Starting phenix.real_space_refine on Thu Mar 13 20:55:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xlm_33284/03_2025/7xlm_33284.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xlm_33284/03_2025/7xlm_33284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xlm_33284/03_2025/7xlm_33284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xlm_33284/03_2025/7xlm_33284.map" model { file = "/net/cci-nas-00/data/ceres_data/7xlm_33284/03_2025/7xlm_33284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xlm_33284/03_2025/7xlm_33284.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 52 5.16 5 C 6090 2.51 5 N 1478 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9268 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4629 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 21, 'TRANS': 573} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 4629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4629 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 21, 'TRANS': 573} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.58, per 1000 atoms: 0.60 Number of scatterers: 9268 At special positions: 0 Unit cell: (105.439, 127.179, 100.004, 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 52 16.00 O 1648 8.00 N 1478 7.00 C 6090 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: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2232 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 2 sheets defined 58.2% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.902A pdb=" N GLY A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.948A pdb=" N GLN A 97 " --> pdb=" O PRO A 94 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TRP A 98 " --> pdb=" O VAL A 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 94 through 98' Processing helix chain 'A' and resid 108 through 121 Processing helix chain 'A' and resid 122 through 133 removed outlier: 3.888A pdb=" N ILE A 127 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 152 removed outlier: 3.615A pdb=" N TYR A 142 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 184 removed outlier: 3.550A pdb=" N GLY A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 239 removed outlier: 3.626A pdb=" N MET A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 268 removed outlier: 4.516A pdb=" N THR A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 296 Processing helix chain 'A' and resid 305 through 324 Proline residue: A 317 - end of helix removed outlier: 4.261A pdb=" N HIS A 324 " --> pdb=" O GLU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 345 removed outlier: 3.683A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.604A pdb=" N LEU A 378 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 403 removed outlier: 3.726A pdb=" N ILE A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 424 removed outlier: 3.847A pdb=" N ILE A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 426 No H-bonds generated for 'chain 'A' and resid 425 through 426' Processing helix chain 'A' and resid 427 through 431 Processing helix chain 'A' and resid 440 through 448 removed outlier: 3.533A pdb=" N LEU A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 471 removed outlier: 4.031A pdb=" N LEU A 464 " --> pdb=" O THR A 460 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 467 " --> pdb=" O VAL A 463 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 490 Processing helix chain 'A' and resid 492 through 497 Processing helix chain 'A' and resid 498 through 500 No H-bonds generated for 'chain 'A' and resid 498 through 500' Processing helix chain 'A' and resid 510 through 524 removed outlier: 3.554A pdb=" N ILE A 514 " --> pdb=" O MET A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 547 removed outlier: 3.998A pdb=" N VAL A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE A 543 " --> pdb=" O ILE A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 603 Processing helix chain 'A' and resid 605 through 616 removed outlier: 3.560A pdb=" N ILE A 609 " --> pdb=" O ASN A 605 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA A 616 " --> pdb=" O ALA A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 678 removed outlier: 3.736A pdb=" N ARG A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA A 676 " --> pdb=" O ARG A 672 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY A 678 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.722A pdb=" N THR A 695 " --> pdb=" O ARG A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 721 removed