Starting phenix.real_space_refine on Mon Feb 19 14:00:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acc_9588/02_2024/6acc_9588.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acc_9588/02_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_9588/02_2024/6acc_9588.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acc_9588/02_2024/6acc_9588.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acc_9588/02_2024/6acc_9588.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acc_9588/02_2024/6acc_9588.pdb" } 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 12.98, per 1000 atoms: 0.52 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: 9.35 Conformation dependent library (CDL) restraints added in 4.9 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: 3.19 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: 9.57 Time building geometry restraints manager: 10.17 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.800 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 65.750 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.120 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.810 ------------------------------------------------------------------------------- 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 : 2.650 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: 0.3721 time to fit residues: 403.8095 Evaluate side-chains 381 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 379 time to evaluate : 2.766 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.8980 chunk 151 optimal weight: 0.6980 chunk 185 optimal weight: 0.9980 chunk 288 optimal weight: 1.9990 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: 0.7244 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 25497 Z= 0.240 Angle : 0.720 13.682 34704 Z= 0.384 Chirality : 0.048 0.234 3930 Planarity : 0.006 0.055 4497 Dihedral : 6.950 57.745 3440 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.73 % Favored : 87.89 % Rotamer: Outliers : 3.29 % Allowed : 8.60 % Favored : 88.11 % 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: -3.77 (0.13), residues: 3171 helix: 0.21 (0.21), residues: 543 sheet: -2.43 (0.20), residues: 579 loop : -3.54 (0.11), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 423 HIS 0.005 0.001 HIS B1030 PHE 0.027 0.002 PHE C1057 TYR 0.022 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 500 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 409 time to evaluate : 2.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.7786 (mmm) cc_final: 0.7376 (mtt) REVERT: A 214 ASN cc_start: 0.7917 (t0) cc_final: 0.7608 (t0) REVERT: A 361 PHE cc_start: 0.7577 (m-10) cc_final: 0.7225 (m-10) REVERT: A 387 PHE cc_start: 0.8157 (p90) cc_final: 0.7868 (p90) REVERT: A 454 ASP cc_start: 0.7181 (m-30) cc_final: 0.6597 (p0) REVERT: B 131 GLU cc_start: 0.6826 (tt0) cc_final: 0.6584 (tp30) REVERT: B 214 ASN cc_start: 0.7581 (t0) cc_final: 0.6950 (t0) REVERT: B 258 LYS cc_start: 0.8021 (tttt) cc_final: 0.7578 (ttmm) REVERT: B 387 PHE cc_start: 0.8162 (p90) cc_final: 0.7860 (p90) REVERT: B 454 ASP cc_start: 0.7052 (m-30) cc_final: 0.6465 (p0) REVERT: B 523 GLN cc_start: 0.8197 (tt0) cc_final: 0.7800 (tt0) REVERT: B 621 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.7962 (pt) REVERT: B 841 THR cc_start: 0.8591 (t) cc_final: 0.8349 (m) REVERT: B 882 MET cc_start: 0.7965 (mtp) cc_final: 0.7662 (mtt) REVERT: B 1011 MET cc_start: 0.8895 (tpp) cc_final: 0.8630 (tpp) REVERT: B 1077 PHE cc_start: 0.5413 (t80) cc_final: 0.5048 (t80) REVERT: C 109 ASN cc_start: 0.6968 (t0) cc_final: 0.6752 (m-40) REVERT: C 214 ASN cc_start: 0.7563 (t0) cc_final: 0.7298 (t0) REVERT: C 302 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8401 (p) REVERT: C 382 VAL cc_start: 0.7016 (m) cc_final: 0.6810 (p) REVERT: C 387 PHE cc_start: 0.8173 (p90) cc_final: 0.7795 (p90) REVERT: C 454 ASP cc_start: 0.7072 (m-30) cc_final: 0.6493 (p0) REVERT: C 523 GLN cc_start: 0.8120 (tt0) cc_final: 0.7740 (tt0) REVERT: C 837 PHE cc_start: 0.6815 (p90) cc_final: 0.6160 (p90) REVERT: C 841 THR cc_start: 0.8547 (t) cc_final: 0.8266 (m) outliers start: 91 outliers final: 58 residues processed: 476 average time/residue: 0.3491 time to fit residues: 269.1222 Evaluate side-chains 386 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 326 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASN 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 302 THR 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 716 THR 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 950 SER Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 