Starting phenix.real_space_refine on Tue Nov 14 04:05:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgj_7096/11_2023/6bgj_7096_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgj_7096/11_2023/6bgj_7096.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgj_7096/11_2023/6bgj_7096.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgj_7096/11_2023/6bgj_7096.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgj_7096/11_2023/6bgj_7096_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgj_7096/11_2023/6bgj_7096_neut.pdb" } resolution = 3.8 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= 1.000 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 48 5.16 5 C 4892 2.51 5 N 1194 2.21 5 O 1282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 7418 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3708 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 19, 'TRANS': 470} Chain breaks: 3 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 171 Chain: "B" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3708 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 19, 'TRANS': 470} Chain breaks: 3 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 171 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.27, per 1000 atoms: 0.58 Number of scatterers: 7418 At special positions: 0 Unit cell: (103.02, 82.62, 99.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 48 16.00 O 1282 8.00 N 1194 7.00 C 4892 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 - 3.50 Amino acid : False - 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: 2.89 Conformation dependent library (CDL) restraints added in 1.9 seconds 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1868 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 74.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 292 through 303 removed outlier: 3.606A pdb=" N LEU A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 324 Processing helix chain 'A' and resid 325 through 362 removed outlier: 3.691A pdb=" N TYR A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 332 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) Proline residue: A 344 - end of helix removed outlier: 3.534A pdb=" N VAL A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 359 " --> pdb=" O TYR A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 390 through 401 removed outlier: 3.847A pdb=" N ARG A 399 " --> pdb=" O CYS A 395 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 407 through 442 removed outlier: 3.670A pdb=" N PHE A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR A 436 " --> pdb=" O MET A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 508 through 522 removed outlier: 3.873A pdb=" N ALA A 519 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 565 removed outlier: 3.584A pdb=" N VAL A 539 " --> pdb=" O THR A 535 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS A 555 " --> pdb=" O GLU A 551 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP A 559 " --> pdb=" O CYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 589 removed outlier: 3.521A pdb=" N PHE A 578 " --> pdb=" O GLU A 574 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 597 Processing helix chain 'A' and resid 627 through 642 removed outlier: 4.265A pdb=" N CYS A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 636 " --> pdb=" O ILE A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 689 removed outlier: 3.684A pdb=" N PHE A 687 " --> pdb=" O GLU A 684 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 689 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 710 removed outlier: 3.615A pdb=" N GLN A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 740 removed outlier: 3.861A pdb=" N ASN A 726 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A 732 " --> pdb=" O ILE A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 771 removed outlier: 3.747A pdb=" N TYR A 757 " --> pdb=" O ILE A 753 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE A 759 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 768 " --> pdb=" O GLY A 764 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 769 " --> pdb=" O LYS A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 776 Processing helix chain 'A' and resid 781 through 790 removed outlier: 5.087A pdb=" N TYR A 787 " --> pdb=" O PRO A 783 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 802 No H-bonds generated for 'chain 'A' and resid 800 through 802' Processing helix chain 'A' and resid 803 through 811 removed outlier: 3.938A pdb=" N SER A 807 " --> pdb=" O HIS A 803 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER A 811 " --> pdb=" O SER A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 825 Processing helix chain 'A' and resid 848 through 850 No H-bonds generated for 'chain 'A' and resid 848 through 850' Processing helix chain 'A' and resid 851 through 882 removed outlier: 3.738A pdb=" N ALA A 855 " --> pdb=" O LYS A 851 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 856 " --> pdb=" O ASP A 852 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN A 869 " --> pdb=" O ILE A 865 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET A 872 " --> pdb=" O GLN A 868 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TRP A 880 " --> pdb=" O ASP A 876 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 882 " --> pdb=" O VAL A 