outlier: 3.734A pdb=" N VAL A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 93 removed outlier: 3.902A pdb=" N GLY B 91 " --> pdb=" O ASN B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.948A pdb=" N GLN B 97 " --> pdb=" O PRO B 94 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TRP B 98 " --> pdb=" O VAL B 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 98' Processing helix chain 'B' and resid 108 through 121 Processing helix chain 'B' and resid 122 through 133 removed outlier: 3.888A pdb=" N ILE B 127 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 152 removed outlier: 3.617A pdb=" N TYR B 142 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 184 removed outlier: 3.550A pdb=" N GLY B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 239 removed outlier: 3.626A pdb=" N MET B 220 " --> pdb=" O CYS B 216 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL B 221 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLY B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 268 removed outlier: 4.517A pdb=" N THR B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 296 Processing helix chain 'B' and resid 305 through 324 Proline residue: B 317 - end of helix removed outlier: 4.260A pdb=" N HIS B 324 " --> pdb=" O GLU B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 345 removed outlier: 3.682A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.604A pdb=" N LEU B 378 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 403 removed outlier: 3.727A pdb=" N ILE B 391 " --> pdb=" O ILE B 387 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 424 removed outlier: 3.848A pdb=" N ILE B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 426 No H-bonds generated for 'chain 'B' and resid 425 through 426' Processing helix chain 'B' and resid 427 through 431 Processing helix chain 'B' and resid 440 through 448 removed outlier: 3.533A pdb=" N LEU B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 471 removed outlier: 4.031A pdb=" N LEU B 464 " --> pdb=" O THR B 460 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 467 " --> pdb=" O VAL B 463 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE B 471 " --> pdb=" O VAL B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 490 Processing helix chain 'B' and resid 492 through 497 Processing helix chain 'B' and resid 498 through 500 No H-bonds generated for 'chain 'B' and resid 498 through 500' Processing helix chain 'B' and resid 510 through 524 removed outlier: 3.554A pdb=" N ILE B 514 " --> pdb=" O MET B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 547 removed outlier: 3.998A pdb=" N VAL B 542 " --> pdb=" O SER B 538 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE B 543 " --> pdb=" O ILE B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 603 Processing helix chain 'B' and resid 605 through 616 removed outlier: 3.560A pdb=" N ILE B 609 " --> pdb=" O ASN B 605 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA B 616 " --> pdb=" O ALA B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 678 removed outlier: 3.736A pdb=" N ARG B 671 " --> pdb=" O LEU B 667 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA B 676 " --> pdb=" O ARG B 672 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY B 678 " --> pdb=" O TYR B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 696 removed outlier: 3.722A pdb=" N THR B 695 " --> pdb=" O ARG B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 721 removed outlier: 3.734A pdb=" N VAL B 721 " --> pdb=" O ALA B 717 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 551 through 552 removed outlier: 3.719A pdb=" N SER A 552 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE A 581 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE A 649 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 551 through 552 removed outlier: 3.720A pdb=" N SER B 552 " --> pdb=" O ARG B 582 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE B 581 " --> pdb=" O ASP B 652 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE B 649 " --> pdb=" O LEU B 682 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2419 1.33 - 1.45: 1627 1.45 - 1.57: 5342 1.57 - 1.69: 0 1.69 - 1.80: 74 Bond restraints: 9462 Sorted by residual: bond pdb=" N ILE A 364 " pdb=" CA ILE A 364 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.23e-02 6.61e+03 1.04e+01 bond pdb=" N ILE B 364 " pdb=" CA ILE B 364 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.23e-02 6.61e+03 8.22e+00 bond pdb=" N ILE B 360 " pdb=" CA