302 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 716 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 779 PHE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1009 THR 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 118 ASN 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 302 THR 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 659 SER Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 716 THR 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 861 SER Chi-restraints excluded: chain C residue 893 VAL 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: 0.0970 chunk 89 optimal weight: 2.9990 chunk 240 optimal weight: 0.7980 chunk 196 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 289 optimal weight: 7.9990 chunk 312 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 chunk 286 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 232 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 721 ASN ** B1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 737 GLN C 759 ASN C 766 GLN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 25497 Z= 0.249 Angle : 0.705 14.815 34704 Z= 0.370 Chirality : 0.048 0.226 3930 Planarity : 0.005 0.059 4497 Dihedral : 6.499 53.798 3436 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.05 % Favored : 87.57 % Rotamer: Outliers : 3.80 % Allowed : 11.17 % Favored : 85.03 % 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: -3.21 (0.14), residues: 3171 helix: 1.21 (0.22), residues: 531 sheet: -2.00 (0.22), residues: 537 loop : -3.33 (0.12), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 868 HIS 0.008 0.001 HIS C1030 PHE 0.024 0.002 PHE A 262 TYR 0.019 0.001 TYR A 689 ARG 0.007 0.000 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 462 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 357 time to evaluate : 3.109 Fit side-chains revert: symmetry clash REVERT: A 107 MET cc_start: 0.8029 (mmm) cc_final: 0.7481 (mmm) REVERT: A 214 ASN cc_start: 0.7967 (t0) cc_final: 0.7593 (t0) REVERT: A 387 PHE cc_start: 0.8161 (p90) cc_final: 0.7935 (p90) REVERT: A 454 ASP cc_start: 0.7155 (m-30) cc_final: 0.6645 (p0) REVERT: A 483 PHE cc_start: 0.7527 (m-10) cc_final: 0.7107 (m-80) REVERT: A 499 LEU cc_start: 0.8620 (mm) cc_final: 0.8411 (mm) REVERT: A 605 ASP cc_start: 0.6834 (t70) cc_final: 0.6581 (t70) REVERT: A 689 TYR cc_start: 0.6427 (t80) cc_final: 0.6213 (t80) REVERT: A 882 MET cc_start: 0.7896 (mtp) cc_final: 0.7673 (mtp) REVERT: A 898 LEU cc_start: 0.6809 (tp) cc_final: 0.6365 (tp) REVERT: A 996 ARG cc_start: 0.7677 (ttm110) cc_final: 0.7385 (ttm-80) REVERT: A 1082 THR cc_start: 0.6106 (OUTLIER) cc_final: 0.5893 (m) REVERT: B 131 GLU cc_start: 0.6738 (tt0) cc_final: 0.6520 (tp30) REVERT: B 214 ASN cc_start: 0.7473 (t0) cc_final: 0.7191 (t0) REVERT: B 258 LYS cc_start: 0.8222 (tttt) cc_final: 0.7686 (ttmm) REVERT: B 417 MET cc_start: 0.3466 (mmm) cc_final: 0.2839 (mmm) REVERT: B 454 ASP cc_start: 0.7372 (m-30) cc_final: 0.6720 (p0) REVERT: B 621 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8022 (pt) REVERT: B 841 THR cc_start: 0.8645 (t) cc_final: 0.8405 (m) REVERT: B 882 MET cc_start: 0.7977 (mtp) cc_final: 0.7763 (mtt) REVERT: C 96 ASN cc_start: 0.7896 (m-40) cc_final: 0.7075 (t0) REVERT: C 183 ARG cc_start: 0.7042 (mtm-85) cc_final: 0.6675 (ttm110) REVERT: C 214 ASN cc_start: 0.7493 (t0) cc_final: 0.7178 (t0) REVERT: C 302 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8503 (p) REVERT: C 382 VAL cc_start: 0.7095 (m) cc_final: 0.6879 (p) REVERT: C 387 PHE cc_start: 0.7976 (p90) cc_final: 0.7747 (p90) REVERT: C 454 ASP cc_start: 0.7035 (m-30) cc_final: 0.6585 (p0) REVERT: C 523 GLN cc_start: 0.8199 (tt0) cc_final: 0.7768 (tt0) REVERT: C 797 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6677 (mtp180) REVERT: C 837 PHE cc_start: 0.6625 (p90) cc_final: 0.5969 (p90) REVERT: C 1082 THR cc_start: 0.6342 (OUTLIER) cc_final: 0.6124 (m) outliers start: 105 outliers final: 79 residues processed: 435 average time/residue: 0.3375 time to fit residues: 238.4968 Evaluate side-chains 382 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 298 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 419 CYS 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 652 ILE Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 861 SER 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 1082 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 530 ASN 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 643 ASP Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 779 PHE Chi-restraints excluded: chain B residue 