Starting phenix.real_space_refine on Mon Feb 19 06:03:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlr_6732/02_2024/5xlr_6732.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlr_6732/02_2024/5xlr_6732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlr_6732/02_2024/5xlr_6732.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlr_6732/02_2024/5xlr_6732.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlr_6732/02_2024/5xlr_6732.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xlr_6732/02_2024/5xlr_6732.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 132 5.16 5 C 15279 2.51 5 N 3954 2.21 5 O 4536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 819": "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: 23901 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7967 Classifications: {'peptide': 1022} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 973} Chain breaks: 6 Chain: "B" Number of atoms: 7967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7967 Classifications: {'peptide': 1022} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 973} Chain breaks: 6 Chain: "C" Number of atoms: 7967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7967 Classifications: {'peptide': 1022} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 973} Chain breaks: 6 Time building chain proxies: 12.49, per 1000 atoms: 0.52 Number of scatterers: 23901 At special positions: 0 Unit cell: (132, 133.32, 163.68, 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 132 16.00 O 4536 8.00 N 3954 7.00 C 15279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.02 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.02 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.02 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.03 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: 9.24 Conformation dependent library (CDL) restraints added in 4.3 seconds 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5736 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 39 sheets defined 23.4% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 267 through 271 removed outlier: 4.059A pdb=" N THR A 271 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.513A pdb=" N LYS A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 390 through 397 removed outlier: 4.215A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 603 through 611 Processing helix chain 'A' and resid 729 through 739 removed outlier: 3.503A pdb=" N GLY A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.809A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 810 Processing helix chain 'A' and resid 815 through 820 removed outlier: 4.197A pdb=" N TYR A 819 " --> pdb=" O PHE A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 865 Processing helix chain 'A' and resid 879 through 892 Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.541A pdb=" N ASN A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 920 Processing helix chain 'A' and resid 927 through 949 removed outlier: 3.665A pdb=" N GLN A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 949 " --> pdb=" O VAL A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 971 through 1015 removed outlier: 4.020A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 982 " --> pdb=" O LEU A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'B' and resid 267 through 271 removed outlier: 4.059A pdb=" N THR B 271 " --> pdb=" O GLU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 removed outlier: 3.512A pdb=" N LYS B 291 " --> pdb=" O LYS B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 390 through 397 removed outlier: 4.214A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 603 through 611 Processing helix chain 'B' and resid 729 through 739 removed outlier: 3.505A pdb=" N GLY B 739 " --> pdb=" O LEU B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 765 removed outlier: 3.811A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 810 Processing helix chain 'B' and resid 815 through 820 removed outlier: 4.197A pdb=" N TYR B 819 " --> pdb=" O PHE B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 865 Processing helix chain 'B' and resid 879 through 892 Processing helix chain 'B' and resid 895 through 901 removed outlier: 3.540A pdb=" N ASN B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 920 Processing helix chain 'B' and resid 927 through 949 removed outlier: 3.665A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER B 949 " --> pdb=" O VAL B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 966 Processing helix chain 'B' and resid 971 through 1015 removed outlier: 4.019A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG B 982 " --> pdb=" O LEU B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'C' and resid 267 through 271 removed outlier: 4.059A pdb=" N THR C 271 " --> pdb=" O GLU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 removed outlier: 3.513A pdb=" N LYS C 291 " --> pdb=" O LYS C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 390 through 397 removed outlier: 4.214A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 603 through 611 Processing helix chain 'C' and resid 729 through 739 removed outlier: 3.504A pdb=" N GLY C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.810A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 810 Processing helix chain 'C' and resid 815 through 820 removed outlier: 4.197A pdb=" N TYR C 819 " --> pdb=" O PHE C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 865 Processing helix chain 'C' and resid 879 through 892 Processing helix chain 'C' and resid 895 through 901 removed outlier: 3.541A pdb=" N ASN C 901 " --> pdb=" O VAL C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 920 Processing helix chain 'C' and resid 927 through 949 removed outlier: 3.665A pdb=" N GLN C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C 949 " --> pdb=" O VAL C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 966 Processing helix chain 'C' and resid 971 through 1015 removed outlier: 