ILE B 360 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.60e+00 bond pdb=" N HIS A 363 " pdb=" CA HIS A 363 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.48e+00 bond pdb=" N THR B 366 " pdb=" CA THR B 366 " ideal model delta sigma weight residual 1.459 1.489 -0.031 1.16e-02 7.43e+03 7.02e+00 ... (remaining 9457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 12142 2.17 - 4.34: 580 4.34 - 6.51: 75 6.51 - 8.68: 35 8.68 - 10.85: 6 Bond angle restraints: 12838 Sorted by residual: angle pdb=" C GLU A 558 " pdb=" N GLU A 559 " pdb=" CA GLU A 559 " ideal model delta sigma weight residual 121.54 129.32 -7.78 1.91e+00 2.74e-01 1.66e+01 angle pdb=" C GLU B 558 " pdb=" N GLU B 559 " pdb=" CA GLU B 559 " ideal model delta sigma weight residual 121.54 129.30 -7.76 1.91e+00 2.74e-01 1.65e+01 angle pdb=" C SER B 508 " pdb=" N ARG B 509 " pdb=" CA ARG B 509 " ideal model delta sigma weight residual 121.54 129.26 -7.72 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C SER A 508 " pdb=" N ARG A 509 " pdb=" CA ARG A 509 " ideal model delta sigma weight residual 121.54 129.22 -7.68 1.91e+00 2.74e-01 1.62e+01 angle pdb=" C ALA A 361 " pdb=" N GLY A 362 " pdb=" CA GLY A 362 " ideal model delta sigma weight residual 121.41 129.21 -7.80 1.96e+00 2.60e-01 1.58e+01 ... (remaining 12833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 4818 16.94 - 33.89: 606 33.89 - 50.83: 150 50.83 - 67.77: 28 67.77 - 84.72: 6 Dihedral angle restraints: 5608 sinusoidal: 2150 harmonic: 3458 Sorted by residual: dihedral pdb=" CA TYR A 699 " pdb=" C TYR A 699 " pdb=" N CYS A 700 " pdb=" CA CYS A 700 " ideal model delta harmonic sigma weight residual -180.00 -132.39 -47.61 0 5.00e+00 4.00e-02 9.07e+01 dihedral pdb=" CA TYR B 699 " pdb=" C TYR B 699 " pdb=" N CYS B 700 " pdb=" CA CYS B 700 " ideal model delta harmonic sigma weight residual 180.00 -132.44 -47.56 0 5.00e+00 4.00e-02 9.05e+01 dihedral pdb=" CA GLY A 697 " pdb=" C GLY A 697 " pdb=" N GLU A 698 " pdb=" CA GLU A 698 " ideal model delta harmonic sigma weight residual -180.00 -137.68 -42.32 0 5.00e+00 4.00e-02 7.16e+01 ... (remaining 5605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 992 0.050 - 0.100: 435 0.100 - 0.151: 88 0.151 - 0.201: 29 0.201 - 0.251: 8 Chirality restraints: 1552 Sorted by residual: chirality pdb=" CB VAL B 557 " pdb=" CA VAL B 557 " pdb=" CG1 VAL B 557 " pdb=" CG2 VAL B 557 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL A 557 " pdb=" CA VAL A 557 " pdb=" CG1 VAL A 557 " pdb=" CG2 VAL A 557 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB VAL B 382 " pdb=" CA VAL B 382 " pdb=" CG1 VAL B 382 " pdb=" CG2 VAL B 382 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1549 not shown) Planarity restraints: 1556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 585 " -0.061 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO B 586 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 586 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 586 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 585 " -0.061 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO A 586 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 586 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 586 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 501 " -0.056 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO A 502 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 502 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 502 " -0.047 5.00e-02 4.00e+02 ... (remaining 1553 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2714 2.81 - 3.33: 8340 3.33 - 3.85: 14387 3.85 - 4.38: 15392 4.38 - 4.90: 27152 Nonbonded interactions: 67985 Sorted by model distance: nonbonded pdb=" OG SER A 538 " pdb=" OH TYR B 589 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR A 589 " pdb=" OG SER B 538 " model vdw 2.287 3.040 nonbonded pdb=" OG SER B 508 " pdb=" OD2 ASP B 511 " model vdw 2.302 3.040 nonbonded pdb=" OG SER A 508 " pdb=" OD2 ASP A 511 " model vdw 2.303 3.040 nonbonded pdb=" O SER B 254 " pdb=" OG SER B 254 " model vdw 2.328 3.040 ... (remaining 67980 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.680 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.980 Find NCS groups from input model: 0.160 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.008 0.065 9462 Z= 0.535 Angle : 1.094 10.847 12838 Z= 0.580 Chirality : 0.060 0.251 1552 Planarity : 0.009 0.091 1556 Dihedral : 15.994 84.719 3376 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 