Starting phenix.real_space_refine on Fri Aug 9 04:12:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acc_9588/08_2024/6acc_9588.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acc_9588/08_2024/6acc_9588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acc_9588/08_2024/6acc_9588.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acc_9588/08_2024/6acc_9588.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acc_9588/08_2024/6acc_9588.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acc_9588/08_2024/6acc_9588.cif" } resolution = 3.6 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: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 15912 2.51 5 N 4122 2.21 5 O 4737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 797": "NH1" <-> "NH2" Residue "A ARG 1001": "NH1" <-> "NH2" Residue "A ARG 1021": "NH1" <-> "NH2" Residue "A ARG 1073": "NH1" <-> "NH2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1001": "NH1" <-> "NH2" Residue "B ARG 1021": "NH1" <-> "NH2" Residue "B ARG 1073": "NH1" <-> "NH2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 797": "NH1" <-> "NH2" Residue "C PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1001": "NH1" <-> "NH2" Residue "C ARG 1021": "NH1" <-> "NH2" Residue "C ARG 1073": "NH1" <-> "NH2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24906 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8302 Classifications: {'peptide': 1065} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1013} Chain breaks: 3 Chain: "B" Number of atoms: 8302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8302 Classifications: {'peptide': 1065} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1013} Chain breaks: 3 Chain: "C" Number of atoms: 8302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8302 Classifications: {'peptide': 1065} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1013} Chain breaks: 3 Time building chain proxies: 12.57, per 1000 atoms: 0.50 Number of scatterers: 24906 At special positions: 0 Unit cell: (149.16, 147.84, 161.04, 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 135 16.00 O 4737 8.00 N 4122 7.00 C 15912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.04 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.02 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.04 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.04 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.04 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.02 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.04 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.04 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.02 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.04 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.04 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.04 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.02 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.04 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.04 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.02 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.04 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.04 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.04 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.02 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.04 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.04 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: 8.07 Conformation dependent library (CDL) restraints added in 4.2 seconds 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5988 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 42 sheets defined 20.7% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.913A pdb=" N ASP A 376 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 377 " --> pdb=" O LEU A 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 373 through 377' Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 604 through 612 Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'A' and resid 740 through 764 Processing helix chain 'A' and resid 798 through 808 removed outlier: 3.835A pdb=" N VAL A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 865 Processing helix chain 'A' and