Starting phenix.real_space_refine on Wed May 14 05:07:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7au2_11923/05_2025/7au2_11923.cif Found real_map, /net/cci-nas-00/data/ceres_data/7au2_11923/05_2025/7au2_11923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7au2_11923/05_2025/7au2_11923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7au2_11923/05_2025/7au2_11923.map" model { file = "/net/cci-nas-00/data/ceres_data/7au2_11923/05_2025/7au2_11923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7au2_11923/05_2025/7au2_11923.cif" } resolution = 2.43 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 7252 2.51 5 N 1886 2.21 5 O 2042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11236 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5540 Classifications: {'peptide': 686} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 45, 'TRANS': 637} Chain breaks: 3 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: E, F, B Time building chain proxies: 12.09, per 1000 atoms: 1.08 Number of scatterers: 11236 At special positions: 0 Unit cell: (91.3379, 102.005, 103.339, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 2042 8.00 N 1886 7.00 C 7252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 793 " - pdb=" SG CYS B 915 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS A 879 " distance=2.04 Simple disulfide: pdb=" SG CYS A 915 " - pdb=" SG CYS B 793 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 400 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 831 " - pdb=" SG CYS B 879 " distance=2.04 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 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA F 3 " - " MAN F 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG C 1 " - " ASN A 592 " " NAG D 1 " - " ASN A 790 " " NAG E 1 " - " ASN B 592 " " NAG F 1 " - " ASN B 790 " Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.3 seconds 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2612 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 11 sheets defined 41.3% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.688A pdb=" N PHE A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 removed outlier: 3.656A pdb=" N ARG A 187 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 252 through 261 Processing helix chain 'A' and resid 286 through 291 removed outlier: 4.361A pdb=" N ASN A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 327 through 331 removed outlier: 3.513A pdb=" N GLU A 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 390 Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.841A pdb=" N LEU A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 458 removed outlier: 3.630A pdb=" N VAL A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 Processing helix chain 'A' and resid 486 through 491 removed outlier: 4.533A pdb=" N THR A 491 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.502A pdb=" N LEU A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 520 Processing helix chain 'A' and resid 522 through 538 Processing helix chain 'A' and resid 591 through 598 Processing helix chain 'A' and resid 599 through 606 Processing helix chain 'A' and resid 626 through 630 Processing helix chain 'A' and resid 638 through 643 removed outlier: 3.889A pdb=" N GLY A 641 " --> pdb=" O PRO A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 653 removed outlier: 3.596A pdb=" N ALA A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 683 removed outlier: 3.677A pdb=" N MET A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 730 removed outlier: 3.548A pdb=" N ARG A 728 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 764 Processing helix chain 'A' and resid 807 through 816 Processing helix chain 'A' and resid 818 through 829 removed outlier: 3.922A pdb=" N ARG A 822 " --> pdb=" O PRO A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 845 Processing helix chain 'A' and resid 870 through 888 removed outlier: 4.127A pdb=" N ARG A 876 " --> pdb=" O HIS A 872 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS A 877 " --> pdb=" O PHE A 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 removed outlier: 3.687A pdb=" N PHE B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 188 removed outlier: 3.656A pdb=" N ARG B 187 " --> pdb=" O ASP B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 206 through 210 Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 252 through 261 Processing helix chain 'B' and resid 286 through 291 removed outlier: 4.361A pdb=" N ASN B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 327 through 331 removed outlier: 3.513A pdb=" N GLU B 330 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 390 removed outlier: 3.500A pdb=" N LYS B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 426 removed outlier: 3.840A pdb=" N LEU B 424 " --> pdb=" O ASP