12.69 % Favored : 87.05 % Rotamer: Outliers : 0.97 % Allowed : 14.44 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -5.14 (0.18), residues: 1174 helix: -2.87 (0.14), residues: 680 sheet: -3.02 (0.83), residues: 36 loop : -4.20 (0.23), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 505 HIS 0.003 0.001 HIS B 324 PHE 0.022 0.002 PHE A 658 TYR 0.022 0.003 TYR B 588 ARG 0.004 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 1.065 Fit side-chains REVERT: A 88 MET cc_start: 0.6574 (ttp) cc_final: 0.6137 (ttp) REVERT: A 131 LEU cc_start: 0.8875 (tp) cc_final: 0.8595 (tt) REVERT: A 384 VAL cc_start: 0.8566 (t) cc_final: 0.8250 (p) REVERT: A 389 ILE cc_start: 0.9278 (pt) cc_final: 0.9073 (pt) REVERT: A 431 PHE cc_start: 0.7892 (m-80) cc_final: 0.7630 (m-80) REVERT: A 543 ILE cc_start: 0.9406 (pt) cc_final: 0.9095 (mt) REVERT: A 544 LEU cc_start: 0.9340 (tp) cc_final: 0.8661 (tt) REVERT: A 682 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8783 (pp) REVERT: B 88 MET cc_start: 0.6576 (ttp) cc_final: 0.6134 (ttp) REVERT: B 131 LEU cc_start: 0.8851 (tp) cc_final: 0.8570 (tt) REVERT: B 384 VAL cc_start: 0.8562 (t) cc_final: 0.8245 (p) REVERT: B 389 ILE cc_start: 0.9276 (pt) cc_final: 0.9073 (pt) REVERT: B 431 PHE cc_start: 0.7872 (m-80) cc_final: 0.7627 (m-80) REVERT: B 543 ILE cc_start: 0.9408 (pt) cc_final: 0.9093 (mt) REVERT: B 544 LEU cc_start: 0.9339 (tp) cc_final: 0.8660 (tt) REVERT: B 682 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8774 (pp) outliers start: 10 outliers final: 4 residues processed: 166 average time/residue: 0.2153 time to fit residues: 51.2528 Evaluate side-chains 132 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 682 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 292 HIS A 363 HIS ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN A 647 HIS B 107 ASN B 292 HIS B 363 HIS ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN B 647 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.155194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.130026 restraints weight = 13138.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.132074 restraints weight = 9362.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.132900 restraints weight = 6448.283| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9462 Z= 0.192 Angle : 0.648 8.060 12838 Z= 0.332 Chirality : 0.041 0.167 1552 Planarity : 0.005 0.059 1556 Dihedral : 6.058 38.975 1261 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 2.62 % Allowed : 18.90 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.11 (0.23), residues: 1174 helix: -0.98 (0.19), residues: 682 sheet: -2.54 (0.92), residues: 36 loop : -3.75 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 505 HIS 0.010 0.001 HIS A 363 PHE 0.029 0.002 PHE A 152 TYR 0.009 0.001 TYR A 674 ARG 0.001 0.000 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.911 Fit side-chains REVERT: A 131 LEU cc_start: 0.8846 (tp) cc_final: 0.8581 (tt) REVERT: A 292 HIS cc_start: 0.8180 (OUTLIER) cc_final: 0.7847 (m170) REVERT: A 384 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8166 (p) REVERT: A 543 ILE cc_start: 0.9310 (pt) cc_final: 0.9040 (mt) REVERT: A 544 LEU cc_start: 0.9305 (tp) cc_final: 0.8727 (tt) REVERT: A 682 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8523 (pp) REVERT: B 131 LEU cc_start: 0.8817 (tp) cc_final: 0.8558 (tt) REVERT: B 292 HIS cc_start: 0.8179 (OUTLIER) cc_final: 0.7840 (m170) REVERT: B 384 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8160 (p) REVERT: B 431 PHE cc_start: 0.7834 (m-80) cc_final: 0.7628 (m-80) REVERT: B 543 ILE cc_start: 0.9311 (pt) cc_final: 0.9042 (mt) REVERT: B 544 LEU cc_start: 0.9309 (tp) cc_final: 0.8728 (tt) REVERT: B 682 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8523 (pp) outliers start: 27 outliers final: 6 residues processed: 170 average time/residue: 0.1523 time to fit residues: 40.4373 Evaluate side-chains 145 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 692 ASP Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 292 HIS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 692 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 55 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 103 optimal weight: 0.0670 chunk 16 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS A 363 HIS ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.167802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143363 restraints weight = 14224.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.145926 restraints weight = 8213.