849 ASP Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1009 THR 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 66 VAL Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 455 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 716 THR 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 861 SER Chi-restraints excluded: chain C residue 884 MET Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 1082 THR Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 138 optimal weight: 0.0040 chunk 194 optimal weight: 3.9990 chunk 290 optimal weight: 3.9990 chunk 307 optimal weight: 2.9990 chunk 151 optimal weight: 0.0030 chunk 275 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.9606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 437 ASN A 627 ASN A 759 ASN A 766 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN C 109 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25497 Z= 0.217 Angle : 0.663 10.520 34704 Z= 0.347 Chirality : 0.047 0.172 3930 Planarity : 0.004 0.060 4497 Dihedral : 6.176 51.132 3436 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.92 % Favored : 87.80 % Rotamer: Outliers : 4.27 % Allowed : 12.62 % Favored : 83.12 % 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: -3.00 (0.14), residues: 3171 helix: 1.63 (0.22), residues: 537 sheet: -1.90 (0.22), residues: 579 loop : -3.27 (0.12), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 868 HIS 0.006 0.001 HIS C1030 PHE 0.020 0.001 PHE A1057 TYR 0.019 0.001 TYR B 689 ARG 0.003 0.000 ARG B 758 *********************** 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 452 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 334 time to evaluate : 2.707 Fit side-chains REVERT: A 214 ASN cc_start: 0.8022 (t0) cc_final: 0.7709 (t0) REVERT: A 263 MET cc_start: 0.8280 (tmm) cc_final: 0.8017 (tmm) REVERT: A 417 MET cc_start: 0.4087 (mmm) cc_final: 0.3738 (mmm) REVERT: A 454 ASP cc_start: 0.7122 (m-30) cc_final: 0.6740 (p0) REVERT: A 483 PHE cc_start: 0.7407 (m-10) cc_final: 0.6979 (m-80) REVERT: A 882 MET cc_start: 0.7892 (mtp) cc_final: 0.7656 (mtp) REVERT: A 898 LEU cc_start: 0.6809 (tp) cc_final: 0.6251 (tp) REVERT: A 1077 PHE cc_start: 0.5660 (t80) cc_final: 0.5349 (t80) REVERT: A 1082 THR cc_start: 0.6095 (OUTLIER) cc_final: 0.5890 (m) REVERT: B 214 ASN cc_start: 0.7445 (t0) cc_final: 0.6894 (t0) REVERT: B 417 MET cc_start: 0.3331 (mmm) cc_final: 0.2716 (mmm) REVERT: B 454 ASP cc_start: 0.7292 (m-30) cc_final: 0.6713 (p0) REVERT: B 621 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.7981 (pt) REVERT: B 841 THR cc_start: 0.8710 (t) cc_final: 0.8447 (m) REVERT: B 882 MET cc_start: 0.7893 (mtp) cc_final: 0.7593 (mtt) REVERT: B 965 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7736 (ptt-90) REVERT: B 1011 MET cc_start: 0.9054 (tpp) cc_final: 0.8809 (tpp) REVERT: C 96 ASN cc_start: 0.7622 (m-40) cc_final: 0.7173 (t0) REVERT: C 214 ASN cc_start: 0.7485 (t0) cc_final: 0.7175 (t0) REVERT: C 265 LYS cc_start: 0.8534 (tmtp) cc_final: 0.8223 (tptt) REVERT: C 302 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8549 (p) REVERT: C 454 ASP cc_start: 0.7013 (m-30) cc_final: 0.6597 (p0) REVERT: C 837 PHE cc_start: 0.6729 (p90) cc_final: 0.6120 (p90) outliers start: 118 outliers final: 87 residues processed: 424 average time/residue: 0.3298 time to fit residues: 227.6482 Evaluate side-chains 385 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 294 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 530 ASN 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 643 ASP Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 895 GLN 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 1082 THR Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 66 VAL 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 231 PHE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 724 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 965 ARG Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1033 SER 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 66 VAL Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 530 ASN Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 616 THR 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 716 THR 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 848 THR Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 884 MET Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain C residue 1116 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 262 optimal weight: 1.9990 chunk 212 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 156 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 