B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 458 removed outlier: 3.630A pdb=" N VAL B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 481 Processing helix chain 'B' and resid 486 through 491 removed outlier: 4.533A pdb=" N THR B 491 " --> pdb=" O PRO B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 removed outlier: 3.502A pdb=" N LEU B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 520 Processing helix chain 'B' and resid 522 through 538 Processing helix chain 'B' and resid 591 through 598 Processing helix chain 'B' and resid 599 through 606 Processing helix chain 'B' and resid 626 through 630 Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.888A pdb=" N GLY B 641 " --> pdb=" O PRO B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 653 removed outlier: 3.596A pdb=" N ALA B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 683 removed outlier: 3.677A pdb=" N MET B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 730 removed outlier: 3.548A pdb=" N ARG B 728 " --> pdb=" O LEU B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 764 Processing helix chain 'B' and resid 807 through 816 Processing helix chain 'B' and resid 818 through 829 removed outlier: 3.921A pdb=" N ARG B 822 " --> pdb=" O PRO B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 845 Processing helix chain 'B' and resid 870 through 888 removed outlier: 4.127A pdb=" N ARG B 876 " --> pdb=" O HIS B 872 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS B 877 " --> pdb=" O PHE B 873 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 198 removed outlier: 6.776A pdb=" N TYR A 197 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N LEU A 241 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR A 238 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE A 276 " --> pdb=" O TYR A 238 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE A 240 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL A 298 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.540A pdb=" N ILE A 443 " --> pdb=" O PHE A 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 395 through 397 removed outlier: 7.409A pdb=" N LEU A 395 " --> pdb=" O TYR A 341 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE A 343 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLU A 397 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE A 345 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N TYR A 341 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA A 431 " --> pdb=" O TYR A 341 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE A 343 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N ILE A 433 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N PHE A 345 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR A 429 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL A 462 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA A 431 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU A 464 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE A 433 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL A 485 " --> pdb=" O PRO A 461 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL A 463 " --> pdb=" O VAL A 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 551 through 552 removed outlier: 4.758A pdb=" N ALA A 551 " --> pdb=" O ARG A 719 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N MET A 716 " --> pdb=" O ASN A 690 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 692 " --> pdb=" O MET A 716 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL A 718 " --> pdb=" O VAL A 692 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 694 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N PHE A 663 " --> pdb=" O LYS A 691 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VAL A 693 " --> pdb=" O PHE A 663 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 665 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL A 695 " --> pdb=" O VAL A 665 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N MET A 667 " --> pdb=" O VAL A 695 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR A 664 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE A 743 " --> pdb=" O THR A 664 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL A 666 " --> pdb=" O ILE A 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 784 through 788 Processing sheet with id=AA6, first strand: chain 'A' and resid 898 through 900 Processing sheet with id=AA7, first strand: chain 'B' and resid 196 through 198 removed outlier: 6.776A pdb=" N TYR B 197 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N LEU B 241 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR B 238 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE B 276 " --> pdb=" O TYR B 238 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE B 240 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL B 298 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 303 through 304 removed outlier: 3.540A pdb=" N ILE B 443 " --> pdb=" O PHE B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 395 through 397 removed outlier: 7.409A pdb=" N LEU B 395 " --> pdb=" O TYR B 341 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE B 343 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLU B 397 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N PHE B 345 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N TYR B 341 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA B 431 " --> pdb=" O TYR B 341 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N PHE B 343 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N ILE B 433 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N PHE B 345 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR B 429 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL B 462 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA B 431 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU B 464 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE B 433 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL B 485 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL B 463 " --> pdb=" O VAL B 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 551 through 552 removed outlier: 4.758A pdb=" N ALA B 551 " --> pdb=" O ARG B 719 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N MET B 716 " --> pdb=" O ASN B 690 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B 692 " --> pdb=" O MET B 716 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL B 718 " --> pdb=" O VAL B 692 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 694 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N PHE B 663 " --> pdb=" O LYS B 691 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VAL B 693 " --> pdb=" O PHE B 663 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B 665 " --> pdb=" O VAL B 693 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL B 695 " --> pdb=" O VAL B 665 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N MET B 667 " --> pdb=" O VAL B 695 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR B 664 " --> pdb=" O LEU B 741 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE B 743 " --> pdb=" O THR B 664 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL B 666 " --> pdb=" O ILE B 743 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 784 through 788 369 hydrogen bonds defined for protein. 957 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: 3.64 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3574 1.34 - 1.46: 2831 1.46 - 1.58: 5061 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 11554 Sorted by residual: bond pdb=" N ILE A 829 " pdb=" CA ILE A 829 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.89e+00 bond pdb=" N ILE B 829 " pdb=" CA ILE B 829 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.82e+00 bond pdb=" N ASN B 830 " pdb=" CA ASN B 830 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.16e-02 7.43e+03 5.95e+00 bond pdb=" N ASN A 830 " pdb=" CA ASN A 830 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.16e-02 7.43e+03 5.94e+00 bond pdb=" N PHE A 918 " pdb=" CA PHE A 918 " ideal model delta sigma weight residual 1.455 1.486 -0.032 1.38e-02 5.25e+03 5.24e+00 ... (remaining 11549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 14726 1.25 - 2.50: 766 2.50 - 3.75: 174 3.75 - 5.00: 39 5.00 - 6.25: 21 Bond angle restraints: 15726 Sorted by residual: angle pdb=" C ASN A 830 " pdb=" N CYS A 831 " pdb=" CA CYS A 831 " ideal model delta sigma weight residual 122.74 128.48 -5.74 1.44e+00 4.82e-01 1.59e+01 angle pdb=" C ASN B 830 " pdb=" N CYS B 831 " pdb=" CA CYS B 831 " ideal model delta sigma weight residual 122.74 128.40 -5.66 1.44e+00 4.82e-01 1.54e+01 angle pdb=" CA CYS A 831 " pdb=" C CYS A 831 " pdb=" O CYS A 831 " ideal model delta sigma weight residual 120.57 116.07 4.50 1.20e+00 6.94e-01 1.41e+01 angle pdb=" CA CYS B 831 " pdb=" C CYS B 831 " pdb=" O CYS B 831 " ideal model delta sigma weight residual 120.57 116.09 4.48 1.20e+00 6.94e-01 1.39e+01 angle pdb=" CA PRO A 583 " pdb=" N PRO A 583 " pdb=" CD PRO A 583 " ideal model delta sigma weight residual 112.00 106.78 5.22 1.40e+00 5.10e-01 1.39e+01 ... (remaining 15721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.80: 6543 20.80 - 41.60: 385 41.60 - 62.40: 76 62.40 - 83.21: 28 83.21 - 104.01: 24 Dihedral angle restraints: 7056 sinusoidal: 3018 harmonic: 4038 Sorted by residual: dihedral pdb=" CA PHE A 520 " pdb=" C PHE A 520 " pdb=" N SER A 521 " pdb=" CA SER A 521 " ideal model delta harmonic sigma weight residual -180.00 -156.32 -23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA PHE B 520 " pdb=" C PHE B 520 " pdb=" N SER B 521 " pdb=" CA SER B 521 " ideal model delta harmonic