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.606A pdb=" N LEU B 300 " --> pdb=" O ASN B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 324 Processing helix chain 'B' and resid 325 through 362 removed outlier: 3.690A pdb=" N TYR B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 332 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) Proline residue: B 344 - end of helix removed outlier: 3.535A pdb=" N VAL B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 359 " --> pdb=" O TYR B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 375 Processing helix chain 'B' and resid 390 through 401 removed outlier: 3.847A pdb=" N ARG B 399 " --> pdb=" O CYS B 395 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 407 through 442 removed outlier: 3.670A pdb=" N PHE B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR B 436 " --> pdb=" O MET B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 508 through 522 removed outlier: 3.873A pdb=" N ALA B 519 " --> pdb=" O ALA B 515 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 565 removed outlier: 3.584A pdb=" N VAL B 539 " --> pdb=" O THR B 535 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 547 " --> pdb=" O LEU B 543 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR B 553 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY B 554 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS B 555 " --> pdb=" O GLU B 551 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP B 559 " --> pdb=" O CYS B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 589 removed outlier: 3.521A pdb=" N PHE B 578 " --> pdb=" O GLU B 574 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 582 " --> pdb=" O PHE B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 597 Processing helix chain 'B' and resid 627 through 642 removed outlier: 4.265A pdb=" N CYS B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 636 " --> pdb=" O ILE B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 689 removed outlier: 3.683A pdb=" N PHE B 687 " --> pdb=" O GLU B 684 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 689 " --> pdb=" O ASP B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 710 removed outlier: 3.614A pdb=" N GLN B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 740 removed outlier: 3.861A pdb=" N ASN B 726 " --> pdb=" O PHE B 722 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE B 729 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 771 removed outlier: 3.748A pdb=" N TYR B 757 " --> pdb=" O ILE B 753 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE B 759 " --> pdb=" O ILE B 755 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 768 " --> pdb=" O GLY B 764 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 769 " --> pdb=" O LYS B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 776 Processing helix chain 'B' and resid 781 through 790 removed outlier: 5.086A pdb=" N TYR B 787 " --> pdb=" O PRO B 783 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR B 789 " --> pdb=" O LEU B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 802 No H-bonds generated for 'chain 'B' and resid 800 through 802' Processing helix chain 'B' and resid 803 through 811 removed outlier: 3.937A pdb=" N SER B 807 " --> pdb=" O HIS B 803 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER B 811 " --> pdb=" O SER B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 825 Processing helix chain 'B' and resid 848 through 850 No H-bonds generated for 'chain 'B' and resid 848 through 850' Processing helix chain 'B' and resid 851 through 882 removed outlier: 3.738A pdb=" N ALA B 855 " --> pdb=" O LYS B 851 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 856 " --> pdb=" O ASP B 852 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN B 869 " --> pdb=" O ILE B 865 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET B 872 " --> pdb=" O GLN B 868 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TRP B 880 " --> pdb=" O ASP B 876 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 882 " --> pdb=" O VAL B 878 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1347 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: 1.84 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2247 1.34 - 1.46: 1907 1.46 - 1.58: 3372 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 7602 Sorted by residual: bond pdb=" C ILE A 782 " pdb=" N PRO A 783 " ideal model delta sigma weight residual 1.334 1.382 -0.048 8.40e-03 1.42e+04 3.28e+01 bond pdb=" C ILE B 782 " pdb=" N PRO B 783 " ideal model delta sigma weight residual 1.334 1.381 -0.047 8.40e-03 1.42e+04 3.15e+01 bond pdb=" CG1 ILE A 775 " pdb=" CD1 ILE A 775 " ideal model delta sigma weight residual 1.513 1.408 0.105 3.90e-02 6.57e+02 7.30e+00 bond pdb=" CG1 ILE B 775 " pdb=" CD1 ILE B 775 " ideal model delta sigma weight residual 1.513 1.408 0.105 3.90e-02 6.57e+02 7.22e+00 bond pdb=" N SER A 811 " pdb=" CA SER A 811 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.29e-02 6.01e+03 5.18e+00 ... (remaining 7597 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.79: 227 106.79 - 113.61: 3990 113.61 - 120.42: 3365 120.42 - 127.24: 2696 127.24 - 134.05: 82 Bond angle restraints: 10360 Sorted by residual: angle pdb=" C ASN A 809 " pdb=" N VAL A 810 " pdb=" CA VAL A 810 " ideal model delta sigma weight residual 121.97 130.80 -8.83 1.80e+00 3.09e-01 