4.019A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG C 982 " --> pdb=" O LEU C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1102 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36 removed outlier: 7.145A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 166 Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 306 removed outlier: 3.859A pdb=" N GLY A 298 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR A 585 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 removed outlier: 3.625A pdb=" N GLY A 311 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 537 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 570 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 345 removed outlier: 5.031A pdb=" N ASN A 381 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU A 502 " --> pdb=" O ASN A 381 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AA8, first strand: chain 'A' and resid 650 through 652 Processing sheet with id=AA9, first strand: chain 'A' and resid 694 through 696 Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 710 Processing sheet with id=AB2, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB3, first strand: chain 'A' and resid 1063 through 1064 removed outlier: 3.582A pdb=" N ILE A1063 " --> pdb=" O TYR A1070 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1077 through 1079 Processing sheet with id=AB5, first strand: chain 'B' and resid 34 through 36 removed outlier: 7.145A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 51 through 55 Processing sheet with id=AB7, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AB8, first strand: chain 'B' and resid 298 through 306 removed outlier: 3.859A pdb=" N GLY B 298 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR B 585 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN B 304 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY B 579 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 315 removed outlier: 3.625A pdb=" N GLY B 311 " --> pdb=" O CYS B 524 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 537 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 570 " --> pdb=" O VAL B 562 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 341 through 345 removed outlier: 5.030A pdb=" N ASN B 381 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU B 502 " --> pdb=" O ASN B 381 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AC3, first strand: chain 'B' and resid 650 through 652 Processing sheet with id=AC4, first strand: chain 'B' and resid 694 through 696 Processing sheet with id=AC5, first strand: chain 'B' and resid 701 through 710 Processing sheet with id=AC6, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AC7, first strand: chain 'B' and resid 1063 through 1064 removed outlier: 3.582A pdb=" N ILE B1063 " --> pdb=" O TYR B1070 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1077 through 1079 Processing sheet with id=AC9, first strand: chain 'C' and resid 34 through 36 removed outlier: 7.145A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 51 through 55 Processing sheet with id=AD2, first strand: chain 'C' and resid 164 through 166 Processing sheet with id=AD3, first strand: chain 'C' and resid 298 through 306 removed outlier: 3.857A pdb=" N GLY C 298 " --> pdb=" O THR C 585 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR C 585 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 315 removed outlier: 3.625A pdb=" N GLY C 311 " --> pdb=" O CYS C 524 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 537 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 570 " --> pdb=" O VAL C 562 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 341 through 345 removed outlier: 5.030A pdb=" N ASN C 381 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU C 502 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AD7, first strand: chain 'C' and resid 650 through 652 Processing sheet with id=AD8, first strand: chain 'C' and resid 694 through 696 Processing sheet with id=AD9, first strand: chain 'C' and resid 701 through 710 Processing sheet with id=AE1, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AE2, first strand: chain 'C' and resid 1063 through 1064 removed outlier: 3.582A pdb=" N ILE C1063 " --> pdb=" O TYR C1070 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1077 through 1079 894 hydrogen bonds defined for protein. 2358 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: 8.49 Time building geometry restraints manager: 9.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7555 1.34 - 1.46: 5559 1.46 - 1.58: 11159 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 24453 Sorted by residual: bond pdb=" C LYS B 411 " pdb=" N LEU B 412 " ideal model delta sigma weight residual 1.331 1.239 0.091 3.12e-02 1.03e+03 8.59e+00 bond pdb=" C LYS C 411 " pdb=" N LEU C 412 " ideal model delta sigma weight residual 1.331 1.239 0.091 3.12e-02 1.03e+03 8.59e+00 bond pdb=" C LYS A 411 " pdb=" N LEU A 412 " ideal model delta sigma weight residual 1.331 1.239 0.091 3.12e-02 1.03e+03 8.58e+00 bond pdb=" C ILE B 787 " pdb=" N LEU B 788 " ideal model delta sigma weight residual 1.331 1.251 0.080 2.83e-02 1.25e+03 7.90e+00 bond pdb=" C LEU A1031 " pdb=" N MET A1032 " ideal model delta sigma weight residual 1.330 1.355 -0.025 1.19e-02 7.06e+03 4.30e+00 ... (remaining 24448 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.44: 533 105.44 - 112.60: 12312 112.60 - 119.77: 8214 119.77 - 126.93: 11934 126.93 - 134.09: 262 Bond angle restraints: 33255 Sorted by residual: angle pdb=" N ASN A 227 " pdb=" CA ASN A 227 " pdb=" C ASN A 227 " ideal model delta sigma weight residual 107.73 115.58 -7.85 1.34e+00 5.57e-01 3.43e+01 angle pdb=" N ASN B 227 " pdb=" CA ASN B 227 " pdb=" C ASN B 227 " ideal model delta sigma weight residual 107.73 115.58 -7.85 1.34e+00 5.57e-01 3.43e+01 angle pdb=" N ASN C 227 " pdb=" CA ASN C 227 " pdb=" C ASN C 227 " ideal model delta sigma weight residual 107.73 115.56 -7.83 1.34e+00 5.57e-01 3.42e+01 angle pdb=" C LYS A 566 " pdb=" N THR A 567 " pdb=" CA THR A 567 " ideal model delta sigma