sigma weight residual -180.00 -156.32 -23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA VAL A 242 " pdb=" C VAL A 242 " pdb=" N GLY A 243 " pdb=" CA GLY A 243 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 7053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1691 0.105 - 0.210: 57 0.210 - 0.316: 2 0.316 - 0.421: 0 0.421 - 0.526: 2 Chirality restraints: 1752 Sorted by residual: chirality pdb=" CB THR A 617 " pdb=" CA THR A 617 " pdb=" OG1 THR A 617 " pdb=" CG2 THR A 617 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" CB THR B 617 " pdb=" CA THR B 617 " pdb=" OG1 THR B 617 " pdb=" CG2 THR B 617 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.53 2.00e-01 2.50e+01 6.91e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 1749 not shown) Planarity restraints: 2008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 582 " 0.041 5.00e-02 4.00e+02 5.96e-02 5.67e+00 pdb=" N PRO A 583 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 582 " -0.041 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO B 583 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 583 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 583 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 890 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO B 891 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 891 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 891 " 0.023 5.00e-02 4.00e+02 ... (remaining 2005 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 4300 2.89 - 3.40: 10155 3.40 - 3.90: 18642 3.90 - 4.40: 22307 4.40 - 4.90: 36722 Nonbonded interactions: 92126 Sorted by model distance: nonbonded pdb=" N ASP A 833 " pdb=" OD1 ASP A 833 " model vdw 2.392 3.120 nonbonded pdb=" N ASP B 833 " pdb=" OD1 ASP B 833 " model vdw 2.393 3.120 nonbonded pdb=" OE1 GLN B 819 " pdb=" NH1 ARG B 822 " model vdw 2.442 3.120 nonbonded pdb=" OE1 GLN A 819 " pdb=" NH1 ARG A 822 " model vdw 2.442 3.120 nonbonded pdb=" O VAL A 851 " pdb=" O VAL A 899 " model vdw 2.444 3.040 ... (remaining 92121 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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 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: 8.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.820 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:9.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 0.086 11576 Z= 0.222 Angle : 0.724 7.985 15782 Z= 0.391 Chirality : 0.049 0.526 1752 Planarity : 0.005 0.060 2004 Dihedral : 15.752 104.007 4414 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.83 % Allowed : 7.93 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.04 (0.22), residues: 1356 helix: 0.45 (0.25), residues: 438 sheet: -0.62 (0.38), residues: 172 loop : -0.04 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 266 HIS 0.005 0.002 HIS B 877 PHE 0.024 0.002 PHE B 600 TYR 0.023 0.002 TYR A 791 ARG 0.017 0.001 ARG B 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 4) link_NAG-ASN : angle 4.26266 ( 12) link_BETA1-4 : bond 0.00570 ( 6) link_BETA1-4 : angle 1.99186 ( 18) link_ALPHA1-3 : bond 0.00980 ( 2) link_ALPHA1-3 : angle 2.75765 ( 6) hydrogen bonds : bond 0.19012 ( 369) hydrogen bonds : angle 6.49082 ( 957) SS BOND : bond 0.00416 ( 10) SS BOND : angle 1.44318 ( 20) covalent geometry : bond 0.00522 (11554) covalent geometry : angle 0.70879 (15726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 1.417 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 138 average time/residue: 1.5746 time to fit residues: 232.0726 Evaluate side-chains 131 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 625 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 469 GLN A 616 HIS A 782 HIS A 881 ASN B 216 GLN B 469 GLN B 616 HIS B 782 HIS B 881 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.140801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.106809 restraints weight = 11347.266| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.71 r_work: 0.3029 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11576 Z= 0.148 Angle : 0.612 6.366 15782 Z= 0.323 Chirality : 0.046 0.148 1752 Planarity : 0.005 0.048 2004 Dihedral : 8.230 67.241 1760 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.07 % Allowed : 7.27 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 0.26 (0.22), residues: 1356 helix: 0.87 (0.25), residues: 452 sheet: -0.66 (0.39), residues: 172 loop : 0.05 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 761 HIS 0.005 0.001 HIS A 776 PHE 0.014 0.002 PHE A 206 TYR 0.016 0.002 TYR A 808 ARG 0.010 0.001 ARG B 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 4) link_NAG-ASN : angle 3.55124 ( 12) link_BETA1-4 : bond 0.00529 ( 6) link_BETA1-4 : angle 2.06626 ( 18) link_ALPHA1-3 : bond 0.01208 ( 2) link_ALPHA1-3 : angle 2.53340 ( 6) hydrogen bonds : bond 0.05718 ( 369) hydrogen bonds : angle 5.36337 ( 957) SS