Starting phenix.real_space_refine on Tue Sep 24 11:32:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln5_0924/09_2024/6ln5_0924.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln5_0924/09_2024/6ln5_0924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln5_0924/09_2024/6ln5_0924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln5_0924/09_2024/6ln5_0924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln5_0924/09_2024/6ln5_0924.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln5_0924/09_2024/6ln5_0924.cif" } resolution = 2.8 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= 0.000 sd= 0.011 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 P 3 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 4988 2.51 5 N 1311 2.21 5 O 1478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7840 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7806 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 46, 'TRANS': 964} Chain breaks: 1 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 2, ' MG': 1, 'ACP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.64, per 1000 atoms: 0.59 Number of scatterers: 7840 At special positions: 0 Unit cell: (103.335, 79.68, 138.195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 2 19.99 S 57 16.00 P 3 15.00 Mg 1 11.99 O 1478 8.00 N 1311 7.00 C 4988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 875 " - pdb=" SG CYS A 887 " distance=2.02 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: 2.00 Conformation dependent library (CDL) restraints added in 965.4 milliseconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 7 sheets defined 53.3% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 8 through 17 Processing helix chain 'A' and resid 25 through 37 removed outlier: 3.686A pdb=" N VAL A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 59 through 78 removed outlier: 3.955A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 118 removed outlier: 3.500A pdb=" N ILE A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.731A pdb=" N THR A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 275 removed outlier: 3.545A pdb=" N LYS A 252 " --> pdb=" O PRO A 248 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 279 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 287 through 307 Processing helix chain 'A' and resid 310 through 329 removed outlier: 3.614A pdb=" N THR A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 343 removed outlier: 4.405A pdb=" N VAL A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 406 removed outlier: 3.828A pdb=" N GLN A 406 " --> pdb=" O ASN A 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 406' Processing helix chain 'A' and resid 407 through 420 Processing helix chain 'A' and resid 439 through 453 removed outlier: 3.833A pdb=" N LEU A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 477 Processing helix chain 'A' and resid 516 through 523 Processing helix chain 'A' and resid 537 through 554 removed outlier: 3.556A pdb=" N LYS A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 removed outlier: 3.539A pdb=" N TYR A 586 " --> pdb=" O ASN A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 removed outlier: 4.322A pdb=" N ALA A 607 " --> pdb=" O ARG A 603 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N SER A 608 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 661 through 670 removed outlier: 3.732A pdb=" N ASP A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 670 " --> pdb=" O ARG A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 692 removed outlier: 3.626A pdb=" N SER A 684 " --> pdb=" O PRO A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 723 through 729 Processing helix chain 'A' and resid 739 through 781 removed outlier: 4.252A pdb=" N VAL A 743 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY A 769 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 799 Processing helix chain 'A' and resid 800 through 805 Processing helix chain 'A' and resid 806 through 809 Processing helix chain 'A' and resid 829 through 857 removed outlier: 3.637A pdb=" N TYR A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 851 " --> pdb=" O THR A 847 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP A 854 " --> pdb=" O ALA A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 871 Processing helix chain 'A' and resid 872 through 875 removed outlier: 3.601A pdb=" N CYS A 875 " --> pdb=" O PHE A 872 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 872 through 875' Processing helix chain 'A' and resid 888 through 891 removed outlier: 3.585A pdb=" N GLU A 891 " --> pdb=" O ALA A 