Starting phenix.real_space_refine on Thu Apr 11 14:16:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2c_22001/04_2024/6x2c_22001_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2c_22001/04_2024/6x2c_22001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2c_22001/04_2024/6x2c_22001.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2c_22001/04_2024/6x2c_22001.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2c_22001/04_2024/6x2c_22001_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2c_22001/04_2024/6x2c_22001_neut.pdb" } resolution = 3.2 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= 0.003 sd= 0.063 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 99 5.16 5 C 14586 2.51 5 N 3777 2.21 5 O 4338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 22800 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7600 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 48, 'TRANS': 922} Chain breaks: 11 Chain: "B" Number of atoms: 7600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7600 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 48, 'TRANS': 922} Chain breaks: 11 Chain: "C" Number of atoms: 7600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7600 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 48, 'TRANS': 922} Chain breaks: 11 Time building chain proxies: 11.68, per 1000 atoms: 0.51 Number of scatterers: 22800 At special positions: 0 Unit cell: (132.25, 138.598, 170.338, 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 99 16.00 O 4338 8.00 N 3777 7.00 C 14586 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.01 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.35 Conformation dependent library (CDL) restraints added in 4.3 seconds 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5478 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 51 sheets defined 27.7% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.945A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.854A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.326A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.693A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.711A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.898A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.391A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.600A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.502A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.556A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.683A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.064A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.394A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.947A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.816A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.314A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.711A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.781A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.911A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.403A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.612A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.540A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.665A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.064A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.434A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.964A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.901A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.310A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.694A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.627A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.911A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.409A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.594A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.530A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.677A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.064A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.449A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.799A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.594A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.594A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.764A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.465A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.511A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.292A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.571A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.604A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 356 Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.685A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.010A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.803A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 