BOND : bond 0.00185 ( 10) SS BOND : angle 0.98895 ( 20) covalent geometry : bond 0.00342 (11554) covalent geometry : angle 0.59761 (15726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 1.341 Fit side-chains REVERT: A 330 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: A 824 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.7990 (tmt) REVERT: B 330 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: B 824 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.7975 (tmt) outliers start: 25 outliers final: 6 residues processed: 147 average time/residue: 1.4649 time to fit residues: 230.8477 Evaluate side-chains 141 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 824 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 97 optimal weight: 0.2980 chunk 103 optimal weight: 0.0970 chunk 71 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS A 216 GLN A 307 GLN B 216 GLN B 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.107204 restraints weight = 11441.331| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.73 r_work: 0.3033 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11576 Z= 0.130 Angle : 0.565 5.844 15782 Z= 0.298 Chirality : 0.044 0.151 1752 Planarity : 0.005 0.042 2004 Dihedral : 6.974 50.911 1754 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.07 % Allowed : 8.84 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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 (0.23), residues: 1356 helix: 1.12 (0.25), residues: 452 sheet: -0.74 (0.38), residues: 172 loop : 0.09 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 266 HIS 0.005 0.001 HIS B 874 PHE 0.012 0.002 PHE A 804 TYR 0.013 0.001 TYR A 808 ARG 0.007 0.000 ARG A 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 4) link_NAG-ASN : angle 3.14629 ( 12) link_BETA1-4 : bond 0.00524 ( 6) link_BETA1-4 : angle 1.76985 ( 18) link_ALPHA1-3 : bond 0.01044 ( 2) link_ALPHA1-3 : angle 1.67611 ( 6) hydrogen bonds : bond 0.05356 ( 369) hydrogen bonds : angle 5.25431 ( 957) SS BOND : bond 0.00186 ( 10) SS BOND : angle 0.89872 ( 20) covalent geometry : bond 0.00293 (11554) covalent geometry : angle 0.55443 (15726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.196 Fit side-chains REVERT: A 330 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: A 824 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.7989 (tmt) REVERT: B 257 GLU cc_start: 0.8332 (tt0) cc_final: 0.8082 (tt0) REVERT: B 330 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: B 824 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.7988 (tmt) outliers start: 25 outliers final: 8 residues processed: 148 average time/residue: 1.4801 time to fit residues: 234.9168 Evaluate side-chains 141 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 824 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN B 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.141314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.106956 restraints weight = 11294.327| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.73 r_work: 0.3031 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11576 Z= 0.129 Angle : 0.559 5.762 15782 Z= 0.294 Chirality : 0.044 0.166 1752 Planarity : 0.005 0.041 2004 Dihedral : 5.861 34.407 1754 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.23 % Allowed : 8.84 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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 (0.22), residues: 1356 helix: 1.17 (0.25), residues: 452 sheet: -0.68 (0.40), residues: 166 loop : 0.02 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 266 HIS 0.003 0.001 HIS B 776 PHE 0.013 0.002 PHE B 600 TYR 0.014 0.001 TYR A 808 ARG 0.009 0.001 ARG B 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00066 ( 4) link_NAG-ASN : angle 3.17935 ( 12) link_BETA1-4 : bond 0.00523 ( 6) link_BETA1-4 : angle 1.78458 ( 18) link_ALPHA1-3 : bond 0.01149 ( 2) link_ALPHA1-3 : angle 2.01650 ( 6) hydrogen bonds : bond 0.05167 ( 369) hydrogen bonds : angle 5.17016 ( 957) SS BOND : bond 0.00176 ( 10) SS BOND : angle 0.89794 ( 20) covalent geometry : bond 0.00292 (11554) covalent geometry : angle 0.54778 (15726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.292 Fit side-chains REVERT: A 330 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: A 672 ARG cc_start: 0.5531 (OUTLIER) cc_final: 0.5185 (mtt-85) REVERT: A 824 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.7949 (tmt) REVERT: B 330 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: B 672 ARG cc_start: 0.5523 (OUTLIER) cc_final: 0.5178 (mtt-85) REVERT: B 824 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.7951 (tmt) outliers start: 27 outliers final: 15 residues processed: 149 average time/residue: 1.4620 time to fit residues: 234.0503 Evaluate side-chains 149 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 672 