resid 880 through 887 removed outlier: 3.626A pdb=" N MET A 884 " --> pdb=" O PHE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 890 No H-bonds generated for 'chain 'A' and resid 888 through 890' Processing helix chain 'A' and resid 895 through 901 removed outlier: 4.049A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 900 " --> pdb=" O ASN A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 922 removed outlier: 3.903A pdb=" N THR A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 950 removed outlier: 3.734A pdb=" N GLN A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 949 " --> pdb=" O VAL A 945 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 950 " --> pdb=" O LYS A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 966 removed outlier: 4.294A pdb=" N ARG A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1014 removed outlier: 3.723A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 373 through 377 removed outlier: 3.913A pdb=" N ASP B 376 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 377 " --> pdb=" O LEU B 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 373 through 377' Processing helix chain 'B' and resid 392 through 397 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 604 through 612 Processing helix chain 'B' and resid 730 through 737 Processing helix chain 'B' and resid 740 through 764 Processing helix chain 'B' and resid 798 through 808 removed outlier: 3.836A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 865 Processing helix chain 'B' and resid 880 through 887 removed outlier: 3.626A pdb=" N MET B 884 " --> pdb=" O PHE B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 890 No H-bonds generated for 'chain 'B' and resid 888 through 890' Processing helix chain 'B' and resid 895 through 901 removed outlier: 4.049A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 900 " --> pdb=" O ASN B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 removed outlier: 3.904A pdb=" N THR B 921 " --> pdb=" O GLN B 917 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 950 removed outlier: 3.735A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 949 " --> pdb=" O VAL B 945 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 950 " --> pdb=" O LYS B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 966 removed outlier: 4.294A pdb=" N ARG B 965 " --> pdb=" O ASP B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 1014 removed outlier: 3.722A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 324 through 329 Processing helix chain 'C' and resid 373 through 377 removed outlier: 3.913A pdb=" N ASP C 376 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU C 377 " --> pdb=" O LEU C 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 373 through 377' Processing helix chain 'C' and resid 392 through 397 Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 604 through 612 Processing helix chain 'C' and resid 730 through 737 Processing helix chain 'C' and resid 740 through 764 Processing helix chain 'C' and resid 798 through 808 removed outlier: 3.796A pdb=" N VAL C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 865 Processing helix chain 'C' and resid 880 through 887 removed outlier: 3.625A pdb=" N MET C 884 " --> pdb=" O PHE C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 890 No H-bonds generated for 'chain 'C' and resid 888 through 890' Processing helix chain 'C' and resid 895 through 901 removed outlier: 4.050A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU C 900 " --> pdb=" O ASN C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 922 removed outlier: 3.903A pdb=" N THR C 921 " --> pdb=" O GLN C 917 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 950 removed outlier: 3.735A pdb=" N GLN C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER C 949 " --> pdb=" O VAL C 945 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 950 " --> pdb=" O LYS C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 966 removed outlier: 4.294A pdb=" N ARG C 965 " --> pdb=" O ASP C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 1014 removed outlier: 3.722A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 34 removed outlier: 3.824A pdb=" N THR A 31 