737 GLN A 766 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 ASN C 70 HIS C 112 GLN C 766 GLN ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 25497 Z= 0.441 Angle : 0.803 10.655 34704 Z= 0.421 Chirality : 0.051 0.187 3930 Planarity : 0.005 0.065 4497 Dihedral : 6.621 49.201 3432 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.38 % Allowed : 15.70 % Favored : 83.92 % Rotamer: Outliers : 5.86 % Allowed : 13.49 % Favored : 80.66 % 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: 1.20 (0.21), residues: 552 sheet: -1.99 (0.21), residues: 579 loop : -3.42 (0.12), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 868 HIS 0.012 0.002 HIS C1030 PHE 0.034 0.003 PHE A 909 TYR 0.023 0.002 TYR A 689 ARG 0.010 0.001 ARG C 620 *********************** 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 467 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 305 time to evaluate : 2.757 Fit side-chains REVERT: A 214 ASN cc_start: 0.7667 (t0) cc_final: 0.7254 (t0) REVERT: A 483 PHE cc_start: 0.7392 (m-10) cc_final: 0.6965 (m-80) REVERT: A 878 ILE cc_start: 0.6619 (OUTLIER) cc_final: 0.6112 (mt) REVERT: B 214 ASN cc_start: 0.7574 (t0) cc_final: 0.7038 (t0) REVERT: B 285 GLU cc_start: 0.8480 (tp30) cc_final: 0.8117 (tp30) REVERT: B 361 PHE cc_start: 0.7799 (m-10) cc_final: 0.7413 (m-80) REVERT: B 454 ASP cc_start: 0.7353 (m-30) cc_final: 0.6986 (p0) REVERT: B 553 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6813 (mtt-85) REVERT: B 621 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8132 (pt) REVERT: B 882 MET cc_start: 0.8262 (mtp) cc_final: 0.7986 (mtp) REVERT: B 965 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7912 (ptt-90) REVERT: B 1032 MET cc_start: 0.6794 (ttm) cc_final: 0.6520 (ttm) REVERT: C 214 ASN cc_start: 0.7546 (t0) cc_final: 0.7264 (t0) REVERT: C 231 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7476 (p90) REVERT: C 382 VAL cc_start: 0.7198 (m) cc_final: 0.6966 (p) REVERT: C 454 ASP cc_start: 0.7122 (m-30) cc_final: 0.6898 (p0) REVERT: C 894 THR cc_start: 0.7820 (t) cc_final: 0.7561 (m) outliers start: 162 outliers final: 119 residues processed: 427 average time/residue: 0.3394 time to fit residues: 240.5172 Evaluate side-chains 409 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 285 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 494 TYR Chi-restraints excluded: chain A residue 530 ASN 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 594 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 895 GLN 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 1087 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 123 VAL 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 296 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 530 ASN 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 553 ARG Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 779 PHE Chi-restraints excluded: chain B residue 848 THR Chi-restraints excluded: chain B residue 849 ASP Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 965 ARG Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1087 THR Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 118 ASN 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 231 PHE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 530 ASN Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 652 ILE 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 848 THR Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 884 MET Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 1087 THR Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain C residue 1116 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 60 optimal weight: 0.0020 chunk 180 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 307 optimal weight: 0.9980 chunk 255 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 GLN A 766 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 304 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN C 766 GLN C 838 ASN C 987 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 25497 Z= 0.279 Angle : 0.705 10.856 34704 Z= 0.369 Chirality : 0.047 0.180 3930 Planarity : 0.005 0.057 4497 Dihedral : 6.322 49.546 3432 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.43 % Favored : 87.20 % Rotamer: Outliers : 4.56 % Allowed : 15.18 % Favored : 80.26 % 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: -3.03 (0.14), residues: 3171 helix: 1.75 (0.22), residues: 534 sheet: -1.90 (0.21), residues: 576 loop : -3.33 (0.12), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 868 HIS 0.007 0.001 HIS