722 removed outlier: 5.778A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.301A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.090A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.774A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.472A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.593A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.593A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.759A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.466A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.519A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.286A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 356 Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.689A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.021A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.813A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 removed outlier: 5.790A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 788 through 790 removed outlier: 6.299A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.092A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.776A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.770A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.455A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.516A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.294A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 356 Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.689A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.014A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.811A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 722 removed outlier: 5.792A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.107A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1053 hydrogen bonds defined for protein. 2829 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: 10.50 Time building geometry restraints manager: 9.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6228 1.34 - 1.46: 4199 1.46 - 1.58: 12754 1.58 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 23304 Sorted by residual: bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.541 -0.024 6.70e-03 2.23e+04 1.26e+01 bond pdb=" CA ASN B 422 " pdb=" C ASN B 422 " ideal model delta sigma weight residual 1.517 1.539 -0.022 6.30e-03 2.52e+04 1.23e+01 bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.539 -0.022 6.70e-03 2.23e+04 1.12e+01 bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.517 1.539 -0.022 6.70e-03 2.23e+04 1.08e+01 bond pdb=" CA ALA A 411 " pdb=" C ALA A 411 " ideal model delta sigma weight residual 1.519 1.549 -0.030 9.50e-03 1.11e+04 9.76e+00 ... (remaining 23299 not shown) Histogram of bond angle deviations from ideal: 97.69 - 105.24: 434 105.24 - 112.80: 10694 112.80 - 120.35: 11763 120.35 - 127.91: 8716 127.91 - 135.46: 97 Bond angle restraints: 31704 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 117.92 -7.22 1.22e+00 6.72e-01 3.50e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 117.89 -7.19 1.22e+00 6.72e-01 3.48e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 117.80 -7.10 1.22e+00 6.72e-01 3.38e+01 angle pdb=" CA ASP B 568 " pdb=" CB ASP B 568 " pdb=" CG ASP B 568 " ideal model delta sigma weight residual 112.60 118.29 -5.69 1.00e+00 1.00e+00 3.24e+01 angle pdb=" CA ASP A 228 " pdb=" CB ASP A 228 " pdb=" CG ASP A 228 " ideal model delta sigma weight residual 112.60 118.27 -5.67 1.00e+00 1.00e+00 3.21e+01 ... (remaining 31699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 12811 17.35 - 34.70: 852 34.70 - 52.04: 138 52.04 - 69.39: 78 69.39 - 86.74: 17 Dihedral angle restraints: 13896 sinusoidal: 5412 harmonic: 8484 Sorted by residual: dihedral pdb=" CA TYR A 451 " pdb=" C TYR A 451 " pdb=" N LEU A 452 " pdb=" CA LEU A 452 " ideal model delta harmonic sigma weight residual -180.00 -150.92 -29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA TYR C 451 " pdb=" C TYR C 451 " pdb=" N LEU C 452 " pdb=" CA LEU C 452 " ideal model delta harmonic sigma weight residual -180.00 -151.13 -28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA TYR B 451 " pdb=" C TYR B 451 " pdb=" N LEU B 452 " pdb=" CA LEU B 452 " ideal model delta harmonic sigma weight residual 180.00 -151.27 -28.73 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 13893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2031 0.073 - 0.146: 1256 0.146 - 0.219: 280 0.219 - 0.292: 54 0.292 - 0.365: 15 Chirality restraints: 3636 Sorted by residual: chirality pdb=" CA GLU C 773 " pdb=" N GLU C 773 " pdb=" C GLU C 773 " pdb=" CB GLU C 773 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA ASP B 568 " pdb=" N ASP B 568 " pdb=" C ASP B 568 " pdb=" CB ASP B 568 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA ASP A 568 " pdb=" N ASP A 