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 66 " --> pdb=" O HIS A 33 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 254 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A 71 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA A 250 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 90 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 255 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL A 186 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 190 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.698A pdb=" N LEU A 264 " --> pdb=" O TYR A 53 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP A 57 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR A 260 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 59 " --> pdb=" O LYS A 258 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.518A pdb=" N SER A 113 " --> pdb=" O CYS A 128 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 141 removed outlier: 5.759A pdb=" N PHE A 138 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N SER A 239 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 140 " --> pdb=" O SER A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 298 through 301 removed outlier: 3.738A pdb=" N GLY A 298 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR A 585 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR A 300 " --> pdb=" O VAL A 583 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 314 removed outlier: 3.548A pdb=" N PHE A 527 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY A 534 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR A 539 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.552A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS A 419 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 439 through 441 removed outlier: 3.589A pdb=" N ASN A 479 " --> pdb=" O TYR A 440 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 650 through 651 Processing sheet with id=AB1, first strand: chain 'A' and resid 683 through 684 removed outlier: 6.121A pdb=" N ALA A 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 709 removed outlier: 3.655A pdb=" N SER A 703 " --> pdb=" O THR A1048 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A1048 " --> pdb=" O SER A 703 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 707 " --> pdb=" O PHE A1044 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A1041 " --> pdb=" O ALA A1038 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A1038 " --> pdb=" O GLY A1041 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB4, first strand: chain 'A' and resid 769 through 770 Processing sheet with id=AB5, first strand: chain 'A' and resid 1063 through 1064 removed outlier: 4.064A pdb=" N PHE A1071 " --> pdb=" O PHE A1103 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A1103 " --> pdb=" O PHE A1071 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1078 through 1079 Processing sheet with id=AB7, first strand: chain 'B' and resid 31 through 34 removed outlier: 3.825A pdb=" N THR B 31 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 66 " --> pdb=" O HIS B 33 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 254 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 71 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA B 250 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 90 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 255 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL B 186 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS B 190 " --> pdb=" O PHE B 193 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.698A pdb=" N LEU B 264 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP B 57 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR B 260 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE B 59 " --> pdb=" O LYS B 258 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.519A pdb=" N SER B 113 " --> pdb=" O CYS B 128 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 138 through 141 removed outlier: 5.759A pdb=" N PHE B 138 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N SER B 239 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 298 through 301 removed outlier: 3.737A