weight residual 122.78 130.94 -8.16 1.52e+00 4.33e-01 2.88e+01 angle pdb=" C LYS C 566 " pdb=" N THR C 567 " pdb=" CA THR C 567 " ideal model delta sigma weight residual 122.78 130.91 -8.13 1.52e+00 4.33e-01 2.86e+01 ... (remaining 33250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.27: 13700 16.27 - 32.55: 719 32.55 - 48.82: 122 48.82 - 65.09: 12 65.09 - 81.36: 6 Dihedral angle restraints: 14559 sinusoidal: 5634 harmonic: 8925 Sorted by residual: dihedral pdb=" CA ILE B 573 " pdb=" C ILE B 573 " pdb=" N SER B 574 " pdb=" CA SER B 574 " ideal model delta harmonic sigma weight residual -180.00 -132.44 -47.56 0 5.00e+00 4.00e-02 9.05e+01 dihedral pdb=" CA ILE C 573 " pdb=" C ILE C 573 " pdb=" N SER C 574 " pdb=" CA SER C 574 " ideal model delta harmonic sigma weight residual -180.00 -132.49 -47.51 0 5.00e+00 4.00e-02 9.03e+01 dihedral pdb=" CA ILE A 573 " pdb=" C ILE A 573 " pdb=" N SER A 574 " pdb=" CA SER A 574 " ideal model delta harmonic sigma weight residual -180.00 -132.51 -47.49 0 5.00e+00 4.00e-02 9.02e+01 ... (remaining 14556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2522 0.057 - 0.113: 929 0.113 - 0.170: 266 0.170 - 0.227: 39 0.227 - 0.284: 6 Chirality restraints: 3762 Sorted by residual: chirality pdb=" CA THR B 567 " pdb=" N THR B 567 " pdb=" C THR B 567 " pdb=" CB THR B 567 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA THR A 567 " pdb=" N THR A 567 " pdb=" C THR A 567 " pdb=" CB THR A 567 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA THR C 567 " pdb=" N THR C 567 " pdb=" C THR C 567 " pdb=" CB THR C 567 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 3759 not shown) Planarity restraints: 4302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 502 " -0.031 2.00e-02 2.50e+03 6.17e-02 3.81e+01 pdb=" C GLU C 502 " 0.107 2.00e-02 2.50e+03 pdb=" O GLU C 502 " -0.041 2.00e-02 2.50e+03 pdb=" N LEU C 503 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 502 " -0.031 2.00e-02 2.50e+03 6.16e-02 3.79e+01 pdb=" C GLU A 502 " 0.107 2.00e-02 2.50e+03 pdb=" O GLU A 502 " -0.040 2.00e-02 2.50e+03 pdb=" N LEU A 503 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 502 " 0.031 2.00e-02 2.50e+03 6.14e-02 3.77e+01 pdb=" C GLU B 502 " -0.106 2.00e-02 2.50e+03 pdb=" O GLU B 502 " 0.040 2.00e-02 2.50e+03 pdb=" N LEU B 503 " 0.035 2.00e-02 2.50e+03 ... (remaining 4299 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 794 2.69 - 3.24: 22807 3.24 - 3.80: 36940 3.80 - 4.35: 46462 4.35 - 4.90: 77525 Nonbonded interactions: 184528 Sorted by model distance: nonbonded pdb=" NE2 GLN A 549 " pdb=" OE1 GLU C 45 " model vdw 2.139 2.520 nonbonded pdb=" ND2 ASN A 304 " pdb=" OD1 ASP C 719 " model vdw 2.147 2.520 nonbonded pdb=" OD1 ASP A 719 " pdb=" ND2 ASN B 304 " model vdw 2.198 2.520 nonbonded pdb=" O PHE C 805 " pdb=" OG1 THR C 809 " model vdw 2.215 2.440 nonbonded pdb=" O PHE A 805 " pdb=" OG1 THR A 809 " model vdw 2.215 2.440 ... (remaining 184523 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: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.220 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 61.050 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 24453 Z= 0.529 Angle : 1.171 12.182 33255 Z= 0.669 Chirality : 0.063 0.284 3762 Planarity : 0.009 0.108 4302 Dihedral : 9.811 55.170 8697 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.30 % Allowed : 14.55 % Favored : 85.15 % Rotamer: Outliers : 0.38 % Allowed : 2.35 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.62 % 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: -4.45 (0.12), residues: 3024 helix: -2.64 (0.13), residues: 699 sheet: -1.59 (0.21), residues: 516 loop : -3.71 (0.12), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 423 HIS 0.021 0.004 HIS A1030 PHE 0.047 0.004 PHE A 193 TYR 0.030 0.004 TYR B 886 ARG 0.007 0.001 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 708 time to evaluate : 2.507 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 PHE cc_start: 0.6028 (t80) cc_final: 0.5759 (t80) REVERT: A 216 LEU cc_start: 0.5945 (OUTLIER) cc_final: 0.5522 (pp) REVERT: A 220 PHE cc_start: 0.5276 (t80) cc_final: 0.4948 (t80) REVERT: A 301 GLN cc_start: 0.8708 (tt0) cc_final: 0.8348 (tm-30) REVERT: A 850 ASP cc_start: 0.8968 (m-30) cc_final: 0.8553 (t0) REVERT: A 884 MET cc_start: 0.6871 (mmm) cc_final: 0.6550 (mmt) REVERT: A 899 TYR cc_start: 0.5974 (t80) cc_final: 0.5646 (t80) REVERT: A 948 LEU cc_start: 0.9482 (tp) cc_final: 0.9262 (tt) REVERT: A 1027 LYS cc_start: 0.8705 (tttt) cc_final: 0.8481 (tppt) REVERT: B 216 LEU cc_start: 0.5953 (OUTLIER) cc_final: 0.5295 (pp) REVERT: B 220 PHE cc_start: 0.5563 (t80) cc_final: 0.5336 (t80) REVERT: B 301 GLN cc_start: 0.8901 (tt0) cc_final: 0.8642 (tm-30) REVERT: B 405 ILE cc_start: 0.7880 (mm) cc_final: 0.7583 (mp) REVERT: B 850 ASP cc_start: 0.9121 (m-30) cc_final: 0.8817 (p0) REVERT: B 894 THR cc_start: 0.8161 (m) cc_final: 0.7954 (p) REVERT: B 973 VAL cc_start: 0.8782 (p) cc_final: 0.8569 (m) REVERT: C 89 PHE cc_start: 0.6230 (t80) cc_final: 0.5898 (t80) REVERT: C 220 PHE cc_start: 0.5565 (t80) cc_final: 0.5328 (t80) REVERT: C 301 GLN cc_start: 0.8787 (tt0) cc_final: 0.8398 (tm-30) REVERT: C 532 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7085 (tm) REVERT: C 733 ASN cc_start: 0.7955 (m-40) cc_final: 0.7567 (m-40) REVERT: C 850 ASP cc_start: 0.9232 (m-30) cc_final: 0.8700 (t0) REVERT: C 868 TRP cc_start: 0.6833 (p-90) cc_final: 0.6417 (p-90) REVERT: C 973 VAL cc_start: 0.8757 (p) cc_final: 0.8375 (m) outliers start: 10 outliers final: 1 residues processed: 718 average time/residue: 0.4152 time to fit residues: 446.9165 Evaluate side-chains 381 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 377 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 532 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.0870 chunk 231 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 239 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 178 optimal weight: 0.2980 chunk 277 optimal weight: 4.