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 888 through 891' Processing helix chain 'A' and resid 892 through 913 removed outlier: 4.447A pdb=" N MET A 896 " --> pdb=" O SER A 892 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A 913 " --> pdb=" O CYS A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 928 Processing helix chain 'A' and resid 929 through 949 Processing helix chain 'A' and resid 951 through 957 Processing helix chain 'A' and resid 962 through 974 Processing helix chain 'A' and resid 974 through 990 removed outlier: 3.791A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1031 Proline residue: A1024 - end of helix removed outlier: 3.593A pdb=" N TRP A1028 " --> pdb=" O PRO A1024 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 141 removed outlier: 4.366A pdb=" N LYS A 128 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE A 150 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL A 222 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LEU A 165 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A 224 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ILE A 163 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 189 removed outlier: 4.700A pdb=" N LEU A 173 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP A 176 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE A 214 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 331 through 333 removed outlier: 6.121A pdb=" N GLY A 716 " --> pdb=" O MET A 732 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU A 734 " --> pdb=" O GLY A 716 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA A 718 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR A 697 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE A 717 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N MET A 699 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N MET A 719 " --> pdb=" O MET A 699 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N GLY A 701 " --> pdb=" O MET A 719 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 347 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N THR A 700 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS A 349 " --> pdb=" O THR A 700 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N PHE A 675 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N MET A 622 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE A 652 " --> pdb=" O ALA A 676 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.597A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 19.868A pdb=" N CYS A 524 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 17.601A pdb=" N PHE A 367 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 14.859A pdb=" N HIS A 526 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N LEU A 369 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ARG A 528 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ARG A 371 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.597A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 19.868A pdb=" N CYS A 524 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 17.601A pdb=" N PHE A 367 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 14.859A pdb=" N HIS A 526 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N LEU A 369 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ARG A 528 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ARG A 371 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU A 590 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLY A 594 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU A 563 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N CYS A 595 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 561 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLY A 597 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG A 559 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER A 493 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU A 486 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N SER A 495 " --> pdb=" O THR A 484 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N THR A 484 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR A 497 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.597A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL A 363 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A 599 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU A 369 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N VAL A 593 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 14.554A pdb=" N ARG A 371 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 16.501A pdb=" N THR A 591 