2.41e+01 angle pdb=" C SER B 522 " pdb=" N SER B 523 " pdb=" CA SER B 523 " ideal model delta sigma weight residual 122.83 128.12 -5.29 1.08e+00 8.57e-01 2.40e+01 angle pdb=" C ASN B 809 " pdb=" N VAL B 810 " pdb=" CA VAL B 810 " ideal model delta sigma weight residual 121.97 130.77 -8.80 1.80e+00 3.09e-01 2.39e+01 angle pdb=" C SER A 522 " pdb=" N SER A 523 " pdb=" CA SER A 523 " ideal model delta sigma weight residual 122.83 128.10 -5.27 1.08e+00 8.57e-01 2.38e+01 angle pdb=" N ASP B 752 " pdb=" CA ASP B 752 " pdb=" C ASP B 752 " ideal model delta sigma weight residual 110.91 116.49 -5.58 1.17e+00 7.31e-01 2.28e+01 ... (remaining 10355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.03: 3780 11.03 - 22.06: 543 22.06 - 33.10: 59 33.10 - 44.13: 28 44.13 - 55.16: 10 Dihedral angle restraints: 4420 sinusoidal: 1538 harmonic: 2882 Sorted by residual: dihedral pdb=" CA GLN A 793 " pdb=" C GLN A 793 " pdb=" N ASN A 794 " pdb=" CA ASN A 794 " ideal model delta harmonic sigma weight residual 180.00 124.84 55.16 0 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" CA GLN B 793 " pdb=" C GLN B 793 " pdb=" N ASN B 794 " pdb=" CA ASN B 794 " ideal model delta harmonic sigma weight residual 180.00 124.90 55.10 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA ASN A 809 " pdb=" C ASN A 809 " pdb=" N VAL A 810 " pdb=" CA VAL A 810 " ideal model delta harmonic sigma weight residual 180.00 134.12 45.88 0 5.00e+00 4.00e-02 8.42e+01 ... (remaining 4417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1014 0.081 - 0.161: 174 0.161 - 0.241: 14 0.241 - 0.322: 0 0.322 - 0.402: 2 Chirality restraints: 1204 Sorted by residual: chirality pdb=" CB ILE A 364 " pdb=" CA ILE A 364 " pdb=" CG1 ILE A 364 " pdb=" CG2 ILE A 364 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CB ILE B 364 " pdb=" CA ILE B 364 " pdb=" CG1 ILE B 364 " pdb=" CG2 ILE B 364 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CB VAL A 713 " pdb=" CA VAL A 713 " pdb=" CG1 VAL A 713 " pdb=" CG2 VAL A 713 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1201 not shown) Planarity restraints: 1298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 379 " -0.059 5.00e-02 4.00e+02 8.88e-02 1.26e+01 pdb=" N PRO A 380 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 380 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 380 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 379 " -0.059 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO B 380 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 380 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 380 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 622 " 0.056 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO B 623 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 623 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 623 " 0.047 5.00e-02 4.00e+02 ... (remaining 1295 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 177 2.69 - 3.25: 7668 3.25 - 3.80: 11542 3.80 - 4.35: 15421 4.35 - 4.90: 24120 Nonbonded interactions: 58928 Sorted by model distance: nonbonded pdb=" OD2 ASP B 383 " pdb=" NH2 ARG B 614 " model vdw 2.142 2.520 nonbonded pdb=" OD2 ASP A 383 " pdb=" NH2 ARG A 614 " model vdw 2.142 2.520 nonbonded pdb=" NH2 ARG B 321 " pdb=" OE2 GLU B 326 " model vdw 2.195 2.520 nonbonded pdb=" NH2 ARG A 321 " pdb=" OE2 GLU A 326 " model vdw 2.195 2.520 nonbonded pdb=" OD2 ASP A 821 " pdb=" N LYS A 846 " model vdw 2.225 2.520 ... (remaining 58923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.770 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: 4.020 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 22.910 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 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 0.105 7602 Z= 0.515 Angle : 1.211 10.576 10360 Z= 0.673 Chirality : 0.060 0.402 1204 Planarity : 0.010 0.089 1298 Dihedral : 10.716 55.160 2552 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.62 % Allowed : 13.69 % Favored : 85.68 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 2.14 % 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: -5.82 (0.19), residues: 964 helix: -3.34 (0.14), residues: 582 sheet: None (None), residues: 0 loop : -4.63 (0.25), residues: 382 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 0.832 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1729 time to fit residues: 51.8795 Evaluate side-chains 157 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.782 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 0.0980 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN A 645 GLN ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 HIS A 809 ASN B 375 ASN B 645 GLN ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 809 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5964 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7602 Z= 0.239 Angle : 0.863 10.756 10360 Z= 0.449 Chirality : 0.047 0.233 1204 Planarity : 0.007 0.056 1298 Dihedral : 8.339 46.996 1048 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.83 % Allowed : 11.72 % Favored : 87.45 % Rotamer: Outliers : 1.93 % Allowed : 10.47 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.28 % 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: -4.19 (0.22), residues: 964 helix: -1.88 (0.17), residues: 660 sheet: None (None), residues: 0 loop : -4.69 (0.29), residues: 