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 149 HIS A 201 GLN A 214 ASN A 437 ASN ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 GLN A 883 GLN A 889 ASN A 904 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 ASN B 109 ASN B 129 ASN B 149 HIS B 201 GLN B 214 ASN B 769 GLN B 883 GLN B 889 ASN B 904 GLN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN B1116 ASN C 129 ASN C 149 HIS C 201 GLN C 214 ASN C 523 GLN C 769 GLN C 883 GLN C 889 ASN C 904 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1046 HIS C1090 ASN C1116 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 24453 Z= 0.239 Angle : 0.789 9.721 33255 Z= 0.414 Chirality : 0.048 0.361 3762 Planarity : 0.007 0.104 4302 Dihedral : 7.473 42.022 3301 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.74 % Favored : 88.16 % Rotamer: Outliers : 2.84 % Allowed : 10.48 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.24 % 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: -3.09 (0.14), residues: 3024 helix: 0.04 (0.19), residues: 681 sheet: -1.05 (0.22), residues: 543 loop : -3.45 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 101 HIS 0.008 0.001 HIS A1065 PHE 0.038 0.002 PHE C 262 TYR 0.025 0.002 TYR A 886 ARG 0.019 0.001 ARG C1089 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 458 time to evaluate : 2.708 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: symmetry clash revert: symmetry clash REVERT: A 216 LEU cc_start: 0.6031 (OUTLIER) cc_final: 0.5504 (pp) REVERT: A 220 PHE cc_start: 0.5198 (t80) cc_final: 0.4967 (t80) REVERT: A 491 TYR cc_start: 0.5744 (OUTLIER) cc_final: 0.5218 (m-10) REVERT: A 545 PHE cc_start: 0.6631 (m-10) cc_final: 0.6355 (m-80) REVERT: A 850 ASP cc_start: 0.8948 (m-30) cc_final: 0.8644 (t0) REVERT: A 899 TYR cc_start: 0.5255 (t80) cc_final: 0.4135 (t80) REVERT: A 966 LEU cc_start: 0.8799 (mp) cc_final: 0.8598 (mm) REVERT: B 216 LEU cc_start: 0.6245 (OUTLIER) cc_final: 0.5238 (pp) REVERT: B 405 ILE cc_start: 0.7788 (mm) cc_final: 0.7395 (mp) REVERT: B 440 TYR cc_start: 0.5762 (p90) cc_final: 0.5374 (p90) REVERT: B 515 LEU cc_start: 0.8864 (mt) cc_final: 0.8561 (tp) REVERT: B 894 THR cc_start: 0.8327 (m) cc_final: 0.7729 (p) REVERT: C 515 LEU cc_start: 0.8901 (mt) cc_final: 0.8603 (tp) REVERT: C 846 LEU cc_start: 0.8722 (tp) cc_final: 0.8503 (tt) REVERT: C 850 ASP cc_start: 0.9226 (m-30) cc_final: 0.8868 (t0) REVERT: C 966 LEU cc_start: 0.8706 (mt) cc_final: 0.8454 (mm) outliers start: 75 outliers final: 44 residues processed: 507 average time/residue: 0.3588 time to fit residues: 287.8911 Evaluate side-chains 413 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 366 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 360 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 737 GLN Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 979 ILE Chi-restraints excluded: chain B residue 1087 THR Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 1087 THR Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1100 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 278 optimal weight: 0.1980 chunk 300 optimal weight: 0.9990 chunk 247 optimal weight: 0.6980 chunk 276 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 223 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 437 ASN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 GLN A 746 ASN A 931 GLN A 935 ASN A 993 GLN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN B 993 GLN B1090 ASN C 109 ASN ** C 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 ASN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 993 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 24453 Z= 0.217 Angle : 0.738 14.199 33255 Z= 0.381 Chirality : 0.048 0.256 3762 Planarity : 0.006 0.096 4302 Dihedral : 6.803 37.113 3299 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.13 % Favored : 86.87 % Rotamer: Outliers : 3.97 % Allowed : 12.49 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 1.39 % 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: 3024 helix: 1.13 (0.20), residues: 669 sheet: -0.71 (0.23), residues: 483 loop : -3.26 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 101 HIS 0.007 0.001 HIS A1065 PHE 0.033 0.002 PHE C 262 TYR 0.022 0.002 TYR A 886 ARG 0.011 0.001 ARG C1089 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 407 time to evaluate : 2.655 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LEU cc_start: 0.6113 (OUTLIER) cc_final: 0.5447 (pp) REVERT: A 491 TYR cc_start: 0.5879 (OUTLIER) cc_final: 0.4896 (m-10) REVERT: A 837 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7764 (m-80) REVERT: A 850 ASP cc_start: 0.8989 (m-30) cc_final: 0.8679 (t0) REVERT: B 216 LEU cc_start: 0.5223 (OUTLIER) cc_final: 0.4475 (pp) REVERT: B 405 ILE cc_start: 0.7827 (mm) cc_final: 0.7463 (mp) REVERT: B 440 TYR cc_start: 0.5830 (p90) cc_final: 0.5452 (p90) REVERT: B 515 LEU cc_start: 0.8882 (mt) cc_final: 0.8583 (tp) REVERT: B 554 ASP cc_start: 0.5100 (t0) cc_final: 0.4727 (t0) REVERT: B 1011 MET cc_start: 0.9106 (ttm) cc_final: 0.8645 (ttm) REVERT: B 1076 VAL cc_start: 0.6907 (OUTLIER) cc_final: 0.6658 (t) REVERT: C 216 LEU cc_start: 0.5177 (OUTLIER) cc_final: 0.4953 (pp) REVERT: C 224 LEU cc_start: 0.6667 (mt) cc_final: 0.6408 (mt) REVERT: C 285 GLU cc_start: 0.8992 (tt0) cc_final: 0.8541 (tm-30) REVERT: C 348 CYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8368 (t) REVERT: C 582 SER cc_start: 0.9492 (m) cc_final: 0.9214 (t) REVERT: C 727 ASP cc_start: 0.8760 (p0) cc_final: 0.8512 (p0) REVERT: C 846 LEU cc_start: 0.8739 (tp) cc_final: 0.8489 (tt) REVERT: C 850 ASP cc_start: 0.9231 (m-30) cc_final: 0.8881 (t0) REVERT: C 966 LEU cc_start: 0.8720 (mt) cc_final: 0.8401 (mm) outliers start: 105 outliers final: 65 residues processed: 472 average time/residue: 0.3402 time to fit residues: 254.9769 Evaluate side-chains 419 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 347 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 360 PHE Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 737 GLN Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 896 ASN Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 