C1030 PHE 0.023 0.002 PHE B 262 TYR 0.024 0.002 TYR C 689 ARG 0.006 0.000 ARG C 620 *********************** 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 440 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 314 time to evaluate : 3.038 Fit side-chains REVERT: A 214 ASN cc_start: 0.7402 (t0) cc_final: 0.7053 (t0) REVERT: A 387 PHE cc_start: 0.8184 (p90) cc_final: 0.7434 (p90) REVERT: A 444 ARG cc_start: 0.5357 (ttt-90) cc_final: 0.4903 (ttt-90) REVERT: A 483 PHE cc_start: 0.7228 (m-10) cc_final: 0.6810 (m-80) REVERT: A 894 THR cc_start: 0.7825 (t) cc_final: 0.7608 (m) REVERT: B 214 ASN cc_start: 0.7467 (t0) cc_final: 0.6928 (t0) REVERT: B 361 PHE cc_start: 0.7619 (m-10) cc_final: 0.7388 (m-80) REVERT: B 454 ASP cc_start: 0.7288 (m-30) cc_final: 0.6960 (p0) REVERT: B 545 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7710 (t80) REVERT: B 553 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.6664 (mtt-85) REVERT: B 621 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8175 (pt) REVERT: B 965 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7371 (ptt-90) REVERT: B 1032 MET cc_start: 0.6595 (ttm) cc_final: 0.6386 (ttm) REVERT: C 214 ASN cc_start: 0.7472 (t0) cc_final: 0.7180 (t0) REVERT: C 302 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8509 (p) REVERT: C 361 PHE cc_start: 0.7017 (m-80) cc_final: 0.6750 (m-80) REVERT: C 483 PHE cc_start: 0.5476 (m-80) cc_final: 0.4384 (m-80) REVERT: C 948 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8733 (mt) outliers start: 126 outliers final: 100 residues processed: 406 average time/residue: 0.3304 time to fit residues: 218.8413 Evaluate side-chains 396 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 290 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 494 TYR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 530 ASN 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 643 ASP Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 741 PHE Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 895 GLN 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 1087 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 149 HIS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 530 ASN 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 545 PHE Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 720 CYS Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 779 PHE Chi-restraints excluded: chain B residue 849 ASP Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 965 ARG Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 215 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 302 THR Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 530 ASN Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 640 GLU 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 861 SER Chi-restraints excluded: chain C residue 884 MET Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 0.0980 chunk 34 optimal weight: 9.9990 chunk 175 optimal weight: 0.9990 chunk 224 optimal weight: 0.7980 chunk 174 optimal weight: 0.9980 chunk 259 optimal weight: 0.2980 chunk 171 optimal weight: 6.9990 chunk 306 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 ASN A 766 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN B 304 ASN B 409 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS C 96 ASN C 109 ASN C 409 ASN C 505 ASN C 766 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25497 Z= 0.196 Angle : 0.655 10.088 34704 Z= 0.341 Chirality : 0.046 0.171 3930 Planarity : 0.004 0.067 4497 Dihedral : 5.938 49.492 3432 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.83 % Favored : 87.89 % Rotamer: Outliers : 3.90 % Allowed : 16.38 % Favored : 79.72 % 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: -2.78 (0.14), residues: 3171 helix: 1.98 (0.22), residues: 537 sheet: -1.71 (0.22), residues: 573 loop : -3.20 (0.12), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 868 HIS 0.005 0.001 HIS C1030 PHE 0.022 0.001 PHE B 262 TYR 0.018 0.001 TYR C 689 ARG 0.006 0.000 ARG C 758 *********************** 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 435 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 327 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ASN cc_start: 0.7437 (t0) cc_final: 0.7170 (t0) REVERT: A 387 PHE cc_start: 0.8172 (p90) cc_final: 0.7418 (p90) REVERT: A 483 PHE cc_start: 0.7192 (m-10) cc_final: 0.6781 (m-80) REVERT: A 545 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.6959 (m-80) REVERT: B 203 ILE cc_start: 0.8474 (pt) cc_final: 0.8247 (pt) REVERT: B 214 ASN cc_start: 0.7547 (t0) cc_final: 0.6988 (t0) REVERT: B 387 PHE cc_start: 0.7937 (p90) cc_final: 0.7468 (p90) REVERT: B 454 ASP cc_start: 0.7343 (m-30) cc_final: 0.7009 (p0) REVERT: B 545 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7651 (t80) REVERT: C 214 ASN cc_start: 0.7476 (t0) cc_final: 0.7172 (t0) REVERT: C 231 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7224 (p90) REVERT: C 387 PHE cc_start: 0.8252 (p90) cc_final: 0.7815 (p90) REVERT: C 483 PHE cc_start: 0.5407 (m-80) cc_final: 0.4305 (m-80) REVERT: C 545 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7764 (t80) REVERT: C 837 PHE cc_start: 0.6871 (p90) cc_final: 0.6183 (p90) REVERT: C 1011 MET cc_start: 0.9124 (tpp) cc_final: 0.8810 (tpp) outliers start: 108 outliers final: 84 residues processed: 403 average time/residue: 0.3362 time to fit residues: 220.4186 Evaluate side-chains 385 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 297 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 494 TYR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 736 LEU 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 1000 ILE 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 66 VAL Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 530 ASN Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 724 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 861 SER Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 965 ARG Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 183 optimal weight: 0.0020 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 208 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN A 766 GLN ** 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 230 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN C 766 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25497 Z= 0.197 Angle : 0.649 10.829 34704 Z= 0.336 Chirality : 0.046 0.329 3930 Planarity : 0.004 0.064 4497 Dihedral : 5.826 48.741 3432 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.70 % Favored : 88.05 % Rotamer: Outliers : 3.69 % Allowed : 16.99 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.15), residues: 3171 helix: 2.10 (0.22), residues: 531 sheet: -1.55 (0.22), residues: 573 loop : -3.09 (0.12), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 868 HIS 0.005 0.001 HIS B1030 PHE 0.028 0.001 PHE B 361 TYR 0.025 0.001 TYR C 677 ARG 0.004 0.000 ARG C 758 *********************** 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 430 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 328 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 ASN cc_start: 0.7263 (t0) cc_final: 0.7027 (t0) REVERT: A 263 MET cc_start: 0.8137 (tmm) cc_final: 0.7887 (tmm) REVERT: A 340 TRP cc_start: 0.5282 (p-90) cc_final: 0.4255 (p-90) REVERT: A 387 PHE cc_start: 0.8162 (p90) cc_final: 0.7283 (p90) REVERT: A 410 TYR cc_start: 0.7028 (t80) cc_final: 0.6758 (m-80) REVERT: A 483 PHE cc_start: 0.7183 (m-10) cc_final: 0.6749 (m-80) REVERT: A 545 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.6970 (m-80) REVERT: B 203 ILE cc_start: 0.8454 (pt) cc_final: 0.8227 (pt) REVERT: B 214 ASN cc_start: 0.7441 (t0) cc_final: 0.6904 (t0) REVERT: B 410 TYR cc_start: 0.6234 (OUTLIER) cc_final: 0.5673 (m-10) REVERT: B 454 ASP cc_start: 0.7230 (m-30) cc_final: 0.7028 (p0) REVERT: B 545 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7635 (t80) REVERT: B 882 MET cc_start: 0.8006 (mtp) cc_final: 0.7527 (mtm) REVERT: B 1011 MET cc_start: 0.8946 (tpp) cc_final: 0.8646 (tpp) REVERT: C 214 ASN cc_start: 0.7461 (t0) cc_final: 0.7156 (t0) REVERT: C 231 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7279 (p90) REVERT: C 265 LYS cc_start: 0.8561 (tmtp) cc_final: 0.8259 (tptt) REVERT: C 387 PHE cc_start: 0.7876 (p90) cc_final: 0.7630 (p90) REVERT: C 545 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7713 (t80) REVERT: C 837 PHE cc_start: 0.6823 (p90) cc_final: 0.6235 (p90) outliers start: 102 outliers final: 85 residues processed: 399 average time/residue: 0.3369 time to fit residues: 219.3672 Evaluate side-chains 389 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 299 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 494 TYR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 410 TYR Chi-restraints excluded: chain B residue 494 TYR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 530 ASN Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 767 VAL 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 1000 ILE 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 66 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 530 ASN Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 648 CYS 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 848 THR Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.9990 chunk 293 optimal weight: 7.9990 chunk 267 optimal weight: 4.9990 chunk 285 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 224 optimal weight: 0.0770 chunk 87 optimal weight: 0.7980 chunk 258 optimal weight: 0.4980 chunk 270 optimal weight: 6.9990 chunk 284 optimal weight: 2.