cc_start: 0.9049 (t) cc_final: 0.8740 (t) outliers start: 36 outliers final: 27 residues processed: 181 average time/residue: 0.1811 time to fit residues: 50.3673 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 : 1.194 ------------------------------------------------------------------------------- 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 198 ASP Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 348 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 381 ILE Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 527 LEU 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: 0.7980 chunk 5 optimal weight: 0.3980 chunk 108 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 40 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.157335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.117411 restraints weight = 19803.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.115478 restraints weight = 16991.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.116438 restraints weight = 13291.669| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2958 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= 0.138 Angle : 0.723 15.833 14517 Z= 0.350 Chirality : 0.043 0.228 1752 Planarity : 0.005 0.063 1794 Dihedral : 5.232 47.781 1475 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.93 % Favored : 88.93 % Rotamer: Outliers : 3.74 % Allowed : 21.77 % Favored : 74.48 % 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: -0.33 (0.24), residues: 1382 helix: 1.29 (0.19), residues: 824 sheet: -1.38 (2.92), residues: 5 loop : -2.72 (0.26), residues: 553 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 0.002 PHE B 513 TYR 0.041 0.002 TYR A 586 ARG 0.006 0.000 ARG B 661 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 644) hydrogen bonds : angle 4.30745 ( 1845) covalent geometry : bond 0.00302 (10616) covalent geometry : angle 0.72324 (14517) *********************** 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 190 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 1.276 Fit side-chains revert: symmetry clash REVERT: A 306 LYS cc_start: 0.8519 (pttp) cc_final: 0.8218 (pttp) REVERT: A 351 ASN cc_start: 0.8582 (t0) cc_final: 0.8361 (t0) REVERT: A 378 MET cc_start: 0.7827 (mmm) cc_final: 0.7366 (mmt) REVERT: B 347 LEU cc_start: 0.8723 (tt) cc_final: 0.8158 (tp) REVERT: B 437 SER cc_start: 0.9051 (t) cc_final: 0.8725 (t) outliers start: 38 outliers final: 27 residues processed: 174 average time/residue: 0.1834 time to fit residues: 49.7194 Evaluate side-chains 177 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 348 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 627 PHE 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 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 630 VAL 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: 0.0070 chunk 127 optimal weight: 0.8980 chunk 137 optimal weight: 0.0000 chunk 123 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.7804 ------------------------------------------------------------------------------- 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 = 0.157123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.118270 restraints weight = 20158.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.116026 restraints weight = 17445.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.116507 restraints weight = 14731.802| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10616 Z= 0.143 Angle : 0.747 19.193 14517 Z= 0.359 Chirality : 0.043 0.248 1752 Planarity : 0.005 0.063 1794 Dihedral : 5.203 47.779 1475 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.71 % Favored : 89.15 % 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: -0.31 (0.24), residues: 1382 helix: 1.32 (0.19), residues: 820 sheet: -1.27 (2.91), residues: 5 loop : -2.69 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 61 HIS 0.003 0.001 HIS A 447 PHE 0.032 0.001 PHE A 416 TYR 0.031 0.001 TYR A 586 ARG 0.007 0.000 ARG B 661 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 644) hydrogen bonds : angle 4.33076 ( 1845) covalent geometry : bond 0.00318 (10616) covalent geometry : angle 0.74690 (14517) *********************** 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 192 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: A 171 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.8489 (t80) REVERT: A 351 ASN cc_start: 0.8593 (t0) cc_final: 0.8371 (t0) REVERT: A 513 PHE cc_start: 0.7067 (m-80) cc_final: 0.6492 (m-80) REVERT: A 517 TYR cc_start: 0.8559 (m-10) cc_final: 0.8130 (m-80) REVERT: B 224 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.7330 (m-80) REVERT: B 300 LYS cc_start: 0.8674 (ttmm) cc_final: 0.8200 (tppt) REVERT: B 437 SER cc_start: 0.9068 (t) cc_final: 0.8720 (t) outliers start: 33 outliers final: 27 residues processed: 177 average time/residue: 0.1805 time to fit residues: 47.8874 Evaluate side-chains 183 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 171 TYR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 348 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 575 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 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 694 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 114 optimal weight: 0.5980 chunk 135 optimal weight: 0.0060 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 60 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 22 optimal weight: 0.0970 chunk 103 optimal weight: 0.4980 chunk 28 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 chunk 136 optimal weight: 0.9980 overall best weight: 0.2994 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.159150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.119361 restraints weight = 19948.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.118563 restraints weight = 16831.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.118711 restraints weight = 12532.916| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10616 Z= 0.135 Angle : 0.764 17.221 14517 Z= 0.366 Chirality : 0.043 0.209 1752 Planarity : 0.005 0.063 1794 Dihedral : 5.177 47.264 1475 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.78 % Favored : 89.07 % Rotamer: Outliers : 3.35 % Allowed : 22.86 % Favored : 73.79 % 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: -0.22 (0.24), residues: 1382 helix: 1.30 (0.19), residues: 828 sheet: -1.37 (2.83), residues: 5 loop : -2.54 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 61 HIS 0.004 0.001 HIS A 447 PHE 0.038 0.002 PHE A 416 TYR 0.029 0.001 TYR A 171 ARG 0.007 0.000 ARG B 661 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 644) hydrogen bonds : angle 4.32742 ( 1845) covalent geometry : bond 0.00290 (10616) covalent geometry : angle 0.76423 (14517) ********************** 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 192 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 1.302 Fit side-chains revert: symmetry clash REVERT: A 171 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.8430 (t80) REVERT: A 517 TYR cc_start: 0.8500 (m-10) cc_final: 0.8095 (m-80) REVERT: B 224 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.7236 (m-80) REVERT: B 300 LYS cc_start: 0.8628 (ttmm) cc_final: 0.8317 (ptpp) REVERT: B 437 SER cc_start: 0.9052 (t) cc_final: 0.8693 (t) outliers start: 34 outliers final: 27 residues processed: 176 average time/residue: 0.1724 time to fit residues: 47.0190 Evaluate side-chains 183 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 348 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 575 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 606 TYR 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 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 630 VAL 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: 3.9990 chunk 38 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 34 optimal weight: 0.3980 chunk 122 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.157437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.116807 restraints weight = 19766.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.116496 restraints weight = 15563.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.116954 restraints weight = 12478.423| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10616 Z= 0.148 Angle : 0.753 16.671 14517 Z= 0.362 Chirality : 0.043 0.204 1752 Planarity : 0.005 0.062 1794 Dihedral : 5.203 47.376 1475 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.85 % Favored : 89.00 % Rotamer: Outliers : 3.15 % Allowed : 23.15 % Favored : 73.69 % 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: -0.17 (0.24), residues: 1382 helix: 1.34 (0.19), residues: 828 sheet: -1.13 (2.91), residues: 5 loop : -2.52 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 61 HIS 0.002 0.001 HIS A 447 PHE 0.030 0.002 PHE B 513 TYR 0.033 0.001 TYR A 171 ARG 0.007 0.000 ARG B 661 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 644) hydrogen bonds : angle 4.29792 ( 1845) covalent geometry : bond 0.00335 (10616) covalent geometry : angle 0.75260 (14517) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3518.02 seconds wall clock time: 63 minutes 22.86 seconds (3802.86 seconds total)