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU A 563 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N CYS A 595 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 561 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLY A 597 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG A 559 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER A 493 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU A 486 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N SER A 495 " --> pdb=" O THR A 484 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N THR A 484 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR A 497 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 424 through 428 433 hydrogen bonds defined for protein. 1257 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2575 1.35 - 1.48: 1793 1.48 - 1.61: 3523 1.61 - 1.73: 4 1.73 - 1.86: 90 Bond restraints: 7985 Sorted by residual: bond pdb=" C1' ACP A2001 " pdb=" O4' ACP A2001 " ideal model delta sigma weight residual 1.390 1.618 -0.228 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C1' ACP A2001 " pdb=" C2' ACP A2001 " ideal model delta sigma weight residual 1.527 1.307 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C4' ACP A2001 " pdb=" O4' ACP A2001 " ideal model delta sigma weight residual 1.428 1.302 0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C6 ACP A2001 " pdb=" N6 ACP A2001 " ideal model delta sigma weight residual 1.335 1.449 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C2' ACP A2001 " pdb=" O2' ACP A2001 " ideal model delta sigma weight residual 1.401 1.493 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 7980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 10792 3.11 - 6.22: 43 6.22 - 9.33: 3 9.33 - 12.44: 5 12.44 - 15.54: 1 Bond angle restraints: 10844 Sorted by residual: angle pdb=" O3A ACP A2001 " pdb=" PA ACP A2001 " pdb=" O5' ACP A2001 " ideal model delta sigma weight residual 93.75 109.29 -15.54 3.00e+00 1.11e-01 2.68e+01 angle pdb=" C3B ACP A2001 " pdb=" PB ACP A2001 " pdb=" O3A ACP A2001 " ideal model delta sigma weight residual 98.05 110.00 -11.95 3.00e+00 1.11e-01 1.59e+01 angle pdb=" N1 ACP A2001 " pdb=" C6 ACP A2001 " pdb=" N6 ACP A2001 " ideal model delta sigma weight residual 119.32 108.11 11.21 3.00e+00 1.11e-01 1.40e+01 angle pdb=" O1B ACP A2001 " pdb=" PB ACP A2001 " pdb=" O2B ACP A2001 " ideal model delta sigma weight residual 119.60 109.01 10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" O1A ACP A2001 " pdb=" PA ACP A2001 " pdb=" O2A ACP A2001 " ideal model delta sigma weight residual 118.95 108.61 10.34 3.00e+00 1.11e-01 1.19e+01 ... (remaining 10839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.94: 4614 21.94 - 43.89: 215 43.89 - 65.83: 16 65.83 - 87.78: 14 87.78 - 109.72: 2 Dihedral angle restraints: 4861 sinusoidal: 1941 harmonic: 2920 Sorted by residual: dihedral pdb=" CA CYS A 887 " pdb=" C CYS A 887 " pdb=" N ALA A 888 " pdb=" CA ALA A 888 " ideal model delta harmonic sigma weight residual 180.00 158.97 21.03 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" O1A ACP A2001 " pdb=" O3A ACP A2001 " pdb=" PA ACP A2001 " pdb=" PB ACP A2001 " ideal model delta sinusoidal sigma weight residual -48.75 60.97 -109.72 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" CA PRO A 951 " pdb=" C PRO A 951 " pdb=" N LEU A 952 " pdb=" CA LEU A 952 " ideal model delta harmonic sigma weight residual -180.00 -161.44 -18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 4858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1177 0.077 - 0.154: 95 0.154 - 0.231: 0 0.231 - 0.308: 0 0.308 - 0.385: 1 Chirality restraints: 1273 Sorted by residual: chirality pdb=" C2' ACP A2001 " pdb=" C1' ACP A2001 " pdb=" C3' ACP A2001 " pdb=" O2' ACP A2001 " both_signs ideal model delta sigma weight residual False -2.75 -2.37 -0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA ILE A 623 " pdb=" N ILE A 623 " pdb=" C ILE A 623 " pdb=" CB ILE A 623 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA VAL A 437 " pdb=" N VAL A 437 " pdb=" C VAL A 437 " pdb=" CB VAL A 437 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 1270 not shown) Planarity restraints: 1377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A1016 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A1017 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A1017 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1017 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 974 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 975 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 787 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A 788 