Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 11 23:58:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acc_9588/07_2023/6acc_9588.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acc_9588/07_2023/6acc_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_9588/07_2023/6acc_9588.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acc_9588/07_2023/6acc_9588.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acc_9588/07_2023/6acc_9588.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acc_9588/07_2023/6acc_9588.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 10.81, per 1000 atoms: 0.43 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: 8.95 Conformation dependent library (CDL) restraints added in 3.4 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: 1.47 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: 9.46 Time building geometry restraints manager: 9.73 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 2.440 nonbonded pdb=" O GLN A 939 " pdb=" OG1 THR A 943 " model vdw 2.297 2.440 ... (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 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: 1.180 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: 7.860 Check model and map are aligned: 0.380 Set scattering table: 0.210 Process input model: 57.770 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.130 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.370 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.886 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 outliers start: 12 outliers final: 1 residues processed: 708 average time/residue: 0.3915 time to fit residues: 427.6875 Evaluate side-chains 359 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 358 time to evaluate : 2.866 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.8270 time to fit residues: 4.7378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.6980 chunk 241 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 chunk 128 optimal weight: 20.0000 chunk 249 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 185 optimal weight: 0.9980 chunk 288 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 437 ASN A 721 ASN A 766 GLN A 987 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 129 ASN B 149 HIS B 181 HIS B 437 ASN 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 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: 0.7242 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 25497 Z= 0.226 Angle : 0.719 13.681 34704 Z= 0.383 Chirality : 0.048 0.236 3930 Planarity : 0.006 0.055 4497 Dihedral : 6.728 55.484 3432 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.70 % Favored : 87.92 % Rotamer Outliers : 3.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.75 (0.13), residues: 3171 helix: 0.25 (0.21), residues: 543 sheet: -2.43 (0.20), residues: 579 loop : -3.53 (0.11), residues: 2049 *********************** 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 510 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 412 time to evaluate : 3.245 Fit side-chains revert: symmetry clash outliers start: 98 outliers final: 66 residues processed: 485 average time/residue: 0.3421 time to fit residues: 271.8508 Evaluate side-chains 383 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 317 time to evaluate : 2.787 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.2203 time to fit residues: 31.6418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 312 optimal weight: 5.9990 chunk 257 optimal weight: 0.9980 chunk 286 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 744 GLN A 759 ASN A 766 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS B 109 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 GLN B 721 ASN B 759 ASN ** B1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN ** C 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 ASN C 766 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.086 25497 Z= 0.424 Angle : 0.812 12.698 34704 Z= 0.429 Chirality : 0.051 0.221 3930 Planarity : 0.006 0.063 4497 Dihedral : 6.835 53.115 3432 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.50 % Allowed : 14.54 % Favored : 84.96 % Rotamer Outliers : 2.28 % 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: -3.57 (0.14), residues: 3171 helix: 0.63 (0.21), residues: 549 sheet: -2.28 (0.21), residues: 594 loop : -3.51 (0.12), residues: 2028 *********************** 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 391 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 328 time to evaluate : 2.909 Fit side-chains revert: symmetry clash outliers start: 63 outliers final: 45 residues processed: 375 average time/residue: 0.3611 time to fit residues: 224.1164 Evaluate side-chains 324 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 279 time to evaluate : 2.880 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.2522 time to fit residues: 25.0054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 194 optimal weight: 0.6980 chunk 290 optimal weight: 0.8980 chunk 307 optimal weight: 0.8980 chunk 151 optimal weight: 7.9990 chunk 275 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 766 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 ASN ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 987 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.086 25497 Z= 0.243 Angle : 0.686 10.324 34704 Z= 0.363 Chirality : 0.047 0.179 3930 Planarity : 0.005 0.062 4497 Dihedral : 6.385 52.295 3432 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.11 % Favored : 87.51 % Rotamer Outliers : 2.31 % 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: -3.24 (0.14), residues: 3171 helix: 1.47 (0.22), residues: 534 sheet: -2.13 (0.21), residues: 609 loop : -3.43 (0.12), residues: 2028 *********************** REFINEMENT MACRO_CYCLE 4 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 389 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 325 time to evaluate : 2.840 Fit side-chains outliers start: 64 outliers final: 35 residues processed: 370 average time/residue: 0.3362 time to fit residues: 204.5333 Evaluate side-chains 325 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 290 time to evaluate : 2.694 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2205 time to fit residues: 18.5048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 228 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 262 optimal weight: 0.7980 chunk 212 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 156 optimal weight: 0.9980 chunk 275 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 737 GLN A 759 ASN A 766 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 ASN B 409 ASN C 70 HIS ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN C 737 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 25497 Z= 0.263 Angle : 0.689 10.510 34704 Z= 0.364 Chirality : 0.047 0.168 3930 Planarity : 0.005 0.061 4497 Dihedral : 6.262 51.482 3432 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.15 % Favored : 86.57 % Rotamer Outliers : 2.10 % 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: -3.12 (0.14), residues: 3171 helix: 1.69 (0.22), residues: 534 sheet: -2.06 (0.21), residues: 609 loop : -3.38 (0.12), residues: 2028 *********************** REFINEMENT MACRO_CYCLE 5 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 369 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 311 time to evaluate : 2.746 Fit side-chains outliers start: 58 outliers final: 38 residues processed: 351 average time/residue: 0.3421 time to fit residues: 198.4353 Evaluate side-chains 326 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 288 time to evaluate : 2.819 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.2296 time to fit residues: 20.3887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 3.9990 chunk 276 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 chunk 255 optimal weight: 0.0070 chunk 142 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 overall best weight: 2.