568 " pdb=" C ASP A 568 " pdb=" CB ASP A 568 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 3633 not shown) Planarity restraints: 4095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 423 " -0.135 2.00e-02 2.50e+03 7.25e-02 1.05e+02 pdb=" CG TYR B 423 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 423 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 TYR B 423 " 0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR B 423 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR B 423 " 0.039 2.00e-02 2.50e+03 pdb=" CZ TYR B 423 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 423 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 423 " -0.132 2.00e-02 2.50e+03 7.09e-02 1.01e+02 pdb=" CG TYR A 423 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 423 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR A 423 " 0.057 2.00e-02 2.50e+03 pdb=" CE1 TYR A 423 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR A 423 " 0.039 2.00e-02 2.50e+03 pdb=" CZ TYR A 423 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 423 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 423 " -0.127 2.00e-02 2.50e+03 6.83e-02 9.32e+01 pdb=" CG TYR C 423 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR C 423 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 TYR C 423 " 0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR C 423 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR C 423 " 0.037 2.00e-02 2.50e+03 pdb=" CZ TYR C 423 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 423 " -0.101 2.00e-02 2.50e+03 ... (remaining 4092 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 11573 3.02 - 3.49: 21525 3.49 - 3.96: 37236 3.96 - 4.43: 41793 4.43 - 4.90: 71634 Nonbonded interactions: 183761 Sorted by model distance: nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU C 918 " model vdw 2.550 2.440 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER B1123 " model vdw 2.557 2.440 nonbonded pdb=" OE2 GLU B 918 " pdb=" OG SER C1123 " model vdw 2.561 2.440 nonbonded pdb=" OD1 ASP C 294 " pdb=" OG SER C 297 " model vdw 2.568 2.440 nonbonded pdb=" OD1 ASP B 294 " pdb=" OG SER B 297 " model vdw 2.571 2.440 ... (remaining 183756 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.060 Check model and map are aligned: 0.320 Set scattering table: 0.230 Process input model: 61.750 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 : 0.013 0.043 23304 Z= 0.818 Angle : 1.808 7.308 31704 Z= 1.226 Chirality : 0.093 0.365 3636 Planarity : 0.016 0.220 4095 Dihedral : 13.390 86.741 8310 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 0.20 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.32 % Favored : 94.37 % Rotamer: Outliers : 3.17 % Allowed : 4.77 % Favored : 92.06 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.14), residues: 2841 helix: -1.64 (0.17), residues: 630 sheet: -0.66 (0.19), residues: 603 loop : -1.09 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.018 TRP C1102 HIS 0.011 0.003 HIS B1058 PHE 0.070 0.011 PHE C 718 TYR 0.135 0.022 TYR B 423 ARG 0.011 0.002 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 252 time to evaluate : 2.608 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 64 TRP cc_start: 0.7785 (t60) cc_final: 0.7571 (t60) REVERT: A 133 PHE cc_start: 0.7918 (m-80) cc_final: 0.7605 (m-80) REVERT: A 392 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.7434 (m-80) REVERT: A 574 ASP cc_start: 0.7396 (t0) cc_final: 0.7158 (t0) REVERT: B 64 TRP cc_start: 0.7874 (t60) cc_final: 0.7573 (t60) REVERT: B 353 TRP cc_start: 0.7867 (p-90) cc_final: 0.7250 (p-90) REVERT: B 399 SER cc_start: 0.8314 (OUTLIER) cc_final: 0.7883 (t) REVERT: B 434 ILE cc_start: 0.8951 (mt) cc_final: 0.8628 (tp) REVERT: B 453 TYR cc_start: 0.7564 (p90) cc_final: 0.7229 (p90) REVERT: B 574 ASP cc_start: 0.7437 (t0) cc_final: 0.7192 (t0) REVERT: B 1004 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8842 (tt) REVERT: C 64 TRP cc_start: 0.7752 (t60) cc_final: 0.7471 (t60) REVERT: C 574 ASP cc_start: 0.7353 (t0) cc_final: 0.7127 (t0) outliers start: 81 outliers final: 38 residues processed: 317 average time/residue: 0.3665 time to fit residues: 179.3648 Evaluate side-chains 178 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 137 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 894 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 0.9980 chunk 220 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 228 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 264 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 955 ASN C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23304 Z= 0.191 Angle : 0.592 7.142 31704 Z= 0.319 Chirality : 0.046 0.173 3636 Planarity : 0.004 0.036 4095 Dihedral : 7.460 58.949 3166 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.82 % Allowed : 7.16 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 2841 helix: 0.66 (0.20), residues: 639 sheet: -0.14 (0.19), residues: 642 loop : -0.71 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 64 HIS 0.002 0.001 HIS B1048 PHE 0.021 0.002 PHE C 140 TYR 0.017 0.001 TYR A1067 ARG 0.007 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 165 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7619 (m-90) cc_final: 0.7331 (m-90) REVERT: A 133 PHE cc_start: 0.7948 (m-80) cc_final: 0.7583 (m-80) REVERT: A 392 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7456 (m-80) REVERT: A 567 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.6894 (mpt90) REVERT: A 574 ASP cc_start: 0.7648 (t0) cc_final: 0.7444 (t0) REVERT: B 133 PHE cc_start: 0.7828 (m-80) cc_final: 0.6224 (t80) REVERT: B 353 TRP cc_start: 0.7915 (p-90) cc_final: 0.7600 (p-90) REVERT: B 377 PHE cc_start: 0.7915 (t80) cc_final: 0.7688 (t80) REVERT: B 574 ASP cc_start: 0.7564 (t0) cc_final: 0.7239 (t0) REVERT: B 1004 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8946 (tt) REVERT: C 104 TRP cc_start: 0.7733 (m-90) cc_final: 0.7212 (m-90) REVERT: C 389 ASP cc_start: 0.7300 (t0) cc_final: 0.7083 (t0) REVERT: C 574 ASP cc_start: 0.7495 (t70) cc_final: 0.7250 (t0) outliers start: 72 outliers final: 48 residues processed: 221 average time/residue: 0.3718 time to fit residues: 129.0030 Evaluate side-chains 175 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 124 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 264 optimal weight: 1.9990 chunk 285 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 262 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 ASN C 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 23304 Z= 0.310 Angle : 0.565 6.858 31704 Z= 0.298 Chirality : 0.045 0.165 3636 Planarity : 0.004 0.039 4095 Dihedral : 6.628 58.980 3159 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.05 % Allowed : 8.22 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2841 helix: 1.44 (0.21), residues: 639 sheet: -0.16 (0.19), residues: 660 loop : -0.63 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 104 HIS 0.004 0.001 HIS B1058 PHE 0.019 0.002 PHE C 133 TYR 0.019 0.001 TYR C1067 ARG 0.005 0.001 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 146 time to evaluate : 2.720 Fit side-chains revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7841 (m-90) cc_final: 0.7499 (m-90) REVERT: A 133 PHE cc_start: 0.8008 (m-80) cc_final: 0.6660 (t80) REVERT: A 392 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7559 (m-80) REVERT: A 453 TYR cc_start: 0.7151 (p90) cc_final: 0.6834 (p90) REVERT: A 567 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7191 (mpt90) REVERT: A 574 ASP cc_start: 0.7652 (t0) cc_final: 0.7404 (t0) REVERT: A 985 ASP cc_start: 0.7950 (p0) cc_final: 0.6748 (p0) REVERT: A 988 GLU cc_start: 0.8010 (mp0) cc_final: 0.7257 (mp0) REVERT: B 100 ILE cc_start: 0.8032 (mm) cc_final: 0.7739 (mm) REVERT: B 133 PHE cc_start: 0.7630 (m-80) cc_final: 0.6362 (t80) REVERT: B 377 PHE cc_start: 0.8191 (t80) cc_final: 0.7842 (t80) REVERT: B 453 TYR cc_start: 0.7261 (p90) cc_final: 0.7017 (p90) REVERT: B 574 ASP cc_start: 0.7415 (t0) cc_final: 0.7117 (t0) REVERT: B 985 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7371 (p0) REVERT: B 988 GLU cc_start: 0.7959 (mp0) cc_final: 0.7523 (mp0) REVERT: B 1004 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8997 (tt) REVERT: B 1029 MET cc_start: 0.8392 (tpp) cc_final: 0.8069 (tpp) REVERT: C 100 ILE cc_start: 0.8073 (mm) cc_final: 0.7727 (mm) REVERT: C 104 TRP cc_start: 0.8036 (m-90) cc_final: 0.7834 (m-90) REVERT: C 133 PHE cc_start: 0.7819 (m-80) cc_final: 0.6310 (t80) REVERT: C 389 ASP cc_start: 0.7392 (t0) cc_final: 0.7130 (t0) REVERT: C 574 ASP cc_start: 0.7520 (t70) cc_final: 0.7242 (t0) outliers start: 78 outliers final: 49 residues processed: 211 average time/residue: 0.3126 time to fit residues: 109.5529 Evaluate side-chains 178 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 125 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 177 optimal weight: 0.6980 chunk 265 optimal weight: 2.9990 chunk 281 optimal weight: 0.6980 chunk 138 optimal weight: 0.2980 chunk 251 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23304 Z= 0.229 Angle : 0.521 7.552 31704 Z= 0.272 Chirality : 0.044 0.160 3636 Planarity : 0.004 0.039 4095 Dihedral : 6.202 55.945 3154 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.01 % Allowed : 8.88 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 2841 helix: 1.69 (0.21), residues: 657 sheet: -0.13 (0.19), residues: 675 loop : -0.62 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 104 HIS 0.002 0.001 HIS B 245 PHE 0.019 0.001 PHE C 140 TYR 0.018 0.001 TYR C1067 ARG 0.004 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 136 time to evaluate : 3.