pdb=" N GLY B 298 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR B 585 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR B 300 " --> pdb=" O VAL B 583 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 313 through 314 removed outlier: 3.548A pdb=" N PHE B 527 " --> pdb=" O GLY B 534 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY B 534 " --> pdb=" O PHE B 527 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 539 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.552A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS B 419 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 439 through 441 removed outlier: 3.589A pdb=" N ASN B 479 " --> pdb=" O TYR B 440 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 709 removed outlier: 3.654A pdb=" N SER B 703 " --> pdb=" O THR B1048 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B1048 " --> pdb=" O SER B 703 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU B 707 " --> pdb=" O PHE B1044 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B1041 " --> pdb=" O ALA B1038 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA B1038 " --> pdb=" O GLY B1041 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AC9, first strand: chain 'B' and resid 769 through 770 Processing sheet with id=AD1, first strand: chain 'B' and resid 1063 through 1064 removed outlier: 4.064A pdb=" N PHE B1071 " --> pdb=" O PHE B1103 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE B1103 " --> pdb=" O PHE B1071 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1078 through 1079 Processing sheet with id=AD3, first strand: chain 'C' and resid 31 through 34 removed outlier: 3.825A pdb=" N THR C 31 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 66 " --> pdb=" O HIS C 33 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 254 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR C 71 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA C 250 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 90 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C 255 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL C 186 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS C 190 " --> pdb=" O PHE C 193 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.697A pdb=" N LEU C 264 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP C 57 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR C 260 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE C 59 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.518A pdb=" N SER C 113 " --> pdb=" O CYS C 128 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 138 through 141 removed outlier: 5.760A pdb=" N PHE C 138 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER C 239 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C 140 " --> pdb=" O SER C 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 298 through 301 removed outlier: 3.738A pdb=" N GLY C 298 " --> pdb=" O THR C 585 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR C 585 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR C 300 " --> pdb=" O VAL C 583 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 313 through 314 removed outlier: 3.548A pdb=" N PHE C 527 " --> pdb=" O GLY C 534 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY C 534 " --> pdb=" O PHE C 527 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR C 539 " --> pdb=" O LEU C 571 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.552A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS C 419 " --> pdb=" O LEU C 499 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 439 through 441 removed outlier: 3.589A pdb=" N ASN C 479 " --> pdb=" O TYR C 440 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 650 through 651 Processing sheet with id=AE3, first strand: chain 'C' and resid 701 through 709 removed outlier: 3.656A pdb=" N SER C 703 " --> pdb=" O THR C1048 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C1048 " --> pdb=" O SER C 703 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU C 707 " --> pdb=" O PHE C1044 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY C1041 " --> pdb=" O ALA C1038 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA C1038 " --> pdb=" O GLY C1041 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AE5, first strand: chain 'C' and resid 1063 through 1064 removed outlier: 4.064A pdb=" N PHE C1071 " --> pdb=" O PHE C1103 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE C1103 " --> pdb=" O PHE C1071 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1078 through 1079 779 hydrogen bonds defined for protein. 