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 788 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 788 " 0.020 5.00e-02 4.00e+02 ... (remaining 1374 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 74 2.60 - 3.18: 6618 3.18 - 3.75: 12044 3.75 - 4.33: 17696 4.33 - 4.90: 29002 Nonbonded interactions: 65434 Sorted by model distance: nonbonded pdb=" OD2 ASP A 351 " pdb="MG MG A2002 " model vdw 2.027 2.170 nonbonded pdb=" OE2 GLU A 309 " pdb=" OD1 ASN A 795 " model vdw 2.027 3.040 nonbonded pdb=" O ILE A 307 " pdb=" OE1 GLU A 309 " model vdw 2.161 3.040 nonbonded pdb=" OD1 ASP A 702 " pdb="MG MG A2002 " model vdw 2.172 2.170 nonbonded pdb=" NH1 ARG A 491 " pdb=" OE2 GLU A 587 " model vdw 2.212 3.120 ... (remaining 65429 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.370 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.228 7985 Z= 0.335 Angle : 0.630 15.544 10844 Z= 0.335 Chirality : 0.042 0.385 1273 Planarity : 0.004 0.039 1377 Dihedral : 12.833 109.724 2966 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.12 % Allowed : 3.12 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.20), residues: 1007 helix: -3.50 (0.13), residues: 500 sheet: -1.77 (0.40), residues: 132 loop : -1.65 (0.27), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 793 HIS 0.006 0.001 HIS A 566 PHE 0.011 0.001 PHE A 367 TYR 0.007 0.001 TYR A 295 ARG 0.002 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 0.872 Fit side-chains REVERT: A 30 LYS cc_start: 0.7917 (ttpp) cc_final: 0.7435 (tttm) REVERT: A 31 LYS cc_start: 0.7380 (mttt) cc_final: 0.7128 (mmtp) REVERT: A 33 LYS cc_start: 0.7988 (tptm) cc_final: 0.7734 (tppt) REVERT: A 135 LYS cc_start: 0.7602 (pttt) cc_final: 0.7264 (mmtp) REVERT: A 143 LYS cc_start: 0.8190 (pttt) cc_final: 0.7820 (ptmt) REVERT: A 153 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8281 (tt) REVERT: A 259 GLN cc_start: 0.8079 (mt0) cc_final: 0.7770 (mt0) REVERT: A 365 ARG cc_start: 0.8105 (ptp-170) cc_final: 0.7899 (ptm160) REVERT: A 371 ARG cc_start: 0.6508 (ptp-110) cc_final: 0.6069 (ptp90) REVERT: A 379 LEU cc_start: 0.8347 (mt) cc_final: 0.8115 (mp) REVERT: A 387 SER cc_start: 0.8261 (p) cc_final: 0.8047 (p) REVERT: A 397 LYS cc_start: 0.7505 (tptp) cc_final: 0.7238 (tmtt) REVERT: A 431 LYS cc_start: 0.8549 (ttmm) cc_final: 0.8139 (mttp) REVERT: A 433 VAL cc_start: 0.8698 (p) cc_final: 0.8447 (m) REVERT: A 510 LYS cc_start: 0.8237 (mttt) cc_final: 0.8031 (mtpp) REVERT: A 541 LYS cc_start: 0.8815 (tttt) cc_final: 0.8578 (ttmt) REVERT: A 549 ARG cc_start: 0.7035 (mtt180) cc_final: 0.6561 (mtm110) REVERT: A 568 ASN cc_start: 0.8016 (m110) cc_final: 0.7636 (m-40) REVERT: A 582 ASN cc_start: 0.7674 (m-40) cc_final: 0.7113 (m-40) REVERT: A 585 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7734 (mttt) REVERT: A 719 MET cc_start: 0.8879 (mmm) cc_final: 0.8209 (mmt) REVERT: A 896 MET cc_start: 0.8490 (mtp) cc_final: 0.8008 (mtm) REVERT: A 968 MET cc_start: 0.8225 (tpt) cc_final: 0.7933 (mmm) outliers start: 1 outliers final: 1 residues processed: 167 average time/residue: 1.4012 time to fit residues: 246.0269 Evaluate side-chains 127 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 153 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 284 HIS A 643 GLN A 874 GLN A 913 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7985 Z= 0.165 Angle : 0.508 6.037 10844 Z= 0.266 Chirality : 0.041 0.129 1273 Planarity : 0.005 0.040 1377 Dihedral : 8.318 148.578 1107 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.55 % Allowed : 9.84 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.24), residues: 1007 helix: -0.64 (0.21), residues: 508 sheet: -1.00 (0.46), residues: 122 loop : -1.07 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1016 HIS 0.002 0.001 HIS A 396 PHE 0.012 0.001 PHE A 367 TYR 0.010 0.001 TYR A 842 ARG 0.005 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 0.906 Fit side-chains REVERT: A 31 LYS cc_start: 0.7409 (mttt) cc_final: 0.7102 (mmtp) REVERT: A 135 LYS cc_start: 0.7480 (pttt) cc_final: 0.7182 (mmtp) REVERT: A 239 MET cc_start: 0.4818 (mtt) cc_final: 0.3755 (tpt) REVERT: A 370 ASP cc_start: 0.6758 (t0) cc_final: 0.6467 (t0) REVERT: A 371 ARG cc_start: 0.6649 (ptp-110) cc_final: 0.6076 (ptp90) REVERT: A 397 LYS cc_start: 0.7596 (tptp) cc_final: 0.7326 (tmtt) REVERT: A 431 LYS cc_start: 0.8706 (ttmm) cc_final: 0.8392 (mttp) REVERT: A 510 LYS cc_start: 0.8281 (mttt) cc_final: 0.8065 (mtpp) REVERT: A 518 GLU cc_start: 0.7848 (mp0) cc_final: 0.7403 (mt-10) REVERT: A 541 LYS cc_start: 0.8676 (tttt) cc_final: 0.8267 (ttmt) REVERT: A 549 ARG cc_start: 0.7178 (mtt180) cc_final: 0.6825 (ttp-110) REVERT: A 568 ASN cc_start: 0.7896 (m110) cc_final: 0.7571 (m-40) REVERT: A 585 LYS cc_start: 0.8269 (mtpp) cc_final: 0.7889 (mttt) REVERT: A 719 MET cc_start: 0.8820 (mmm) cc_final: 0.8205 (mmt) REVERT: A 797 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8053 (p) REVERT: A 896 MET cc_start: 0.8441 (mtp) cc_final: 0.7915 (mtm) REVERT: A 917 GLU cc_start: 0.7728 (tt0) cc_final: 0.7470 (tp30) REVERT: A 968 MET cc_start: 0.7944 (tpt) cc_final: 0.7561 (mmm) outliers start: 22 outliers final: 8 residues processed: 148 average time/residue: 1.3345 time to fit residues: 208.1600 Evaluate side-chains 123 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 797 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 469 ASN A 643 GLN A 874 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7985 Z= 0.186 Angle : 0.502 5.686 10844 Z= 0.259 Chirality : 0.042 0.130 1273 Planarity : 0.004 0.037 1377 Dihedral : 8.423 155.073 1107 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.55 % Allowed : 14.24 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.25), residues: 1007 helix: 0.49 (0.23), residues: 510 sheet: -0.94 (0.46), residues: 119 loop : -0.70 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1016 HIS 0.002 0.001 HIS A 15 PHE 0.013 0.001 PHE A 367 TYR 0.013 0.001 TYR A 842 ARG 0.007 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 0.866 Fit side-chains REVERT: A 31 LYS cc_start: 0.7388 (mttt) cc_final: 0.7083 (mmtp) REVERT: A 135 LYS cc_start: 0.7407 (pttt) cc_final: 0.7139 (mmtp) REVERT: A 239 MET cc_start: 0.4801 (mtt) cc_final: 0.3709 (tpt) REVERT: A 370 ASP cc_start: 0.6561 (t0) cc_final: 0.6306 (t0) REVERT: A 371 ARG cc_start: 0.6555 (ptp-110) cc_final: 0.5940 (ptp90) REVERT: A 397 LYS cc_start: 0.7781 (tptp) cc_final: 0.7290 (tmtt) REVERT: A 431 LYS cc_start: 0.8728 (ttmm) cc_final: 0.8443 (mttp) REVERT: A 510 LYS cc_start: 0.8169 (mttt) cc_final: 0.7957 (mtpp) REVERT: A 528 ARG cc_start: 0.8723 (tpp-160) cc_final: 0.8476 (tpp-160) REVERT: A 541 LYS cc_start: 0.8668 (tttt) cc_final: 0.8270 (ttmt) REVERT: A 549 ARG cc_start: 0.7192 (mtt180) cc_final: 0.6814 (ttp-110) REVERT: A 568 ASN cc_start: 0.7827 (m110) cc_final: 0.7486 (m-40) REVERT: A 585 LYS cc_start: 0.8288 (mtpp) cc_final: 0.7702 (mttt) REVERT: A 714 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.6798 (mp0) REVERT: A 719 MET cc_start: 0.8786 (mmm) cc_final: 0.8160 (mmt) REVERT: A 797 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.8110 (p) REVERT: A 896 MET cc_start: 0.8436 (mtp) cc_final: 0.7961 (mtm) outliers start: 22 outliers final: 12 residues processed: 139 average time/residue: 1.3200 time to fit residues: 193.6876 Evaluate side-chains 128 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 812 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.0980 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 81 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 GLN A 874 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7985 Z= 0.140 Angle : 0.474 5.686 10844 Z= 0.243 Chirality : 0.040 0.125 1273 Planarity : 0.004 0.036 1377 Dihedral : 8.251 154.663 1107 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.31 % Allowed : 14.70 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.26), residues: 1007 helix: 1.13 (0.24), residues: 508 sheet: -0.65 (0.45), residues: 124 loop : -0.49 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 927 HIS 0.001 0.000 HIS A 278 PHE 0.016 0.001 PHE A 367 TYR 0.011 0.001 TYR A 842 ARG 0.004 0.000 ARG A 923 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 0.939 Fit side-chains REVERT: A 31 LYS cc_start: 0.7353 (mttt) cc_final: 0.7044 (mmtp) REVERT: A 239 MET cc_start: 0.4679 (mtt) cc_final: 0.3652 (tpt) REVERT: A 371 ARG cc_start: 0.6431 (ptp-110) cc_final: 0.5735 (ptp90) REVERT: A 397 LYS cc_start: 0.7785 (tptp) cc_final: 0.7373 (tmtt) REVERT: A 398 ASP cc_start: 0.6606 (OUTLIER) cc_final: 0.6190 (m-30) REVERT: A 431 LYS cc_start: 0.8738 (ttmm) cc_final: 0.8448 (mttp) REVERT: A 510 LYS cc_start: 0.8126 (mttt) cc_final: 0.7911 (mtpp) REVERT: A 528 ARG cc_start: 0.8714 (tpp-160) cc_final: 0.8481 (tpp-160) REVERT: A 529 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8307 (m) REVERT: A 541 LYS cc_start: 0.8639 (tttt) cc_final: 0.8374 (ttmt) REVERT: A 549 ARG cc_start: 0.7186 (mtt180) cc_final: 0.6790 (ttp-110) REVERT: A 585 LYS cc_start: 0.8298 (mtpp) cc_final: 0.7826 (mttt) REVERT: A 719 MET cc_start: 0.8788 (mmm) cc_final: 0.8260 (mmp) REVERT: A 797 VAL cc_start: 0.8365 (OUTLIER) cc_final: 0.8000 (p) REVERT: A 896 MET cc_start: 0.8433 (mtp) cc_final: 0.7996 (mtm) REVERT: A 917 GLU cc_start: 