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 GLN A 766 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS C 109 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 25497 Z= 0.358 Angle : 0.749 10.333 34704 Z= 0.393 Chirality : 0.049 0.176 3930 Planarity : 0.005 0.057 4497 Dihedral : 6.452 49.673 3432 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.35 % Allowed : 15.29 % Favored : 84.36 % Rotamer Outliers : 2.17 % 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: -3.18 (0.14), residues: 3171 helix: 1.56 (0.22), residues: 534 sheet: -2.02 (0.21), residues: 573 loop : -3.41 (0.12), residues: 2064 *********************** REFINEMENT MACRO_CYCLE 6 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 360 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 300 time to evaluate : 2.954 Fit side-chains outliers start: 60 outliers final: 36 residues processed: 339 average time/residue: 0.3247 time to fit residues: 185.8639 Evaluate side-chains 313 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 277 time to evaluate : 2.767 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.2218 time to fit residues: 19.2547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 224 optimal weight: 9.9990 chunk 174 optimal weight: 0.8980 chunk 259 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 306 optimal weight: 0.8980 chunk 191 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 25497 Z= 0.242 Angle : 0.683 10.577 34704 Z= 0.358 Chirality : 0.047 0.163 3930 Planarity : 0.004 0.052 4497 Dihedral : 6.190 49.394 3432 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.39 % Favored : 87.32 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -3.00 (0.14), residues: 3171 helix: 1.78 (0.22), residues: 534 sheet: -1.92 (0.21), residues: 582 loop : -3.31 (0.12), residues: 2055 *********************** REFINEMENT MACRO_CYCLE 7 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 326 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 299 time to evaluate : 2.794 Fit side-chains outliers start: 27 outliers final: 18 residues processed: 316 average time/residue: 0.3439 time to fit residues: 180.6930 Evaluate side-chains 294 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 276 time to evaluate : 2.941 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2282 time to fit residues: 11.9301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 0.2980 chunk 122 optimal weight: 7.9990 chunk 183 optimal weight: 0.0770 chunk 92 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 overall best weight: 1.0744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 25497 Z= 0.239 Angle : 0.674 10.302 34704 Z= 0.352 Chirality : 0.047 0.165 3930 Planarity : 0.005 0.070 4497 Dihedral : 6.075 49.146 3432 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.80 % Favored : 86.94 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.14), residues: 3171 helix: 1.84 (0.22), residues: 534 sheet: -1.83 (0.21), residues: 582 loop : -3.24 (0.12), residues: 2055 *********************** REFINEMENT MACRO_CYCLE 8 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 327 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 303 time to evaluate : 2.839 Fit side-chains outliers start: 24 outliers final: 18 residues processed: 316 average time/residue: 0.3398 time to fit residues: 177.7413 Evaluate side-chains 299 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 281 time to evaluate : 2.707 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2210 time to fit residues: 11.4963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.4980 chunk 293 optimal weight: 4.9990 chunk 267 optimal weight: 1.9990 chunk 285 optimal weight: 0.9980 chunk 171 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 258 optimal weight: 0.9980 chunk 270 optimal weight: 0.4980 chunk 284 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN A 766 GLN A 947 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 ASN ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 ASN ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 25497 Z= 0.200 Angle : 0.653 11.616 34704 Z= 0.339 Chirality : 0.046 0.156 3930 Planarity : 0.004 0.061 4497 Dihedral : 5.881 49.258 3432 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.86 % Favored : 87.89 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.15), residues: 3171 helix: 1.98 (0.22), residues: 531 sheet: -1.76 (0.22), residues: 573 loop : -3.11 (0.12), residues: 2067 *********************** REFINEMENT MACRO_CYCLE 9 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 338 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 323 time to evaluate : 3.000 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 334 average time/residue: 0.3441 time to fit residues: 190.6260 Evaluate side-chains 299 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 288 time to evaluate : 2.935 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2194 time to fit residues: 8.4494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 6.9990 chunk 302 optimal weight: 4.9990 chunk 184 optimal weight: 0.2980 chunk 143 optimal weight: 5.9990 chunk 209 optimal weight: 0.0010 chunk 316 optimal weight: 5.9990 chunk 291 optimal weight: 1.9990 chunk 252 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 154 optimal weight: 0.3980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 25497 Z= 0.200 Angle : 0.659 12.505 34704 Z= 0.340 Chirality : 0.046 0.159 3930 Planarity : 0.004 0.057 4497 Dihedral : 5.807 48.443 3432 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.02 % Favored : 87.73 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.15), residues: 3171 helix: 2.09 (0.22), residues: 531 sheet: -1.60 (0.22), residues: 570 loop : -3.06 (0.12), residues: 2070 ********************** REFINEMENT MACRO_CYCLE 10 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 317 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 309 time to evaluate : 3.003 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 316 average time/residue: 0.3423 time to fit residues: 179.3925 Evaluate side-chains 287 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 282 time to evaluate : 2.680 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2333 time to fit residues: 5.8168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 252 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 259 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 112 GLN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN C 437 ASN C 766 GLN ** C 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 838 ASN ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.172418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.136519 restraints weight = 39479.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.137433 restraints weight = 25416.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.138579 restraints weight = 22940.227| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.080 25497 Z= 0.551 Angle : 0.855 12.818 34704 Z= 0.446 Chirality : 0.054 0.455 3930 Planarity : 0.005 0.066 4497 Dihedral : 6.598 46.447 3432 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.32 % Allowed : 16.93 % Favored : 82.75 % Rotamer Outliers : 0.61 % 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: -3.14 (0.14), residues: 3171 helix: 0.99 (0.21), residues: 570 sheet: -1.97 (0.21), residues: 597 loop : -3.28 (0.12), residues: 2004 =============================================================================== Job complete usr+sys time: 4774.53 seconds wall clock time: 88 minutes 17.73 seconds (5297.73 seconds total)