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.146780 restraints weight = 5873.707| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9462 Z= 0.237 Angle : 0.652 7.754 12838 Z= 0.329 Chirality : 0.042 0.179 1552 Planarity : 0.004 0.053 1556 Dihedral : 5.676 38.744 1256 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 3.10 % Allowed : 23.16 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.48 (0.24), residues: 1174 helix: -0.32 (0.20), residues: 680 sheet: -2.43 (0.94), residues: 36 loop : -3.72 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 505 HIS 0.005 0.001 HIS A 363 PHE 0.033 0.002 PHE A 152 TYR 0.010 0.001 TYR A 588 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.968 Fit side-chains REVERT: A 131 LEU cc_start: 0.8847 (tp) cc_final: 0.8588 (tt) REVERT: A 349 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6975 (m-80) REVERT: A 384 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8218 (p) REVERT: A 543 ILE cc_start: 0.9339 (pt) cc_final: 0.9053 (mt) REVERT: A 544 LEU cc_start: 0.9350 (tp) cc_final: 0.8780 (tt) REVERT: A 682 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8729 (pp) REVERT: B 131 LEU cc_start: 0.8817 (tp) cc_final: 0.8557 (tt) REVERT: B 349 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.7012 (m-80) REVERT: B 384 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8221 (p) REVERT: B 431 PHE cc_start: 0.7936 (m-80) cc_final: 0.7718 (m-80) REVERT: B 543 ILE cc_start: 0.9335 (pt) cc_final: 0.9054 (mt) REVERT: B 544 LEU cc_start: 0.9373 (tp) cc_final: 0.8818 (tt) REVERT: B 682 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8700 (pp) outliers start: 32 outliers final: 20 residues processed: 158 average time/residue: 0.1528 time to fit residues: 37.5043 Evaluate side-chains 160 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 349 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 349 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 88 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 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 = 0.4017 r_free = 0.4017 target = 0.167742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.142250 restraints weight = 14010.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145103 restraints weight = 8303.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.146959 restraints weight = 5816.473| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9462 Z= 0.278 Angle : 0.648 8.281 12838 Z= 0.331 Chirality : 0.043 0.184 1552 Planarity : 0.004 0.052 1556 Dihedral : 5.586 37.349 1256 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 4.26 % Allowed : 24.52 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.02 (0.24), residues: 1174 helix: 0.13 (0.20), residues: 680 sheet: -2.33 (0.98), residues: 36 loop : -3.67 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 505 HIS 0.002 0.001 HIS B 363 PHE 0.034 0.002 PHE B 152 TYR 0.011 0.001 TYR A 588 ARG 0.002 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 1.191 Fit side-chains REVERT: A 131 LEU cc_start: 0.8806 (tp) cc_final: 0.8562 (tt) REVERT: A 384 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8248 (p) REVERT: A 543 ILE cc_start: 0.9335 (pt) cc_final: 0.9083 (mt) REVERT: A 544 LEU cc_start: 0.9385 (tp) cc_final: 0.9079 (tt) REVERT: A 682 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8762 (pp) REVERT: B 131 LEU cc_start: 0.8766 (tp) cc_final: 0.8531 (tt) REVERT: B 384 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8270 (p) REVERT: B 431 PHE cc_start: 0.7931 (m-80) cc_final: 0.7650 (m-80) REVERT: B 543 ILE cc_start: 0.9335 (pt) cc_final: 0.9078 (mt) REVERT: B 544 LEU cc_start: 0.9386 (tp) cc_final: 0.9086 (tt) REVERT: B 682 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8757 (pp) outliers start: 44 outliers final: 28 residues processed: 169 average time/residue: 0.1921 time to fit residues: 49.2005 Evaluate side-chains 165 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 36 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 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 = 0.4066 r_free = 0.4066 target = 0.172418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.147408 restraints weight = 13955.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.150409 restraints weight = 8113.