896 ASN Chi-restraints excluded: chain C residue 1073 ARG Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain C residue 1100 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 132 optimal weight: 0.1980 chunk 186 optimal weight: 0.9980 chunk 279 optimal weight: 1.9990 chunk 295 optimal weight: 3.9990 chunk 145 optimal weight: 0.0870 chunk 264 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- 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 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 GLN A 935 ASN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 931 GLN ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN B1046 HIS ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 627 ASN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24453 Z= 0.237 Angle : 0.744 17.604 33255 Z= 0.381 Chirality : 0.048 0.308 3762 Planarity : 0.006 0.100 4302 Dihedral : 6.522 38.239 3298 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.06 % Favored : 86.94 % Rotamer: Outliers : 4.05 % Allowed : 13.96 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.10 % 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: -2.33 (0.15), residues: 3024 helix: 1.35 (0.20), residues: 681 sheet: -0.52 (0.23), residues: 489 loop : -3.21 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 101 HIS 0.006 0.001 HIS A1065 PHE 0.037 0.002 PHE C 262 TYR 0.021 0.002 TYR A 886 ARG 0.010 0.001 ARG C1089 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 369 time to evaluate : 2.821 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: symmetry clash revert: symmetry clash REVERT: A 216 LEU cc_start: 0.6334 (OUTLIER) cc_final: 0.5692 (pp) REVERT: A 491 TYR cc_start: 0.6110 (OUTLIER) cc_final: 0.5075 (m-10) REVERT: A 837 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: A 850 ASP cc_start: 0.9011 (m-30) cc_final: 0.8747 (t0) REVERT: B 216 LEU cc_start: 0.5243 (OUTLIER) cc_final: 0.4590 (pp) REVERT: B 405 ILE cc_start: 0.7963 (mm) cc_final: 0.7681 (mp) REVERT: B 415 ASP cc_start: 0.5668 (p0) cc_final: 0.5396 (p0) REVERT: B 440 TYR cc_start: 0.5863 (p90) cc_final: 0.5489 (p90) REVERT: B 735 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9110 (tt) REVERT: B 931 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8045 (tp40) REVERT: B 1011 MET cc_start: 0.9212 (ttm) cc_final: 0.8914 (ttm) REVERT: C 216 LEU cc_start: 0.5203 (OUTLIER) cc_final: 0.4992 (pp) REVERT: C 285 GLU cc_start: 0.8956 (tt0) cc_final: 0.8537 (tm-30) REVERT: C 348 CYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8444 (t) REVERT: C 615 LEU cc_start: 0.7513 (tp) cc_final: 0.7180 (mt) REVERT: C 727 ASP cc_start: 0.8809 (p0) cc_final: 0.8585 (p0) REVERT: C 850 ASP cc_start: 0.9137 (m-30) cc_final: 0.8834 (t0) REVERT: C 966 LEU cc_start: 0.8765 (mt) cc_final: 0.8405 (mm) outliers start: 107 outliers final: 74 residues processed: 430 average time/residue: 0.3290 time to fit residues: 225.5219 Evaluate side-chains 427 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 345 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 360 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 737 GLN Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 931 GLN Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 894 THR Chi-restraints excluded: chain C residue 896 ASN Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain C residue 1100 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 7.9990 chunk 167 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 220 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 252 optimal weight: 4.9990 chunk 204 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 265 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 24453 Z= 0.234 Angle : 0.734 18.667 33255 Z= 0.375 Chirality : 0.047 0.297 3762 Planarity : 0.005 0.096 4302 Dihedral : 6.398 36.796 3298 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.00 % Favored : 87.00 % Rotamer: Outliers : 4.20 % Allowed : 14.76 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.24 (0.15), residues: 3024 helix: 1.48 (0.21), residues: 681 sheet: -0.42 (0.24), residues: 477 loop : -3.19 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 101 HIS 0.005 0.001 HIS A1065 PHE 0.034 0.002 PHE B 185 TYR 0.024 0.001 TYR C 886 ARG 0.009 0.000 ARG C1089 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 361 time to evaluate : 2.583 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.5611 (pp) REVERT: A 491 TYR cc_start: 0.6128 (OUTLIER) cc_final: 0.5008 (m-10) REVERT: A 503 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7084 (mm) REVERT: A 735 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8845 (tt) REVERT: A 837 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7879 (m-80) REVERT: B 216 LEU cc_start: 0.5220 (OUTLIER) cc_final: 0.4697 (pp) REVERT: B 405 ILE cc_start: 0.7978 (mm) cc_final: 0.7605 (mp) REVERT: B 440 TYR cc_start: 0.5799 (p90) cc_final: 0.5447 (p90) REVERT: B 735 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9094 (tt) REVERT: B 966 LEU cc_start: 0.8713 (mm) cc_final: 0.8236 (mm) REVERT: B 1011 MET cc_start: 0.9237 (ttm) cc_final: 0.8963 (ttm) REVERT: C 348 CYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8457 (t) REVERT: C 615 LEU cc_start: 0.7566 (tp) cc_final: 0.7147 (mt) REVERT: C 837 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8130 (m-80) REVERT: C 850 ASP cc_start: 0.9087 (m-30) cc_final: 0.8814 (t0) REVERT: C 966 LEU cc_start: 0.8768 (mt) cc_final: 0.8415 (mm) outliers start: 111 outliers final: 79 residues processed: 433 average time/residue: 0.3328 time to fit residues: 230.1309 Evaluate side-chains 419 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 331 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 360 PHE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 737 GLN Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 896 ASN Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 348 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 896 ASN Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain C residue 1100 