ARG Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 672 ARG Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 824 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.141863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.107542 restraints weight = 11344.479| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.73 r_work: 0.3041 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 11576 Z= 0.119 Angle : 0.542 5.651 15782 Z= 0.284 Chirality : 0.044 0.146 1752 Planarity : 0.005 0.040 2004 Dihedral : 5.252 28.788 1754 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.23 % Allowed : 9.67 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: 0.44 (0.23), residues: 1356 helix: 1.24 (0.25), residues: 452 sheet: -0.68 (0.40), residues: 166 loop : 0.03 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 266 HIS 0.003 0.001 HIS A 616 PHE 0.011 0.001 PHE B 600 TYR 0.013 0.001 TYR A 808 ARG 0.009 0.000 ARG A 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00081 ( 4) link_NAG-ASN : angle 3.11554 ( 12) link_BETA1-4 : bond 0.00536 ( 6) link_BETA1-4 : angle 1.64823 ( 18) link_ALPHA1-3 : bond 0.01046 ( 2) link_ALPHA1-3 : angle 1.78622 ( 6) hydrogen bonds : bond 0.04894 ( 369) hydrogen bonds : angle 5.12945 ( 957) SS BOND : bond 0.00145 ( 10) SS BOND : angle 0.84079 ( 20) covalent geometry : bond 0.00264 (11554) covalent geometry : angle 0.53077 (15726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.190 Fit side-chains REVERT: A 257 GLU cc_start: 0.8333 (tt0) cc_final: 0.8073 (tt0) REVERT: A 330 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: A 672 ARG cc_start: 0.5559 (OUTLIER) cc_final: 0.5214 (mtt-85) REVERT: A 824 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.7944 (tmt) REVERT: B 330 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: B 672 ARG cc_start: 0.5575 (OUTLIER) cc_final: 0.5197 (mtt-85) REVERT: B 824 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.7947 (tmt) outliers start: 27 outliers final: 14 residues processed: 140 average time/residue: 1.5117 time to fit residues: 226.4879 Evaluate side-chains 147 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 672 ARG Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 503 SER Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 672 ARG Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 824 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.0856 > 50: distance: 81 - 86: 27.000 distance: 86 - 87: 26.813 distance: 87 - 88: 9.698 distance: 87 - 90: 38.700 distance: 88 - 89: 23.327 distance: 88 - 94: 32.563 distance: 90 - 91: 10.402 distance: 91 - 92: 31.191 distance: 91 - 93: 30.274 distance: 94 - 95: 26.145 distance: 95 - 96: 19.150 distance: 95 - 98: 15.996 distance: 96 - 97: 31.049 distance: 96 - 105: 19.947 distance: 98 - 99: 23.462 distance: 99 - 100: 10.809 distance: 99 - 101: 11.883 distance: 100 - 102: 37.676 distance: 101 - 103: 23.375 distance: 102 - 104: 20.013 distance: 103 - 104: 20.842 distance: 105 - 106: 14.823 distance: 105 - 111: 48.899 distance: 106 - 107: 33.299 distance: 106 - 109: 6.567 distance: 107 - 108: 19.570 distance: 107 - 112: 29.112 distance: 109 - 110: 42.392 distance: 110 - 111: 57.104 distance: 112 - 113: 17.326 distance: 113 - 114: 47.046 distance: 113 - 116: 16.814 distance: 114 - 115: 40.552 distance: 114 - 122: 30.880 distance: 116 - 117: 25.775 distance: 117 - 118: 19.572 distance: 117 - 119: 10.687 distance: 118 - 120: 5.880 distance: 119 - 121: 9.044 distance: 120 - 121: 6.612 distance: 122 - 123: 27.507 distance: 123 - 124: 35.460 distance: 123 - 126: 22.896 distance: 124 - 125: 40.234 distance: 124 - 129: 32.903 distance: 126 - 127: 16.451 distance: 126 - 128: 23.598 distance: 129 - 130: 34.484 distance: 129 - 135: 26.687 distance: 130 - 131: 7.844 distance: 130 - 133: 11.185 distance: 131 - 132: 11.930 distance: 131 - 136: 21.925 distance: 133 - 134: 27.178 distance: 134 - 135: 25.473 distance: 136 - 137: 8.429 distance: 137 - 138: 54.682 distance: 137 - 140: 39.701 distance: 138 - 139: 12.076 distance: 138 - 147: 45.517 distance: 140 - 141: 11.969 distance: 141 - 142: 23.718 distance: 141 - 143: 26.907 distance: 142 - 144: 21.947 distance: 143 - 145: 20.973 distance: 144 - 146: 30.238 distance: 145 - 146: 29.031 distance: 147 - 148: 40.190 distance: 148 - 149: 13.693 distance: 148 - 151: 14.709 distance: 149 - 150: 47.817 distance: 149 - 155: 12.044 distance: 151 - 152: 22.301 distance: 152 - 153: 26.868 distance: 152 - 154: 32.738 distance: 155 - 156: 29.662 distance: 155 - 161: 13.114 distance: 156 - 157: 10.762 distance: 156 - 159: 25.803 distance: 157 - 158: 23.349 distance: 157 - 162: 6.632 distance: 159 - 160: 29.126 distance: 160 - 161: 24.066 distance: 162 - 163: 17.391 distance: 163 - 164: 19.685 distance: 163 - 166: 25.145 distance: 164 - 165: 17.909 distance: 164 - 169: 22.893 distance: 166 - 167: 25.296 distance: 166 - 168: 4.517