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.152411 restraints weight = 5619.168| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9462 Z= 0.150 Angle : 0.602 10.264 12838 Z= 0.299 Chirality : 0.040 0.199 1552 Planarity : 0.004 0.046 1556 Dihedral : 5.230 34.340 1256 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 3.20 % Allowed : 27.03 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.72 (0.25), residues: 1174 helix: 0.40 (0.21), residues: 688 sheet: -2.20 (1.01), residues: 36 loop : -3.67 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 505 HIS 0.001 0.000 HIS A 292 PHE 0.034 0.001 PHE B 152 TYR 0.007 0.001 TYR B 142 ARG 0.002 0.000 ARG B 672 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 1.218 Fit side-chains REVERT: A 131 LEU cc_start: 0.8781 (tp) cc_final: 0.8530 (tt) REVERT: A 376 TRP cc_start: 0.6247 (m-10) cc_final: 0.5939 (t60) REVERT: A 384 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8168 (p) REVERT: A 544 LEU cc_start: 0.9308 (tp) cc_final: 0.9025 (tt) REVERT: A 682 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8664 (pp) REVERT: B 131 LEU cc_start: 0.8735 (tp) cc_final: 0.8500 (tt) REVERT: B 376 TRP cc_start: 0.6261 (m-10) cc_final: 0.5958 (t60) REVERT: B 384 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8183 (p) REVERT: B 431 PHE cc_start: 0.7897 (m-80) cc_final: 0.7574 (m-80) REVERT: B 544 LEU cc_start: 0.9317 (tp) cc_final: 0.9035 (tt) REVERT: B 682 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8656 (pp) outliers start: 33 outliers final: 18 residues processed: 173 average time/residue: 0.2064 time to fit residues: 56.9116 Evaluate side-chains 152 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 692 ASP Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 692 ASP Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 25 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN ** B 490 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 = 0.4008 r_free = 0.4008 target = 0.167303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.142492 restraints weight = 14065.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.145302 restraints weight = 10697.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.146280 restraints weight = 6504.085| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9462 Z= 0.247 Angle : 0.631 8.972 12838 Z= 0.317 Chirality : 0.042 0.184 1552 Planarity : 0.004 0.047 1556 Dihedral : 5.239 33.741 1256 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 4.65 % Allowed : 27.81 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.66 (0.25), residues: 1174 helix: 0.42 (0.21), residues: 694 sheet: -2.19 (1.01), residues: 36 loop : -3.63 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 505 HIS 0.002 0.000 HIS B 324 PHE 0.035 0.001 PHE A 152 TYR 0.010 0.001 TYR A 588 ARG 0.001 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 137 time to evaluate : 1.131 Fit side-chains REVERT: A 131 LEU cc_start: 0.8803 (tp) cc_final: 0.8578 (tt) REVERT: A 376 TRP cc_start: 0.6260 (m-10) cc_final: 0.6058 (t60) REVERT: A 384 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8179 (p) REVERT: A 544 LEU cc_start: 0.9245 (tp) cc_final: 0.8994 (tt) REVERT: A 682 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8725 (pp) REVERT: B 131 LEU cc_start: 0.8768 (tp) cc_final: 0.8550 (tt) REVERT: B 376 TRP cc_start: 0.6438 (m-10) cc_final: 0.6167 (t60) REVERT: B 384 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8231 (p) REVERT: B 431 PHE cc_start: 0.7930 (m-80) cc_final: 0.7686 (m-80) REVERT: B 544 LEU cc_start: 0.9249 (tp) cc_final: 0.8993 (tt) REVERT: B 682 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8719 (pp) outliers start: 48 outliers final: 31 residues processed: 171 average time/residue: 0.1829 time to fit residues: 47.1794 Evaluate side-chains 164 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 50 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 54 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 2 optimal weight: 0.0870 chunk 103 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 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 = 0.4076 r_free = 0.4076 target = 0.173361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.148268 restraints weight = 13945.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.151335 restraints weight = 8094.