0.7917 (tt0) cc_final: 0.7510 (tp30) outliers start: 20 outliers final: 6 residues processed: 131 average time/residue: 1.3338 time to fit residues: 184.4692 Evaluate side-chains 117 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 812 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 87 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 GLN A 822 ASN A 874 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7985 Z= 0.167 Angle : 0.492 5.670 10844 Z= 0.251 Chirality : 0.041 0.127 1273 Planarity : 0.004 0.035 1377 Dihedral : 8.314 155.626 1107 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.36 % Allowed : 15.39 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.27), residues: 1007 helix: 1.31 (0.24), residues: 509 sheet: -0.62 (0.47), residues: 119 loop : -0.32 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 854 HIS 0.002 0.001 HIS A 15 PHE 0.015 0.001 PHE A 367 TYR 0.013 0.001 TYR A 842 ARG 0.004 0.000 ARG A 923 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 108 time to evaluate : 0.813 Fit side-chains REVERT: A 31 LYS cc_start: 0.7360 (mttt) cc_final: 0.7051 (mmtt) REVERT: A 239 MET cc_start: 0.4706 (mtt) cc_final: 0.3631 (tpt) REVERT: A 371 ARG cc_start: 0.6389 (ptp-110) cc_final: 0.5899 (ptp90) REVERT: A 397 LYS cc_start: 0.7795 (tptp) cc_final: 0.7390 (tmtt) REVERT: A 398 ASP cc_start: 0.6594 (OUTLIER) cc_final: 0.6226 (m-30) REVERT: A 431 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8467 (mttp) REVERT: A 510 LYS cc_start: 0.8123 (mttt) cc_final: 0.7906 (mtpp) REVERT: A 528 ARG cc_start: 0.8730 (tpp-160) cc_final: 0.8488 (tpp-160) REVERT: A 529 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8302 (m) REVERT: A 541 LYS cc_start: 0.8615 (tttt) cc_final: 0.8350 (ttmt) REVERT: A 549 ARG cc_start: 0.7168 (mtt180) cc_final: 0.6722 (mtp180) REVERT: A 568 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7836 (m-40) REVERT: A 585 LYS cc_start: 0.8347 (mtpp) cc_final: 0.7753 (mttt) REVERT: A 719 MET cc_start: 0.8790 (mmm) cc_final: 0.8079 (mmt) REVERT: A 797 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8057 (p) REVERT: A 896 MET cc_start: 0.8413 (mtp) cc_final: 0.8021 (mtm) REVERT: A 917 GLU cc_start: 0.7846 (tt0) cc_final: 0.7494 (tp30) outliers start: 29 outliers final: 14 residues processed: 128 average time/residue: 1.3307 time to fit residues: 179.9659 Evaluate side-chains 125 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 812 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 24 optimal weight: 0.0870 chunk 97 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 GLN A 874 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7985 Z= 0.235 Angle : 0.534 6.257 10844 Z= 0.272 Chirality : 0.043 0.135 1273 Planarity : 0.004 0.035 1377 Dihedral : 8.721 162.604 1107 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.59 % Allowed : 14.93 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1007 helix: 1.29 (0.24), residues: 509 sheet: -0.46 (0.45), residues: 129 loop : -0.35 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1016 HIS 0.003 0.001 HIS A 15 PHE 0.014 0.001 PHE A 367 TYR 0.015 0.002 TYR A 842 ARG 0.004 0.000 ARG A 923 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 111 time to evaluate : 0.909 Fit side-chains REVERT: A 31 LYS cc_start: 0.7458 (mttt) cc_final: 0.7062 (mmtp) REVERT: A 65 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.7987 (mp) REVERT: A 143 LYS cc_start: 0.8179 (pttt) cc_final: 0.7755 (ptmt) REVERT: A 239 MET cc_start: 0.4696 (mtt) cc_final: 0.3771 (tpt) REVERT: A 371 ARG cc_start: 0.6384 (ptp-110) cc_final: 0.5925 (ptp90) REVERT: A 397 LYS cc_start: 0.7836 (tptp) cc_final: 0.7393 (tmtt) REVERT: A 398 ASP cc_start: 0.6597 (OUTLIER) cc_final: 0.6187 (m-30) REVERT: A 431 LYS cc_start: 0.8739 (ttmm) cc_final: 0.8512 (mttp) REVERT: A 528 ARG cc_start: 0.8740 (tpp-160) cc_final: 0.8175 (tpp-160) REVERT: A 529 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8304 (m) REVERT: A 541 LYS cc_start: 0.8625 (tttt) cc_final: 0.8317 (ttmt) REVERT: A 549 ARG cc_start: 0.7184 (mtt180) cc_final: 0.6773 (mtp180) REVERT: A 585 LYS cc_start: 0.8278 (mtpp) cc_final: 0.7664 (mttt) REVERT: A 719 MET cc_start: 0.8813 (mmm) cc_final: 0.7997 (mmt) REVERT: A 797 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8245 (p) REVERT: A 891 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: A 896 MET cc_start: 0.8419 (mtp) cc_final: 0.8052 (mtm) outliers start: 31 outliers final: 16 residues processed: 131 average time/residue: 1.2717 time to fit residues: 175.9841 Evaluate side-chains 128 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 891 