2085 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: 9.04 Time building geometry restraints manager: 9.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 4085 1.28 - 1.42: 6849 1.42 - 1.56: 14377 1.56 - 1.70: 3 1.70 - 1.84: 183 Bond restraints: 25497 Sorted by residual: bond pdb=" C LEU C 804 " pdb=" O LEU C 804 " ideal model delta sigma weight residual 1.237 1.146 0.091 1.16e-02 7.43e+03 6.12e+01 bond pdb=" CA LEU C 804 " pdb=" C LEU C 804 " ideal model delta sigma weight residual 1.524 1.450 0.074 1.26e-02 6.30e+03 3.42e+01 bond pdb=" N PHE C 805 " pdb=" CA PHE C 805 " ideal model delta sigma weight residual 1.459 1.391 0.068 1.23e-02 6.61e+03 3.04e+01 bond pdb=" C LEU C 804 " pdb=" N PHE C 805 " ideal model delta sigma weight residual 1.335 1.277 0.058 1.30e-02 5.92e+03 2.01e+01 bond pdb=" CD ARG B 797 " pdb=" NE ARG B 797 " ideal model delta sigma weight residual 1.458 1.400 0.058 1.40e-02 5.10e+03 1.71e+01 ... (remaining 25492 not shown) Histogram of bond angle deviations from ideal: 98.96 - 105.98: 621 105.98 - 113.00: 13281 113.00 - 120.02: 8963 120.02 - 127.04: 11598 127.04 - 134.06: 241 Bond angle restraints: 34704 Sorted by residual: angle pdb=" N LEU C 804 " pdb=" CA LEU C 804 " pdb=" C LEU C 804 " ideal model delta sigma weight residual 111.14 103.35 7.79 1.08e+00 8.57e-01 5.21e+01 angle pdb=" C LEU C 804 " pdb=" N PHE C 805 " pdb=" CA PHE C 805 " ideal model delta sigma weight residual 120.38 112.41 7.97 1.37e+00 5.33e-01 3.38e+01 angle pdb=" N ASP C 961 " pdb=" CA ASP C 961 " pdb=" C ASP C 961 " ideal model delta sigma weight residual 114.04 107.12 6.92 1.24e+00 6.50e-01 3.11e+01 angle pdb=" N ASP A 961 " pdb=" CA ASP A 961 " pdb=" C ASP A 961 " ideal model delta sigma weight residual 114.04 107.12 6.92 1.24e+00 6.50e-01 3.11e+01 angle pdb=" N ASP B 961 " pdb=" CA ASP B 961 " pdb=" C ASP B 961 " ideal model delta sigma weight residual 114.04 107.16 6.88 1.24e+00 6.50e-01 3.08e+01 ... (remaining 34699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 14566 17.68 - 35.36: 462 35.36 - 53.04: 100 53.04 - 70.72: 25 70.72 - 88.40: 9 Dihedral angle restraints: 15162 sinusoidal: 5850 harmonic: 9312 Sorted by residual: dihedral pdb=" CA GLU B1074 " pdb=" C GLU B1074 " pdb=" N GLY B1075 " pdb=" CA GLY B1075 " ideal model delta harmonic sigma weight residual -180.00 -121.08 -58.92 0 5.00e+00 4.00e-02 1.39e+02 dihedral pdb=" CA GLU C1074 " pdb=" C GLU C1074 " pdb=" N GLY C1075 " pdb=" CA GLY C1075 " ideal model delta harmonic sigma weight residual -180.00 -121.09 -58.91 0 5.00e+00 4.00e-02 1.39e+02 dihedral pdb=" CA GLU A1074 " pdb=" C GLU A1074 " pdb=" N GLY A1075 " pdb=" CA GLY A1075 " ideal model delta harmonic sigma weight residual -180.00 -121.12 -58.88 0 5.00e+00 4.00e-02 1.39e+02 ... (remaining 15159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2880 0.059 - 0.117: 840 0.117 - 0.176: 187 0.176 - 0.235: 21 0.235 - 0.294: 2 Chirality restraints: 3930 Sorted by residual: chirality pdb=" CA ARG A 797 " pdb=" N ARG A 797 " pdb=" C ARG A 797 " pdb=" CB ARG A 797 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA PHE C 805 " pdb=" N PHE C 805 " pdb=" C PHE C 805 " pdb=" CB PHE C 805 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ASN A1117 " pdb=" N ASN A1117 " pdb=" C ASN A1117 " pdb=" CB ASN A1117 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 3927 not shown) Planarity restraints: 4497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 797 " -0.015 2.00e-02 2.50e+03 3.14e-02 9.88e+00 pdb=" C ARG B 797 " 0.054 2.00e-02 2.50e+03 pdb=" O ARG B 797 " -0.021 2.00e-02 2.50e+03 pdb=" N SER B 798 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 678 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.07e+00 pdb=" C THR C 678 " 0.052 2.00e-02 2.50e+03 pdb=" O THR C 678 " -0.019 2.00e-02 2.50e+03 pdb=" N MET