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.153338 restraints weight = 5592.215| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9462 Z= 0.145 Angle : 0.603 9.552 12838 Z= 0.296 Chirality : 0.040 0.194 1552 Planarity : 0.003 0.043 1556 Dihedral : 4.970 31.720 1256 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 3.20 % Allowed : 28.39 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.49 (0.25), residues: 1174 helix: 0.56 (0.21), residues: 704 sheet: -2.04 (1.02), residues: 36 loop : -3.67 (0.25), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 505 HIS 0.002 0.000 HIS B 452 PHE 0.035 0.001 PHE A 152 TYR 0.008 0.001 TYR B 142 ARG 0.001 0.000 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 1.042 Fit side-chains REVERT: A 131 LEU cc_start: 0.8782 (tp) cc_final: 0.8539 (tt) REVERT: A 376 TRP cc_start: 0.6419 (m-10) cc_final: 0.5838 (t60) REVERT: A 384 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8150 (p) REVERT: A 544 LEU cc_start: 0.9192 (tp) cc_final: 0.8947 (tt) REVERT: A 682 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8627 (pp) REVERT: A 720 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7410 (tm-30) REVERT: B 131 LEU cc_start: 0.8740 (tp) cc_final: 0.8510 (tt) REVERT: B 376 TRP cc_start: 0.6435 (m-10) cc_final: 0.5851 (t60) REVERT: B 384 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8155 (p) REVERT: B 431 PHE cc_start: 0.7889 (m-80) cc_final: 0.7542 (m-80) REVERT: B 544 LEU cc_start: 0.9199 (tp) cc_final: 0.8955 (tt) REVERT: B 682 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8621 (pp) REVERT: B 720 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7409 (tm-30) outliers start: 33 outliers final: 27 residues processed: 164 average time/residue: 0.1954 time to fit residues: 50.6854 Evaluate side-chains 158 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 682 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 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 = 0.4058 r_free = 0.4058 target = 0.171778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.146421 restraints weight = 14171.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.149364 restraints weight = 8377.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.151393 restraints weight = 5838.415| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9462 Z= 0.190 Angle : 0.613 9.504 12838 Z= 0.302 Chirality : 0.041 0.190 1552 Planarity : 0.003 0.044 1556 Dihedral : 4.959 32.622 1256 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 3.68 % Allowed : 28.00 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.49 (0.25), residues: 1174 helix: 0.57 (0.21), residues: 708 sheet: -2.05 (1.01), residues: 36 loop : -3.72 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 505 HIS 0.001 0.000 HIS A 324 PHE 0.034 0.001 PHE A 152 TYR 0.008 0.001 TYR B 589 ARG 0.001 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 0.985 Fit side-chains REVERT: A 131 LEU cc_start: 0.8834 (tp) cc_final: 0.8605 (tt) REVERT: A 376 TRP cc_start: 0.6428 (m-10) cc_final: 0.5860 (t60) REVERT: A 384 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8164 (p) REVERT: A 544 LEU cc_start: 0.9234 (tp) cc_final: 0.8981 (tt) REVERT: A 682 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8674 (pp) REVERT: A 720 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7392 (tm-30) REVERT: B 131 LEU cc_start: 0.8794 (tp) cc_final: 0.8575 (tt) REVERT: B 376 TRP cc_start: 0.6437 (m-10) cc_final: 0.5866 (t60) REVERT: B 384 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8186 (p) REVERT: B 544 LEU cc_start: 0.9233 (tp) cc_final: 0.8985 (tt) REVERT: B 682 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8712 (pp) REVERT: B 720 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7392 (tm-30) outliers start: 38 outliers final: 30 residues processed: 164 average time/residue: 0.1511 time to fit residues: 38.7247 Evaluate side-chains 161 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 66 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 44 optimal weight: 0.1980 chunk 104 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 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 = 0.4068 r_free = 0.4068 target = 0.172668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.147501 restraints weight = 13953.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.150472 restraints weight = 8260.