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 437 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN C 759 ASN C1101 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25497 Z= 0.195 Angle : 0.642 12.142 34704 Z= 0.333 Chirality : 0.046 0.308 3930 Planarity : 0.004 0.062 4497 Dihedral : 5.728 48.584 3432 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.54 % Favored : 88.24 % Rotamer: Outliers : 3.80 % Allowed : 17.17 % Favored : 79.03 % 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: -2.57 (0.15), residues: 3171 helix: 2.15 (0.22), residues: 531 sheet: -1.56 (0.22), residues: 579 loop : -3.05 (0.12), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 868 HIS 0.004 0.001 HIS C1030 PHE 0.027 0.001 PHE A 262 TYR 0.028 0.001 TYR B 677 ARG 0.004 0.000 ARG C 758 *********************** 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 423 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 318 time to evaluate : 2.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ASN cc_start: 0.7252 (t0) cc_final: 0.7021 (t0) REVERT: A 263 MET cc_start: 0.8110 (tmm) cc_final: 0.7751 (tmm) REVERT: A 387 PHE cc_start: 0.8171 (p90) cc_final: 0.7285 (p90) REVERT: A 410 TYR cc_start: 0.7138 (t80) cc_final: 0.6821 (m-80) REVERT: A 483 PHE cc_start: 0.7186 (m-10) cc_final: 0.6749 (m-80) REVERT: A 545 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.6978 (m-80) REVERT: A 689 TYR cc_start: 0.6125 (t80) cc_final: 0.5919 (t80) REVERT: A 837 PHE cc_start: 0.7126 (p90) cc_final: 0.6881 (p90) REVERT: B 203 ILE cc_start: 0.8450 (pt) cc_final: 0.8224 (pt) REVERT: B 214 ASN cc_start: 0.7366 (t0) cc_final: 0.6818 (t0) REVERT: B 410 TYR cc_start: 0.6159 (OUTLIER) cc_final: 0.5412 (m-10) REVERT: B 454 ASP cc_start: 0.7235 (m-30) cc_final: 0.7031 (p0) REVERT: B 545 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7616 (t80) REVERT: B 882 MET cc_start: 0.8015 (mtp) cc_final: 0.7520 (mtm) REVERT: C 214 ASN cc_start: 0.7469 (t0) cc_final: 0.7176 (t0) REVERT: C 231 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7211 (p90) REVERT: C 265 LYS cc_start: 0.8607 (tmtp) cc_final: 0.8285 (tptt) REVERT: C 387 PHE cc_start: 0.7873 (p90) cc_final: 0.7643 (p90) REVERT: C 410 TYR cc_start: 0.5981 (OUTLIER) cc_final: 0.5690 (m-10) REVERT: C 545 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7738 (t80) REVERT: C 837 PHE cc_start: 0.6840 (p90) cc_final: 0.6231 (p90) outliers start: 105 outliers final: 89 residues processed: 394 average time/residue: 0.3396 time to fit residues: 220.8882 Evaluate side-chains 393 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 298 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 494 TYR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 779 PHE Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1057 PHE Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 410 TYR Chi-restraints excluded: chain B residue 494 TYR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 530 ASN Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 741 PHE Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 779 PHE Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 1000 ILE Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1057 PHE Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 124 VAL 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 231 PHE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 410 TYR Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 530 ASN Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 562 VAL 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 724 ILE Chi-restraints excluded: chain C residue 729 THR 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 861 SER Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 5.9990 chunk 302 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 316 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 252 optimal weight: 20.0000 chunk 26 optimal weight: 0.6980 chunk 194 optimal weight: 0.7980 chunk 154 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN ** 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** A1101 ASN B 230 ASN B 409 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25497 