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 0.6980 chunk 266 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 296 optimal weight: 0.9980 chunk 245 optimal weight: 6.9990 chunk 137 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 155 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 947 GLN B 993 GLN ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN C 904 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24453 Z= 0.224 Angle : 0.723 15.230 33255 Z= 0.368 Chirality : 0.047 0.238 3762 Planarity : 0.005 0.078 4302 Dihedral : 6.249 35.958 3298 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.13 % Favored : 86.87 % Rotamer: Outliers : 4.24 % Allowed : 15.82 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.15 (0.15), residues: 3024 helix: 1.61 (0.21), residues: 681 sheet: -0.55 (0.23), residues: 489 loop : -3.11 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 101 HIS 0.005 0.001 HIS A1065 PHE 0.034 0.002 PHE C 262 TYR 0.017 0.001 TYR C 886 ARG 0.008 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 358 time to evaluate : 2.656 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: symmetry clash REVERT: A 216 LEU cc_start: 0.6245 (OUTLIER) cc_final: 0.5580 (pp) REVERT: A 441 ARG cc_start: 0.5860 (mtp85) cc_final: 0.5441 (mtp85) REVERT: A 491 TYR cc_start: 0.6118 (OUTLIER) cc_final: 0.5042 (m-10) REVERT: A 503 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7676 (mm) REVERT: A 735 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8852 (tt) REVERT: A 837 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7908 (m-80) REVERT: B 42 TYR cc_start: 0.6571 (OUTLIER) cc_final: 0.5365 (t80) REVERT: B 405 ILE cc_start: 0.8122 (mm) cc_final: 0.7749 (mp) REVERT: B 440 TYR cc_start: 0.5888 (p90) cc_final: 0.5601 (p90) REVERT: B 735 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9145 (tt) REVERT: B 944 LEU cc_start: 0.9355 (tp) cc_final: 0.9135 (tp) REVERT: B 1011 MET cc_start: 0.9238 (ttm) cc_final: 0.8981 (ttm) REVERT: C 285 GLU cc_start: 0.8947 (tt0) cc_final: 0.8580 (tm-30) REVERT: C 615 LEU cc_start: 0.7531 (tp) cc_final: 0.7106 (mt) REVERT: C 837 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8215 (m-80) REVERT: C 850 ASP cc_start: 0.9097 (m-30) cc_final: 0.8816 (t0) REVERT: C 966 LEU cc_start: 0.8847 (mt) cc_final: 0.8486 (mm) outliers start: 112 outliers final: 85 residues processed: 432 average time/residue: 0.3436 time to fit residues: 236.1025 Evaluate side-chains 417 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 324 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 737 GLN Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 896 ASN Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 993 GLN Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 896 ASN Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain C residue 1100 ASP Chi-restraints excluded: chain C residue 1102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 216 optimal weight: 0.5980 chunk 167 optimal weight: 1.9990 chunk 249 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 294 optimal weight: 0.9980 chunk 184 optimal weight: 5.9990 chunk 179 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 GLN B 931 GLN B 993 GLN ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24453 Z= 0.209 Angle : 0.717 17.150 33255 Z= 0.363 Chirality : 0.047 0.272 3762 Planarity : 0.005 0.081 4302 Dihedral : 6.136 36.374 3298 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.76 % Favored : 87.24 % Rotamer: Outliers : 4.46 % Allowed : 15.82 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.08 (0.15), residues: 3024 helix: 1.64 (0.21), residues: 684 sheet: -0.47 (0.23), residues: 480 loop : -3.06 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 101 HIS 0.005 0.001 HIS A1065 PHE 0.032 0.002 PHE C 262 TYR 0.018 0.001 TYR C 886 ARG 0.003 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 356 time to evaluate : 2.659 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 216 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.5867 (pp) REVERT: A 441 ARG cc_start: 0.5852 (mtp85) cc_final: 0.5640 (mtp85) REVERT: A 491 TYR cc_start: 0.6093 (OUTLIER) cc_final: 0.5371 (m-10) REVERT: A 503 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7692 (mm) REVERT: A 554 ASP cc_start: 0.4683 (t0) cc_final: 0.4410 (t0) REVERT: A 556 SER cc_start: 0.8462 (OUTLIER) cc_final: 0.8038 (p) REVERT: A 735 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8866 (tt) REVERT: A 837 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: A 1011 MET cc_start: 0.9524 (tpp) cc_final: 0.9243 (ttp) REVERT: A 1032 MET cc_start: 0.8233 (ttp) cc_final: 0.8013 (mtm) REVERT: B 42 TYR cc_start: 0.6822 (OUTLIER) cc_final: 0.5333 (t80) REVERT: B 396 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.7161 (tt0) REVERT: B 405 ILE cc_start: 0.8299 (mm) cc_final: 0.8012 (mp) REVERT: B 440 TYR cc_start: 0.5877 (p90) cc_final: 0.5580 (p90) REVERT: B 605 ASP cc_start: 0.5076 (OUTLIER) cc_final: 0.4665 (p0) REVERT: B 735 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9092 (tt) REVERT: B 1011 MET cc_start: 0.9224 (ttm) cc_final: 0.8973 (ttm) REVERT: C 42 TYR cc_start: 0.6774 (OUTLIER) cc_final: 0.5417 (t80) REVERT: C 285 GLU cc_start: 0.8914 (tt0) cc_final: 0.8558 (tm-30) REVERT: C 615 LEU cc_start: 0.7663 (tp) cc_final: 0.7250 (mt) REVERT: C 837 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.8266 (m-80) REVERT: C 966 LEU cc_start: 0.8837 (mt) cc_final: 0.8407 (mm) outliers start: 118 outliers final: 87 residues processed: 439 average time/residue: 0.3519 time to fit residues: 249.9105 Evaluate side-chains 427 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 328 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 737 GLN Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 896 ASN Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain C residue 42 TYR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 744 GLN Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 896 ASN Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain C residue 1100 ASP Chi-restraints excluded: chain C residue 1102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 145 optimal weight: 0.0770 chunk 27 optimal weight: 0.9980 chunk 231 optimal weight: 0.5980 chunk 268 optimal weight: 1.