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.152453 restraints weight = 5796.733| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9462 Z= 0.180 Angle : 0.633 14.046 12838 Z= 0.304 Chirality : 0.041 0.180 1552 Planarity : 0.003 0.042 1556 Dihedral : 4.915 32.023 1256 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 3.59 % Allowed : 28.00 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.39 (0.25), residues: 1174 helix: 0.65 (0.21), residues: 708 sheet: -2.06 (1.01), residues: 36 loop : -3.69 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 505 HIS 0.001 0.000 HIS B 363 PHE 0.034 0.001 PHE A 152 TYR 0.008 0.001 TYR B 589 ARG 0.001 0.000 ARG B 671 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.945 Fit side-chains REVERT: A 376 TRP cc_start: 0.6427 (m-10) cc_final: 0.5864 (t60) REVERT: A 384 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8171 (p) REVERT: A 544 LEU cc_start: 0.9234 (tp) cc_final: 0.8984 (tt) REVERT: A 682 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8661 (pp) REVERT: A 720 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7372 (tm-30) REVERT: B 376 TRP cc_start: 0.6435 (m-10) cc_final: 0.5871 (t60) REVERT: B 384 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8170 (p) REVERT: B 544 LEU cc_start: 0.9231 (tp) cc_final: 0.8983 (tt) REVERT: B 682 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8653 (pp) REVERT: B 720 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7379 (tm-30) outliers start: 37 outliers final: 28 residues processed: 164 average time/residue: 0.1495 time to fit residues: 37.7683 Evaluate side-chains 160 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 682 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 55 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 2 optimal weight: 0.0570 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.174352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.149329 restraints weight = 14039.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.152275 restraints weight = 8252.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.154341 restraints weight = 5771.399| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9462 Z= 0.150 Angle : 0.647 14.064 12838 Z= 0.303 Chirality : 0.040 0.190 1552 Planarity : 0.003 0.043 1556 Dihedral : 4.802 31.155 1256 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 3.10 % Allowed : 29.07 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.28 (0.25), residues: 1174 helix: 0.75 (0.21), residues: 708 sheet: -1.96 (1.02), residues: 36 loop : -3.66 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 505 HIS 0.001 0.000 HIS A 363 PHE 0.035 0.001 PHE A 152 TYR 0.007 0.001 TYR B 142 ARG 0.002 0.000 ARG A 671 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.966 Fit side-chains REVERT: A 88 MET cc_start: 0.6164 (ttp) cc_final: 0.3700 (tpt) REVERT: A 376 TRP cc_start: 0.6492 (m-10) cc_final: 0.5703 (t60) REVERT: A 384 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8138 (p) REVERT: A 544 LEU cc_start: 0.9262 (tp) cc_final: 0.9000 (tt) REVERT: A 682 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8536 (pp) REVERT: B 88 MET cc_start: 0.6163 (ttp) cc_final: 0.3695 (tpt) REVERT: B 376 TRP cc_start: 0.6494 (m-10) cc_final: 0.5702 (t60) REVERT: B 384 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8156 (p) REVERT: B 544 LEU cc_start: 0.9256 (tp) cc_final: 0.8748 (tt) REVERT: B 682 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8529 (pp) REVERT: B 720 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7448 (tm-30) outliers start: 32 outliers final: 27 residues processed: 159 average time/residue: 0.1765 time to fit residues: 43.8360 Evaluate side-chains 161 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 682 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 9 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 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 = 0.3966 r_free = 0.3966 target = 0.163414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.136793 restraints weight = 14307.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.139587 restraints weight = 8695.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.141483 restraints weight = 6216.188| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 9462 Z= 0.476 Angle : 0.794 13.751 12838 Z= 0.389 Chirality : 0.048 0.178 1552 Planarity : 0.004 0.047 1556 Dihedral : 5.484 37.527 1256 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.01 % Favored : 87.99 % Rotamer: Outliers : 3.29 % Allowed : 28.78 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.66 (0.25), residues: 1174 helix: 0.41 (0.20), residues: 696 sheet: -2.41 (0.96), residues: 36 loop : -3.60 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 505 HIS 0.004 0.001 HIS B 324 PHE 0.038 0.002 PHE A 152 TYR 0.016 0.002 TYR A 588 ARG 0.003 0.000 ARG B 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2891.76 seconds wall clock time: 53 minutes 34.13 seconds (3214.13 seconds total)