Z= 0.281 Angle : 0.686 12.915 34704 Z= 0.355 Chirality : 0.047 0.212 3930 Planarity : 0.004 0.063 4497 Dihedral : 5.886 46.609 3432 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.15 % Favored : 86.63 % Rotamer: Outliers : 3.80 % Allowed : 17.28 % Favored : 78.92 % 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: -2.62 (0.15), residues: 3171 helix: 2.03 (0.22), residues: 531 sheet: -1.54 (0.22), residues: 579 loop : -3.06 (0.12), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 868 HIS 0.007 0.001 HIS C1030 PHE 0.033 0.002 PHE A 262 TYR 0.026 0.002 TYR B 677 ARG 0.004 0.000 ARG C 620 ********************** 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 405 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 300 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 ASN cc_start: 0.7163 (t0) cc_final: 0.6952 (t0) REVERT: A 263 MET cc_start: 0.8245 (tmm) cc_final: 0.7935 (tmm) REVERT: A 387 PHE cc_start: 0.8179 (p90) cc_final: 0.7300 (p90) REVERT: A 410 TYR cc_start: 0.7218 (t80) cc_final: 0.6835 (m-80) REVERT: A 483 PHE cc_start: 0.7204 (m-10) cc_final: 0.6755 (m-80) REVERT: A 545 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7107 (m-80) REVERT: B 203 ILE cc_start: 0.8457 (pt) cc_final: 0.8227 (pt) REVERT: B 214 ASN cc_start: 0.7426 (t0) cc_final: 0.6879 (t0) REVERT: B 387 PHE cc_start: 0.7857 (p90) cc_final: 0.7292 (p90) REVERT: B 410 TYR cc_start: 0.6163 (OUTLIER) cc_final: 0.5446 (m-10) REVERT: B 454 ASP cc_start: 0.7257 (m-30) cc_final: 0.7035 (p0) REVERT: B 545 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7799 (t80) REVERT: B 882 MET cc_start: 0.8025 (mtp) cc_final: 0.7694 (mtm) REVERT: C 214 ASN cc_start: 0.7532 (t0) cc_final: 0.7252 (t0) REVERT: C 231 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7268 (p90) REVERT: C 387 PHE cc_start: 0.7903 (p90) cc_final: 0.7701 (p90) REVERT: C 410 TYR cc_start: 0.5931 (OUTLIER) cc_final: 0.5669 (m-10) REVERT: C 545 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7655 (t80) outliers start: 105 outliers final: 92 residues processed: 377 average time/residue: 0.3146 time to fit residues: 196.0633 Evaluate side-chains 387 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 289 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 494 TYR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 410 TYR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 530 ASN Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 767 VAL Chi-restraints excluded: chain B residue 779 PHE Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1000 ILE 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 66 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 124 VAL 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 231 PHE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 409 ASN Chi-restraints excluded: chain C residue 410 TYR Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 530 ASN Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 643 ASP 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 719 ASP Chi-restraints excluded: chain C residue 729 THR 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 861 SER Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 0.9990 chunk 268 optimal weight: 0.9990 chunk 77 optimal weight: 0.0020 chunk 232 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 252 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 chunk 259 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 230 ASN B 304 ASN B 505 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.189578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.156476 restraints weight = 40185.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.157794 restraints weight = 27821.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.158524 restraints weight = 23259.075| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25497 Z= 0.200 Angle : 0.665 13.288 34704 Z= 0.341 Chirality : 0.046 0.183 3930 Planarity : 0.004 0.060 4497 Dihedral : 5.753 47.665 3432 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.73 % Favored : 88.05 % Rotamer: Outliers : 3.47 % Allowed : 18.00 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.52 (0.15), residues: 3171 helix: 2.16 (0.22), residues: 528 sheet: -1.49 (0.22), residues: 579 loop : -3.01 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 868 HIS 0.004 0.001 HIS C1030 PHE 0.023 0.001 PHE B 483 TYR 0.031 0.001 TYR C 677 ARG 0.004 0.000 ARG C 758 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5261.37 seconds wall clock time: 97 minutes 23.13 seconds (5843.13 seconds total)