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 ASN A1090 ASN ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 931 GLN ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 24453 Z= 0.229 Angle : 0.720 15.018 33255 Z= 0.366 Chirality : 0.047 0.225 3762 Planarity : 0.005 0.110 4302 Dihedral : 6.117 39.871 3298 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.06 % Favored : 86.94 % Rotamer: Outliers : 4.16 % Allowed : 16.99 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.07 (0.15), residues: 3024 helix: 1.60 (0.21), residues: 684 sheet: -0.76 (0.22), residues: 540 loop : -2.99 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 101 HIS 0.005 0.001 HIS A1065 PHE 0.034 0.002 PHE C 231 TYR 0.028 0.001 TYR B 677 ARG 0.006 0.000 ARG B 426 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 342 time to evaluate : 2.631 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 216 LEU cc_start: 0.6361 (OUTLIER) cc_final: 0.5500 (pp) REVERT: A 441 ARG cc_start: 0.5818 (mtp85) cc_final: 0.5617 (mtp85) REVERT: A 491 TYR cc_start: 0.6010 (OUTLIER) cc_final: 0.5309 (m-10) REVERT: A 503 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7706 (mm) REVERT: A 556 SER cc_start: 0.8577 (OUTLIER) cc_final: 0.8188 (p) REVERT: A 735 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8897 (tt) REVERT: A 837 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.8035 (m-80) REVERT: A 1011 MET cc_start: 0.9541 (tpp) cc_final: 0.9196 (ttp) REVERT: A 1078 VAL cc_start: 0.6413 (t) cc_final: 0.6064 (t) REVERT: B 42 TYR cc_start: 0.6969 (OUTLIER) cc_final: 0.5441 (t80) REVERT: B 405 ILE cc_start: 0.8336 (mm) cc_final: 0.8081 (mp) REVERT: B 440 TYR cc_start: 0.5867 (p90) cc_final: 0.5608 (p90) REVERT: B 605 ASP cc_start: 0.5129 (OUTLIER) cc_final: 0.4785 (p0) REVERT: B 723 TYR cc_start: 0.8907 (t80) cc_final: 0.8682 (t80) REVERT: B 735 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9037 (tt) REVERT: B 802 ASP cc_start: 0.8236 (m-30) cc_final: 0.7893 (t0) REVERT: B 899 TYR cc_start: 0.4627 (t80) cc_final: 0.3693 (t80) REVERT: B 1011 MET cc_start: 0.9202 (ttm) cc_final: 0.8979 (ttm) REVERT: C 42 TYR cc_start: 0.6793 (OUTLIER) cc_final: 0.5395 (t80) REVERT: C 107 MET cc_start: 0.6419 (mpp) cc_final: 0.6063 (mpp) REVERT: C 285 GLU cc_start: 0.8900 (tt0) cc_final: 0.8539 (tm-30) REVERT: C 615 LEU cc_start: 0.7674 (tp) cc_final: 0.7213 (mt) REVERT: C 837 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.8370 (m-80) REVERT: C 966 LEU cc_start: 0.8828 (mt) cc_final: 0.8402 (mm) outliers start: 110 outliers final: 88 residues processed: 418 average time/residue: 0.3685 time to fit residues: 250.0244 Evaluate side-chains 420 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 321 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 896 ASN Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain C residue 42 TYR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 744 GLN Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 896 ASN Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain C residue 1100 ASP Chi-restraints excluded: chain C residue 1102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 0.3980 chunk 257 optimal weight: 1.9990 chunk 274 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 259 optimal weight: 0.9980 chunk 273 optimal weight: 7.9990 chunk 180 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 ASN A1101 ASN B 381 ASN ** B 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 931 GLN ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24453 Z= 0.206 Angle : 0.716 14.613 33255 Z= 0.363 Chirality : 0.047 0.252 3762 Planarity : 0.006 0.115 4302 Dihedral : 6.063 39.055 3298 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.40 % Favored : 87.60 % Rotamer: Outliers : 4.50 % Allowed : 17.33 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.07 (0.15), residues: 3024 helix: 1.50 (0.21), residues: 705 sheet: -0.76 (0.22), residues: 540 loop : -2.99 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP B 101 HIS 0.004 0.001 HIS A1065 PHE 0.040 0.002 PHE C 231 TYR 0.029 0.001 TYR B 677 ARG 0.018 0.000 ARG B1089 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 338 time to evaluate : 2.670 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: symmetry clash REVERT: A 42 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.5485 (t80) REVERT: A 216 LEU cc_start: 0.6038 (OUTLIER) cc_final: 0.5419 (pp) REVERT: A 285 GLU cc_start: 0.8784 (tt0) cc_final: 0.8526 (tm-30) REVERT: A 441 ARG cc_start: 0.5807 (mtp85) cc_final: 0.5600 (mtp85) REVERT: A 491 TYR cc_start: 0.6087 (OUTLIER) cc_final: 0.5342 (m-10) REVERT: A 503 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7864 (mm) REVERT: A 556 SER cc_start: 0.8625 (OUTLIER) cc_final: 0.8268 (p) REVERT: A 605 ASP cc_start: 0.4543 (OUTLIER) cc_final: 0.4111 (p0) REVERT: A 735 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8901 (tt) REVERT: A 837 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8096 (m-80) REVERT: A 1011 MET cc_start: 0.9541 (tpp) cc_final: 0.9167 (ttp) REVERT: A 1078 VAL cc_start: 0.6507 (t) cc_final: 0.6182 (t) REVERT: B 42 TYR cc_start: 0.6980 (OUTLIER) cc_final: 0.5367 (t80) REVERT: B 440 TYR cc_start: 0.5863 (p90) cc_final: 0.5636 (p90) REVERT: B 605 ASP cc_start: 0.5139 (OUTLIER) cc_final: 0.4868 (p0) REVERT: B 735 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9027 (tt) REVERT: B 802 ASP cc_start: 0.8231 (m-30) cc_final: 0.7889 (t0) REVERT: B 899 TYR cc_start: 0.4824 (t80) cc_final: 0.3849 (t80) REVERT: B 1011 MET cc_start: 0.9185 (ttm) cc_final: 0.8976 (ttm) REVERT: C 42 TYR cc_start: 0.6957 (OUTLIER) cc_final: 0.5439 (t80) REVERT: C 107 MET cc_start: 0.6534 (mpp) cc_final: 0.6289 (mpp) REVERT: C 285 GLU cc_start: 0.8931 (tt0) cc_final: 0.8572 (tm-30) REVERT: C 548 PHE cc_start: 0.6419 (m-80) cc_final: 