C 679 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 678 " -0.015 2.00e-02 2.50e+03 3.00e-02 8.98e+00 pdb=" C THR A 678 " 0.052 2.00e-02 2.50e+03 pdb=" O THR A 678 " -0.019 2.00e-02 2.50e+03 pdb=" N MET A 679 " -0.018 2.00e-02 2.50e+03 ... (remaining 4494 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 754 2.69 - 3.24: 22914 3.24 - 3.80: 37195 3.80 - 4.35: 49007 4.35 - 4.90: 80924 Nonbonded interactions: 190794 Sorted by model distance: nonbonded pdb=" NH2 ARG A 797 " pdb=" CD2 PHE A 805 " model vdw 2.139 3.420 nonbonded pdb=" CB PRO A 789 " pdb=" O ARG A 797 " model vdw 2.172 3.440 nonbonded pdb=" NH2 ARG C 797 " pdb=" CD2 PHE C 805 " model vdw 2.237 3.420 nonbonded pdb=" OD1 ASN B 896 " pdb=" OG SER C1105 " model vdw 2.282 3.040 nonbonded pdb=" O GLN A 939 " pdb=" OG1 THR A 943 " model vdw 2.297 3.040 ... (remaining 190789 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.130 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: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 60.390 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 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 0.097 25497 Z= 0.348 Angle : 0.955 9.470 34704 Z= 0.543 Chirality : 0.059 0.294 3930 Planarity : 0.008 0.066 4497 Dihedral : 9.618 78.319 9057 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.60 % Allowed : 11.95 % Favored : 87.45 % Rotamer: Outliers : 0.43 % Allowed : 1.55 % Favored : 98.01 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -4.74 (0.12), residues: 3171 helix: -1.84 (0.17), residues: 567 sheet: -2.99 (0.20), residues: 483 loop : -3.84 (0.10), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 868 HIS 0.009 0.002 HIS C1030 PHE 0.047 0.003 PHE C 837 TYR 0.015 0.002 TYR B 252 ARG 0.008 0.001 ARG A 797 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 701 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 SER cc_start: 0.7922 (t) cc_final: 0.7266 (p) REVERT: A 214 ASN cc_start: 0.8014 (t0) cc_final: 0.7697 (t0) REVERT: A 226 ILE cc_start: 0.7312 (pt) cc_final: 0.7093 (pt) REVERT: A 229 THR cc_start: 0.7165 (p) cc_final: 0.6963 (p) REVERT: A 230 ASN cc_start: 0.7092 (m-40) cc_final: 0.6854 (m-40) REVERT: A 261 THR cc_start: 0.8561 (m) cc_final: 0.8300 (p) REVERT: A 361 PHE cc_start: 0.7506 (m-10) cc_final: 0.7134 (m-80) REVERT: A 365 LYS cc_start: 0.7608 (tttt) cc_final: 0.7326 (mmtt) REVERT: A 372 THR cc_start: 0.8462 (p) cc_final: 0.8179 (p) REVERT: A 387 PHE cc_start: 0.8043 (p90) cc_final: 0.7782 (p90) REVERT: A 454 ASP cc_start: 0.7140 (m-30) cc_final: 0.6443 (p0) REVERT: A 797 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6624 (mtm-85) REVERT: A 1116 ASN cc_start: 0.7771 (m-40) cc_final: 0.7461 (p0) REVERT: B 49 SER cc_start: 0.7961 (t) cc_final: 0.7531 (p) REVERT: B 131 GLU cc_start: 0.6858 (tt0) cc_final: 0.6655 (tp30) REVERT: B 184 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7284 (tt0) REVERT: B 214 ASN cc_start: 0.7669 (t0) cc_final: 0.7347 (t0) REVERT: B 230 ASN cc_start: 0.7016 (m-40) cc_final: 0.6791 (m-40) REVERT: B 258 LYS cc_start: 0.8051 (tttt) cc_final: 0.7622 (ttmm) REVERT: B 361 PHE cc_start: 0.7513 (m-10) cc_final: 0.7258 (m-10) REVERT: B 365 LYS cc_start: 0.7575 (tttt) cc_final: 0.7196 (mmtm) REVERT: B 367 TYR cc_start: 0.7626 (m-10) cc_final: 0.7366 (m-10) REVERT: B 372 THR cc_start: 0.8262 (p) cc_final: 0.7970 (p) REVERT: B 387 PHE cc_start: 0.8105 (p90) cc_final: 0.7789 (p90) REVERT: B 454 ASP cc_start: 0.7275 (m-30) cc_final: 0.6464 (p0) REVERT: B 500 SER cc_start: 0.9030 (t) cc_final: 0.8586 (p) REVERT: B 573 ILE cc_start: 0.7385 (mt) cc_final: 0.7101 (mt) REVERT: B 837 PHE cc_start: 0.7037 (p90) cc_final: 0.6808 (p90) REVERT: B 841 THR cc_start: 0.8821 (t) cc_final: 0.8523 (m) REVERT: B 1019 SER cc_start: 0.8503 (t) cc_final: 0.8279 (m) REVERT: C 49 SER cc_start: 0.8031 (t) cc_final: 0.7190 (p) REVERT: C 361 PHE cc_start: 0.7421 (m-10) cc_final: 0.7208 (m-10) REVERT: C 372 THR cc_start: 0.8290 (p) cc_final: 0.8027 (p) REVERT: C 387 PHE cc_start: 0.8043 (p90) cc_final: 0.7736 (p90) REVERT: C 454 ASP cc_start: 0.7287 (m-30) cc_final: 0.6141 (p0) REVERT: C 497 VAL cc_start: 0.8913 (t) cc_final: 0.8687 (p) REVERT: C 500 SER cc_start: 0.8999 (t) cc_final: 0.8531 (p) REVERT: C 527 PHE cc_start: 0.7003 (m-10) cc_final: 0.6718 (m-80) REVERT: C 562 VAL cc_start: 0.8118 (m) cc_final: 0.7909 (p) REVERT: C 837 PHE cc_start: 0.7151 (p90) cc_final: 0.6407 (p90) REVERT: C 1013 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6760 (mm-30) REVERT: C 1116 ASN cc_start: 0.8108 (m-40) cc_final: 0.7882 (p0) outliers start: 12 outliers final: 1 residues processed: 708 average time/residue: 0.3731 time to fit residues: 405.0066 Evaluate side-chains 381 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 379 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 797 ARG Chi-restraints excluded: chain C residue 797 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.9980 chunk 241 optimal weight: 3.9990 chunk 133 optimal weight: 0.2980 chunk 82 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 128 optimal weight: 20.0000 chunk 249 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 151 optimal weight: 0.1980 chunk 185 optimal weight: 0.7980 chunk 288 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 181 HIS A 321 ASN A 721 ASN A 766 GLN A 987 GLN A 993 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 149 HIS B 181 HIS B 721 ASN B 759 ASN B 766 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 HIS C 181 HIS C 214 ASN C 321 ASN C 737 GLN C 744 GLN C 766 GLN C 939 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 25497 Z= 0.221 Angle : 0.723 12.570 34704 Z= 0.387 Chirality : 0.048 0.196 3930 Planarity : 0.006 0.055 4497 Dihedral : 6.945 59.512 3440 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.48 % Favored : 88.17 % Rotamer: Outliers : 3.04 % Allowed : 8.71 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -3.74 (0.13), residues: 3171 helix: 0.26 (0.21), residues: 552 sheet: -2.40 (0.20), residues: 579 loop : -3.55 (0.11), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 423 HIS 0.005 0.001 HIS A 181 PHE 0.027 0.002 PHE A 364 TYR 0.023 0.001 TYR C 163 ARG 0.006 0.001 ARG B 758 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 434 time to evaluate : 2.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.7782 (mmm) cc_final: 0.7427 (mtt) REVERT: A 214 ASN cc_start: 0.8090 (t0) cc_final: 0.7737 (t0) REVERT: A 361 PHE cc_start: 0.7599 (m-10) cc_final: 0.7227 (m-10) REVERT: A 387 PHE cc_start: 0.8166 (p90) cc_final: 0.7876 (p90) REVERT: A 454 ASP cc_start: 0.7141 (m-30) cc_final: 0.6619 (p0) REVERT: A 522 ASN cc_start: 0.8253 (m-40) cc_final: 0.8033 (m110) REVERT: A 605 ASP cc_start: 0.7029 (t70) cc_final: 0.6601 (t70) REVERT: A 687 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8038 (pp) REVERT: B 131 GLU cc_start: 0.6826 (tt0) cc_final: 0.6592 (tp30) REVERT: B 184 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6738 (tt0) REVERT: B 214 ASN cc_start: 0.7667 (t0) cc_final: 0.7258 (t0) REVERT: B 258 LYS cc_start: 0.7992 (tttt) cc_final: 0.7553 (ttmm) REVERT: B 387 PHE cc_start: 0.8176 (p90) cc_final: 0.7886 (p90) REVERT: B 454 ASP cc_start: 0.7228 (m-30) cc_final: 0.6574 (p0) REVERT: B 523 GLN cc_start: 0.8182 (tt0) cc_final: 0.7821 (tt0) REVERT: B 756 GLN cc_start: 0.7240 (mp10) cc_final: 0.7039 (mp10) REVERT: B 837 PHE cc_start: 0.6639 (p90) cc_final: 0.6437 (p90) REVERT: B 882 MET cc_start: 0.7904 (mtp) cc_final: 0.7546 (mtp) REVERT: B 1011 MET cc_start: 0.8928 (tpp) cc_final: 0.8584 (tpp) REVERT: C 214 ASN cc_start: 0.7564 (t0) cc_final: 0.7315 (t0) REVERT: C 382 VAL cc_start: 0.6963 (m) cc_final: 0.6747 (p) REVERT: C 387 PHE cc_start: 0.8022 (p90) cc_final: 0.7719 (p90) REVERT: C 454 ASP cc_start: 0.7024 (m-30) cc_final: 0.6513 (p0) REVERT: C 523 GLN cc_start: 0.8074 (tt0) cc_final: 0.7727 (tt0) REVERT: C 797 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6580 (mtp180) REVERT: C 837 PHE cc_start: 0.6675 (p90) cc_final: 0.5459 (p90) REVERT: C 841 THR cc_start: 0.8475 (t) cc_final: 0.8196 (m) REVERT: C 996 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.7099 (ttp-170) outliers start: 84 outliers final: 48 residues processed: 492 average time/residue: 0.3219 time to fit residues: 254.8074 Evaluate side-chains 377 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 326 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 779 