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 172 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 174 average time/residue: 0.1630 time to fit residues: 39.8243 Evaluate side-chains 151 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 0.829 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0846 time to fit residues: 1.5926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN B 645 GLN ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7602 Z= 0.236 Angle : 0.802 13.661 10360 Z= 0.416 Chirality : 0.046 0.205 1204 Planarity : 0.006 0.046 1298 Dihedral : 7.729 41.155 1048 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.73 % Allowed : 12.97 % Favored : 86.31 % Rotamer: Outliers : 1.65 % Allowed : 12.53 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.28 % 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: -3.41 (0.24), residues: 964 helix: -1.18 (0.18), residues: 674 sheet: None (None), residues: 0 loop : -4.80 (0.28), residues: 290 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 157 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 161 average time/residue: 0.1627 time to fit residues: 36.6088 Evaluate side-chains 142 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 0.763 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0778 time to fit residues: 1.9302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 0.0770 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 42 optimal weight: 0.0970 chunk 59 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.7938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 GLN ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5972 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7602 Z= 0.230 Angle : 0.773 9.602 10360 Z= 0.402 Chirality : 0.046 0.246 1204 Planarity : 0.005 0.045 1298 Dihedral : 7.326 38.905 1048 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.52 % Allowed : 13.38 % Favored : 86.10 % Rotamer: Outliers : 0.69 % Allowed : 13.64 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.96 % 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: -2.63 (0.25), residues: 964 helix: -0.61 (0.19), residues: 680 sheet: None (None), residues: 0 loop : -4.55 (0.30), residues: 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 153 time to evaluate : 1.024 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 156 average time/residue: 0.1740 time to fit residues: 37.9548 Evaluate side-chains 136 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 0.799 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1065 time to fit residues: 1.4183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN A 633 GLN A 645 GLN ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5979 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7602 Z= 0.234 Angle : 0.763 8.340 10360 Z= 0.396 Chirality : 0.045 0.190 1204 Planarity : 0.005 0.045 1298 Dihedral : 7.120 48.866 1048 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.80 % Favored : 85.89 % Rotamer: Outliers : 1.65 % Allowed : 13.64 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.96 % 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: -2.01 (0.26), residues: 964 helix: -0.12 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -4.37 (0.30), residues: 286 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 0.919 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 153 average time/residue: 0.1703 time to fit residues: 36.2994 Evaluate side-chains 146 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 0.827 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.0883 time to fit residues: 2.0316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 94 optimal weight: 0.0770 chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5944 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 7602 Z= 0.210 Angle : 0.751 7.767 10360 Z= 0.385 Chirality : 0.044 0.210 1204 Planarity : 0.005 0.044 1298 Dihedral : 6.837 45.779 1048 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.41 % Allowed : 13.28 % Favored : 86.31 % Rotamer: Outliers : 1.52 % Allowed : 14.46 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % 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: -1.70 (0.27), residues: 964 helix: 0.10 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -4.37 (0.31), residues: 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 0.873 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 151 average time/residue: 0.1669 time to fit residues: 35.5346 Evaluate side-chains 142 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 137 time to evaluate : 0.871 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0826 time to fit residues: 1.9426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 94 optimal weight: 0.0060 chunk 59 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5955 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7602 Z= 0.233 Angle : 0.768 9.907 10360 Z= 0.393 Chirality : 0.045 0.202 1204 Planarity : 0.005 0.049 1298 Dihedral : 6.712 39.969 1048 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.28 % Favored : 86.41 % Rotamer: Outliers : 1.52 % Allowed : 15.56 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % 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: -1.53 (0.27), residues: 964 helix: 0.23 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -4.35 (0.30), residues: 274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 150 average time/residue: 0.1723 time to fit residues: 36.3598 Evaluate side-chains 144 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 0.861 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0911 time to fit residues: 2.3888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.1980 chunk 56 optimal weight: 4.9990 chunk 28 optimal weight: 0.0970 chunk 18 optimal weight: 0.0010 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.0060 chunk 74 optimal weight: 0.4980 chunk 85 optimal weight: 5.9990 chunk 90 optimal weight: 0.0980 overall best weight: 0.