0.6123 (m-80) REVERT: C 615 LEU cc_start: 0.7707 (tp) cc_final: 0.7276 (mt) REVERT: C 837 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8210 (m-80) REVERT: C 966 LEU cc_start: 0.8843 (mt) cc_final: 0.8392 (mm) outliers start: 119 outliers final: 91 residues processed: 423 average time/residue: 0.3262 time to fit residues: 223.9101 Evaluate side-chains 428 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 324 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 42 TYR Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 657 CYS Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 737 GLN Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 896 ASN Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain C residue 42 TYR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 744 GLN Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 896 ASN Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 1089 ARG Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain C residue 1100 ASP Chi-restraints excluded: chain C residue 1102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 137 optimal weight: 20.0000 chunk 202 optimal weight: 5.9990 chunk 304 optimal weight: 1.9990 chunk 280 optimal weight: 0.8980 chunk 242 optimal weight: 0.0050 chunk 25 optimal weight: 10.0000 chunk 187 optimal weight: 0.5980 chunk 148 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 611 HIS ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 ASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 HIS ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 987 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24453 Z= 0.270 Angle : 0.748 14.430 33255 Z= 0.380 Chirality : 0.048 0.213 3762 Planarity : 0.006 0.111 4302 Dihedral : 6.160 39.180 3298 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.53 % Favored : 86.47 % Rotamer: Outliers : 4.09 % Allowed : 17.78 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.11 (0.15), residues: 3024 helix: 1.46 (0.21), residues: 705 sheet: -0.80 (0.22), residues: 555 loop : -3.03 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP B 101 HIS 0.005 0.001 HIS A1046 PHE 0.043 0.002 PHE C 231 TYR 0.037 0.002 TYR B 723 ARG 0.018 0.001 ARG B1089 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 333 time to evaluate : 2.600 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: A 216 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.5639 (pp) REVERT: A 441 ARG cc_start: 0.5881 (mtp85) cc_final: 0.5621 (mtp85) REVERT: A 491 TYR cc_start: 0.5993 (OUTLIER) cc_final: 0.5183 (m-10) REVERT: A 556 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8398 (p) REVERT: A 605 ASP cc_start: 0.4447 (OUTLIER) cc_final: 0.3980 (p0) REVERT: A 735 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8968 (tt) REVERT: A 837 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.8054 (m-80) REVERT: A 1011 MET cc_start: 0.9561 (tpp) cc_final: 0.9106 (ttp) REVERT: A 1023 ASP cc_start: 0.8508 (m-30) cc_final: 0.7762 (m-30) REVERT: B 802 ASP cc_start: 0.8341 (m-30) cc_final: 0.7891 (t0) REVERT: B 899 TYR cc_start: 0.4721 (t80) cc_final: 0.3752 (t80) REVERT: B 1011 MET cc_start: 0.9200 (ttm) cc_final: 0.8984 (ttm) REVERT: C 42 TYR cc_start: 0.6942 (OUTLIER) cc_final: 0.5528 (t80) REVERT: C 285 GLU cc_start: 0.8936 (tt0) cc_final: 0.8551 (tm-30) REVERT: C 615 LEU cc_start: 0.7628 (tp) cc_final: 0.7217 (mt) REVERT: C 837 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.8349 (m-80) REVERT: C 966 LEU cc_start: 0.8896 (mt) cc_final: 0.8458 (mm) outliers start: 108 outliers final: 90 residues processed: 410 average time/residue: 0.3192 time to fit residues: 212.2520 Evaluate side-chains 410 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 312 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 896 ASN Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1093 SER Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 737 GLN Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 896 ASN Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 1082 THR Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain B residue 1093 SER Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain C residue 42 TYR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 367 TYR Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 744 GLN Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 896 ASN Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1098 THR Chi-restraints excluded: chain C residue 1100 ASP Chi-restraints excluded: chain C residue 1102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.0040 chunk 74 optimal weight: 0.0370 chunk 223 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 243 optimal weight: 0.0470 chunk 101 optimal weight: 0.0170 chunk 249 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 213 optimal weight: 7.9990 overall best weight: 0.2206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 ASN B 381 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 889 ASN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.133618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.104108 restraints weight = 56765.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.106897 restraints weight = 32467.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.108769 restraints weight = 21983.219| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24453 Z= 0.175 Angle : 0.721 14.022 33255 Z= 0.363 Chirality : 0.046 0.187 3762 Planarity : 0.005 0.104 4302 Dihedral : 5.956 38.321 3298 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.47 % Favored : 88.53 % Rotamer: Outliers : 3.14 % Allowed : 19.22 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.15), residues: 3024 helix: 1.74 (0.21), residues: 690 sheet: -0.77 (0.21), residues: 567 loop : -3.00 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B 101 HIS 0.004 0.001 HIS B1030 PHE 0.050 0.002 PHE C 231 TYR 0.030 0.001 TYR B 723 ARG 0.017 0.001 ARG B1089 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5301.45 seconds wall clock time: 97 minutes 4.89 seconds (5824.89 seconds total)