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 779 PHE Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 996 ARG Chi-restraints excluded: chain C residue 1057 PHE Chi-restraints excluded: chain C residue 1059 THR Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 7.9990 chunk 89 optimal weight: 0.7980 chunk 240 optimal weight: 0.9980 chunk 196 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 289 optimal weight: 7.9990 chunk 312 optimal weight: 5.9990 chunk 257 optimal weight: 1.9990 chunk 286 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 232 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 321 ASN A 550 GLN A 721 ASN A 744 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 70 HIS B 109 ASN B 721 ASN B 737 GLN B 759 ASN C 109 ASN C 321 ASN C 759 ASN C 766 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 GLN C1101 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 25497 Z= 0.321 Angle : 0.753 12.404 34704 Z= 0.397 Chirality : 0.049 0.220 3930 Planarity : 0.005 0.059 4497 Dihedral : 6.740 56.308 3436 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.36 % Favored : 87.26 % Rotamer: Outliers : 3.43 % Allowed : 12.22 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.34 (0.14), residues: 3171 helix: 1.04 (0.21), residues: 555 sheet: -2.20 (0.21), residues: 582 loop : -3.42 (0.12), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 868 HIS 0.010 0.001 HIS C1030 PHE 0.024 0.002 PHE A 59 TYR 0.020 0.002 TYR C 689 ARG 0.007 0.001 ARG C 620 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 343 time to evaluate : 2.612 Fit side-chains REVERT: A 107 MET cc_start: 0.7945 (mmm) cc_final: 0.7427 (mmm) REVERT: A 214 ASN cc_start: 0.7992 (t0) cc_final: 0.7652 (t0) REVERT: A 387 PHE cc_start: 0.8134 (p90) cc_final: 0.7896 (p90) REVERT: A 454 ASP cc_start: 0.7250 (m-30) cc_final: 0.6765 (p0) REVERT: A 483 PHE cc_start: 0.7562 (m-10) cc_final: 0.7154 (m-80) REVERT: A 499 LEU cc_start: 0.8581 (mm) cc_final: 0.8336 (mm) REVERT: A 605 ASP cc_start: 0.6755 (t70) cc_final: 0.6496 (t70) REVERT: A 996 ARG cc_start: 0.7650 (ttm110) cc_final: 0.7444 (ttm-80) REVERT: B 184 GLU cc_start: 0.7476 (mt-10) cc_final: 0.6960 (tt0) REVERT: B 214 ASN cc_start: 0.7659 (t0) cc_final: 0.7187 (t0) REVERT: B 361 PHE cc_start: 0.7647 (m-10) cc_final: 0.7433 (m-80) REVERT: B 387 PHE cc_start: 0.8153 (p90) cc_final: 0.7948 (p90) REVERT: B 454 ASP cc_start: 0.7345 (m-30) cc_final: 0.6634 (p0) REVERT: B 523 GLN cc_start: 0.8332 (tt0) cc_final: 0.7896 (tt0) REVERT: B 621 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8033 (pt) REVERT: B 882 MET cc_start: 0.8030 (mtp) cc_final: 0.7696 (mtt) REVERT: B 1011 MET cc_start: 0.9104 (tpp) cc_final: 0.8885 (tpp) REVERT: C 214 ASN cc_start: 0.7506 (t0) cc_final: 0.7191 (t0) REVERT: C 361 PHE cc_start: 0.7850 (m-10) cc_final: 0.7639 (m-80) REVERT: C 382 VAL cc_start: 0.7135 (m) cc_final: 0.6928 (p) REVERT: C 387 PHE cc_start: 0.8007 (p90) cc_final: 0.7759 (p90) REVERT: C 454 ASP cc_start: 0.7022 (m-30) cc_final: 0.6598 (p0) REVERT: C 523 GLN cc_start: 0.8224 (tt0) cc_final: 0.7806 (tt0) REVERT: C 1011 MET cc_start: 0.9127 (tpp) cc_final: 0.8892 (tpp) outliers start: 95 outliers final: 70 residues processed: 411 average time/residue: 0.3290 time to fit residues: 220.2048 Evaluate side-chains 360 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 289 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 779 PHE Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1057 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 779 PHE Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 1012 SER Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.7248 > 50: distance: 24 - 180: 7.975 distance: 124 - 125: 4.461 distance: 130 - 131: 5.167 distance: 131 - 132: 3.177 distance: 132 - 133: 3.461 distance: 132 - 136: 3.575 distance: 137 - 138: 22.098 distance: 138 - 139: 22.094 distance: 138 - 148: 53.535 distance: 148 - 149: 54.725 distance: 149 - 150: 22.791 distance: 149 - 152: 23.965 distance: 150 - 151: 4.018 distance: 150 - 162: 3.317 distance: 163 - 166: 3.561 distance: 164 - 165: 3.076 distance: 167 - 168: 3.676 distance: 171 - 172: 3.897 distance: 171 - 177: 3.252 distance: 179 - 180: 3.267 distance: 179 - 185: 3.292