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 874 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7985 Z= 0.177 Angle : 0.508 6.464 10844 Z= 0.259 Chirality : 0.042 0.128 1273 Planarity : 0.004 0.033 1377 Dihedral : 8.667 161.556 1107 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.01 % Allowed : 16.20 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.27), residues: 1007 helix: 1.43 (0.24), residues: 509 sheet: -0.49 (0.43), residues: 140 loop : -0.25 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 854 HIS 0.002 0.001 HIS A 15 PHE 0.014 0.001 PHE A 367 TYR 0.013 0.001 TYR A 842 ARG 0.005 0.000 ARG A 923 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 0.888 Fit side-chains REVERT: A 31 LYS cc_start: 0.7413 (mttt) cc_final: 0.7041 (mmtp) REVERT: A 65 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.7983 (mp) REVERT: A 143 LYS cc_start: 0.8163 (pttt) cc_final: 0.7742 (ptmt) REVERT: A 239 MET cc_start: 0.4714 (mtt) cc_final: 0.3616 (tpt) REVERT: A 371 ARG cc_start: 0.6374 (ptp-110) cc_final: 0.5891 (ptp90) REVERT: A 397 LYS cc_start: 0.7837 (tptp) cc_final: 0.7406 (tmtt) REVERT: A 431 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8512 (mttp) REVERT: A 528 ARG cc_start: 0.8731 (tpp-160) cc_final: 0.8187 (tpp-160) REVERT: A 529 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8298 (m) REVERT: A 541 LYS cc_start: 0.8600 (tttt) cc_final: 0.8270 (ttmt) REVERT: A 549 ARG cc_start: 0.7184 (mtt180) cc_final: 0.6682 (mtm110) REVERT: A 585 LYS cc_start: 0.8303 (mtpp) cc_final: 0.7679 (mttt) REVERT: A 719 MET cc_start: 0.8819 (mmm) cc_final: 0.8243 (mmt) REVERT: A 797 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8103 (p) REVERT: A 891 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: A 896 MET cc_start: 0.8399 (mtp) cc_final: 0.8040 (mtm) outliers start: 26 outliers final: 15 residues processed: 126 average time/residue: 1.3053 time to fit residues: 173.9950 Evaluate side-chains 125 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 891 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 0.0000 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 88 optimal weight: 0.0970 chunk 93 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 874 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7985 Z= 0.142 Angle : 0.492 6.882 10844 Z= 0.248 Chirality : 0.041 0.124 1273 Planarity : 0.004 0.032 1377 Dihedral : 8.371 159.653 1107 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.43 % Allowed : 17.25 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.27), residues: 1007 helix: 1.57 (0.24), residues: 513 sheet: -0.39 (0.44), residues: 140 loop : -0.16 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 927 HIS 0.001 0.000 HIS A 15 PHE 0.015 0.001 PHE A 367 TYR 0.011 0.001 TYR A 842 ARG 0.005 0.000 ARG A 923 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 0.956 Fit side-chains REVERT: A 31 LYS cc_start: 0.7392 (mttt) cc_final: 0.7050 (mmtp) REVERT: A 65 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.7941 (mp) REVERT: A 174 ARG cc_start: 0.8176 (mtp180) cc_final: 0.7925 (mtp-110) REVERT: A 239 MET cc_start: 0.4756 (mtt) cc_final: 0.3633 (tpt) REVERT: A 371 ARG cc_start: 0.6363 (ptp-110) cc_final: 0.5909 (ptp90) REVERT: A 397 LYS cc_start: 0.7821 (tptp) cc_final: 0.7600 (tmtt) REVERT: A 431 LYS cc_start: 0.8716 (ttmm) cc_final: 0.8503 (mttp) REVERT: A 528 ARG cc_start: 0.8650 (tpp-160) cc_final: 0.8401 (tpp-160) REVERT: A 529 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8297 (m) REVERT: A 541 LYS cc_start: 0.8501 (tttt) cc_final: 0.8202 (ttmt) REVERT: A 549 ARG cc_start: 0.7224 (mtt180) cc_final: 0.6701 (mtm110) REVERT: A 585 LYS cc_start: 0.8307 (mtpp) cc_final: 0.7692 (mttt) REVERT: A 719 MET cc_start: 0.8783 (mmm) cc_final: 0.8352 (mmp) REVERT: A 797 VAL cc_start: 0.8414 (OUTLIER) cc_final: 0.8053 (p) REVERT: A 896 MET cc_start: 0.8373 (mtp) cc_final: 0.8027 (mtm) REVERT: A 917 GLU cc_start: 0.7853 (tt0) cc_final: 0.7487 (tp30) outliers start: 21 outliers final: 11 residues processed: 130 average time/residue: 1.2784 time to fit residues: 175.7063 Evaluate side-chains 120 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 812 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 874 GLN A 965 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7985 Z= 0.176 Angle : 0.517 8.738 10844 Z= 0.260 Chirality : 0.042 0.128 1273 Planarity : 0.004 0.033 1377 Dihedral : 8.452 159.948 1107 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.97 % Allowed : 18.06 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.27), residues: 1007 helix: 1.52 (0.24), residues: 513 sheet: -0.25 (0.45), residues: 134 loop : -0.15 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 854 HIS 0.002 0.001 HIS A 15 PHE 0.015 0.001 PHE A 73 TYR 0.013 0.001 TYR A 842 ARG 0.006 0.000 ARG A 923 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 1.032 Fit side-chains REVERT: A 31 LYS cc_start: 0.7336 (mttt) cc_final: 0.7044 (mmtp) REVERT: A 65 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.7954 (mp) REVERT: A 143 LYS cc_start: 0.8164 (pttt) cc_final: 0.7737 (ptmt) REVERT: A 239 MET cc_start: 0.4770 (mtt) cc_final: 0.3628 (tpt) REVERT: A 371 ARG cc_start: 0.6338 (ptp-110) cc_final: 0.5933 (ptp90) REVERT: A 397 LYS cc_start: 0.7832 (tptp) cc_final: 0.7616 (tmtt) REVERT: A 431 LYS cc_start: 0.8716 (ttmm) cc_final: 0.8509 (mttp) REVERT: A 462 LEU cc_start: 0.8191 (mt) cc_final: 0.7928 (mt) REVERT: A 528 ARG cc_start: 0.8710 (tpp-160) cc_final: 0.8465 (tpp-160) REVERT: A 529 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8316 (m) REVERT: A 541 LYS cc_start: 0.8528 (tttt) cc_final: 0.8203 (ttmt) REVERT: A 549 ARG cc_start: 0.7240 (mtt180) cc_final: 0.6704 (mtm110) REVERT: A 585 LYS cc_start: 0.8307 (mtpp) cc_final: 0.7687 (mttt) REVERT: A 719 MET cc_start: 0.8800 (mmm) cc_final: 0.7968 (mmt) REVERT: A 797 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8090 (p) REVERT: A 891 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: A 896 MET cc_start: 0.8390 (mtp) cc_final: 0.8056 (mtm) outliers start: 17 outliers final: 12 residues processed: 121 average time/residue: 1.3666 time to fit residues: 174.4132 Evaluate side-chains 120 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 891 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7985 Z= 0.239 Angle : 0.555 9.122 10844 Z= 0.279 Chirality : 0.043 0.134 1273 Planarity : 0.004 0.034 1377 Dihedral : 8.788 166.328 1107 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.43 % Allowed : 17.59 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.27), residues: 1007 helix: 1.39 (0.24), residues: 510 sheet: -0.29 (0.44), residues: 134 loop : -0.19 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1016 HIS 0.002 0.001 HIS A 15 PHE 0.014 0.001 PHE A 367 TYR 0.015 0.002 TYR A 842 ARG 0.005 0.000 ARG A 923 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 0.937 Fit side-chains REVERT: A 31 LYS cc_start: 0.7384 (mttt) cc_final: 0.7071 (mmtp) REVERT: A 65 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.7998 (mp) REVERT: A 143 LYS cc_start: 0.8162 (pttt) cc_final: 0.7748 (ptmt) REVERT: A 239 MET cc_start: 0.4747 (mtt) cc_final: 0.3767 (tpt) REVERT: A 371 ARG cc_start: 0.6349 (ptp-110) cc_final: 0.5904 (ptp90) REVERT: A 397 LYS cc_start: 0.7872 (tptp) cc_final: 0.7415 (tmtt) REVERT: A 462 LEU cc_start: 0.8207 (mt) cc_final: 0.7939 (mt) REVERT: A 528 ARG cc_start: 0.8724 (tpp-160) cc_final: 0.8456 (tpp-160) REVERT: A 529 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8327 (m) REVERT: A 541 LYS cc_start: 0.8574 (tttt) cc_final: 0.8263 (ttmt) REVERT: A 549 ARG cc_start: 0.7207 (mtt180) cc_final: 0.6774 (mtp180) REVERT: A 585 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7712 (mttt) REVERT: A 604 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.8016 (mm) REVERT: A 719 MET cc_start: 0.8829 (mmm) cc_final: 0.8296 (mmt) REVERT: A 797 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8275 (p) REVERT: A 896 MET cc_start: 0.8408 (mtp) cc_final: 0.8022 (mtm) outliers start: 21 outliers final: 14 residues processed: 123 average time/residue: 1.4221 time to fit residues: 184.5984 Evaluate side-chains 121 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 812 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 0.0060 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 874 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.136016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.107760 restraints weight = 8848.145| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.53 r_work: 0.2996 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7985 Z= 0.159 Angle : 0.513 9.021 10844 Z= 0.257 Chirality : 0.041 0.125 1273 Planarity : 0.004 0.031 1377 Dihedral : 8.561 164.093 1107 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.08 % Allowed : 18.06 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.27), residues: 1007 helix: 1.53 (0.24), residues: 513 sheet: -0.25 (0.45), residues: 134 loop : -0.14 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 854 HIS 0.002 0.001 HIS A 15 PHE 0.014 0.001 PHE A 367 TYR 0.012 0.001 TYR A 295 ARG 0.006 0.000 ARG A 923 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3501.31 seconds wall clock time: 61 minutes 33.22 seconds (3693.22 seconds total)