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 ASN ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 ASN ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5876 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7602 Z= 0.189 Angle : 0.783 10.984 10360 Z= 0.398 Chirality : 0.045 0.283 1204 Planarity : 0.005 0.051 1298 Dihedral : 6.535 49.231 1048 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.41 % Allowed : 13.17 % Favored : 86.41 % Rotamer: Outliers : 0.83 % Allowed : 16.39 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -1.50 (0.27), residues: 964 helix: 0.30 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -4.41 (0.29), residues: 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 148 time to evaluate : 0.752 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 151 average time/residue: 0.1756 time to fit residues: 36.9595 Evaluate side-chains 137 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 0.817 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2937 time to fit residues: 1.8855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9990 chunk 88 optimal weight: 0.0970 chunk 90 optimal weight: 0.0040 chunk 52 optimal weight: 0.0770 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 27 optimal weight: 0.0670 chunk 79 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 87 optimal weight: 0.1980 chunk 57 optimal weight: 0.0670 overall best weight: 0.0624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 ASN ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 727 ASN ** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5831 moved from start: 0.5836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7602 Z= 0.200 Angle : 0.780 11.257 10360 Z= 0.399 Chirality : 0.045 0.206 1204 Planarity : 0.005 0.051 1298 Dihedral : 6.432 47.228 1048 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.07 % Favored : 86.62 % Rotamer: Outliers : 0.55 % Allowed : 18.73 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -1.43 (0.27), residues: 964 helix: 0.32 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -4.34 (0.30), residues: 276 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 152 time to evaluate : 0.842 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 152 average time/residue: 0.1792 time to fit residues: 37.6876 Evaluate side-chains 137 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 0.829 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0946 time to fit residues: 1.4978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 5.9990 chunk 56 optimal weight: 0.0010 chunk 44 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 GLN ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5859 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7602 Z= 0.212 Angle : 0.821 16.534 10360 Z= 0.415 Chirality : 0.048 0.395 1204 Planarity : 0.005 0.045 1298 Dihedral : 6.385 46.398 1048 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.66 % Favored : 86.93 % Rotamer: Outliers : 0.41 % Allowed : 18.87 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -1.26 (0.27), residues: 964 helix: 0.45 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -4.25 (0.31), residues: 278 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 0.786 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 135 average time/residue: 0.1697 time to fit residues: 32.7009 Evaluate side-chains 134 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1679 time to fit residues: 2.2727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 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 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 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 = 0.4884 r_free = 0.4884 target = 0.235387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.198493 restraints weight = 10441.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.201967 restraints weight = 7196.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.204520 restraints weight = 5639.268| |-----------------------------------------------------------------------------| r_work (final): 0.4580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.6079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7602 Z= 0.236 Angle : 0.820 17.408 10360 Z= 0.415 Chirality : 0.047 0.211 1204 Planarity : 0.005 0.044 1298 Dihedral : 6.441 48.920 1048 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.07 % Favored : 86.62 % Rotamer: Outliers : 0.14 % Allowed : 19.97 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -1.19 (0.28), residues: 964 helix: 0.48 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -4.21 (0.32), residues: 276 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1745.79 seconds wall clock time: 32 minutes 17.46 seconds (1937.46 seconds total)