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7818 (m-90) cc_final: 0.7445 (m-90) REVERT: A 133 PHE cc_start: 0.7944 (m-80) cc_final: 0.6678 (t80) REVERT: A 392 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7525 (m-80) REVERT: A 453 TYR cc_start: 0.7173 (p90) cc_final: 0.6876 (p90) REVERT: A 567 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7338 (mpt90) REVERT: A 574 ASP cc_start: 0.7665 (t0) cc_final: 0.7423 (t0) REVERT: A 985 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.6797 (p0) REVERT: A 988 GLU cc_start: 0.7944 (mp0) cc_final: 0.7238 (mp0) REVERT: B 133 PHE cc_start: 0.7710 (m-80) cc_final: 0.6458 (t80) REVERT: B 377 PHE cc_start: 0.8212 (t80) cc_final: 0.7888 (t80) REVERT: B 453 TYR cc_start: 0.7140 (p90) cc_final: 0.6914 (p90) REVERT: B 574 ASP cc_start: 0.7463 (t0) cc_final: 0.7145 (t0) REVERT: B 900 MET cc_start: 0.7550 (mtp) cc_final: 0.7258 (mtm) REVERT: B 985 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7286 (p0) REVERT: B 988 GLU cc_start: 0.7885 (mp0) cc_final: 0.7528 (mp0) REVERT: B 1004 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8922 (tt) REVERT: B 1029 MET cc_start: 0.8331 (tpp) cc_final: 0.8054 (tpp) REVERT: C 100 ILE cc_start: 0.8038 (mm) cc_final: 0.7682 (mm) REVERT: C 133 PHE cc_start: 0.7853 (m-80) cc_final: 0.6427 (t80) REVERT: C 574 ASP cc_start: 0.7496 (t70) cc_final: 0.7214 (t0) REVERT: C 1106 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8198 (pt0) outliers start: 77 outliers final: 55 residues processed: 200 average time/residue: 0.3314 time to fit residues: 110.0872 Evaluate side-chains 184 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 123 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 209 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 240 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 252 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23304 Z= 0.343 Angle : 0.547 8.098 31704 Z= 0.286 Chirality : 0.045 0.196 3636 Planarity : 0.004 0.040 4095 Dihedral : 6.198 53.869 3154 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.60 % Allowed : 9.12 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2841 helix: 1.78 (0.21), residues: 657 sheet: -0.35 (0.19), residues: 672 loop : -0.73 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 104 HIS 0.004 0.001 HIS B1064 PHE 0.017 0.002 PHE A1121 TYR 0.019 0.001 TYR C1067 ARG 0.004 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 123 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7815 (m-90) cc_final: 0.7407 (m-90) REVERT: A 133 PHE cc_start: 0.7898 (m-80) cc_final: 0.6678 (t80) REVERT: A 392 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7613 (m-80) REVERT: A 453 TYR cc_start: 0.7145 (p90) cc_final: 0.6884 (p90) REVERT: A 567 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7486 (mpt90) REVERT: A 574 ASP cc_start: 0.7677 (t0) cc_final: 0.7444 (t0) REVERT: A 985 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.6811 (p0) REVERT: A 988 GLU cc_start: 0.7959 (mp0) cc_final: 0.7251 (mp0) REVERT: B 133 PHE cc_start: 0.7766 (m-80) cc_final: 0.6549 (t80) REVERT: B 377 PHE cc_start: 0.8232 (t80) cc_final: 0.7915 (t80) REVERT: B 453 TYR cc_start: 0.7168 (p90) cc_final: 0.6965 (p90) REVERT: B 574 ASP cc_start: 0.7467 (t0) cc_final: 0.7152 (t0) REVERT: B 988 GLU cc_start: 0.7819 (mp0) cc_final: 0.7476 (mp0) REVERT: B 1004 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8953 (tt) REVERT: B 1029 MET cc_start: 0.8375 (tpp) cc_final: 0.8147 (tpp) REVERT: C 100 ILE cc_start: 0.8094 (mm) cc_final: 0.7737 (mm) REVERT: C 133 PHE cc_start: 0.7718 (m-80) cc_final: 0.6564 (t80) REVERT: C 574 ASP cc_start: 0.7509 (t70) cc_final: 0.7212 (t0) REVERT: C 1106 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8266 (pt0) outliers start: 92 outliers final: 69 residues processed: 202 average time/residue: 0.3282 time to fit residues: 111.7450 Evaluate side-chains 193 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 119 time to evaluate : 3.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 0.9990 chunk 253 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 165 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 281 optimal weight: 0.8980 chunk 233 optimal weight: 7.9990 chunk 130 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23304 Z= 0.146 Angle : 0.473 8.331 31704 Z= 0.248 Chirality : 0.042 0.154 3636 Planarity : 0.004 0.038 4095 Dihedral : 5.761 52.351 3152 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.17 % Allowed : 9.66 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.16), residues: 2841 helix: 2.22 (0.21), residues: 654 sheet: -0.24 (0.19), residues: 681 loop : -0.61 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 104 HIS 0.002 0.000 HIS A1048 PHE 0.017 0.001 PHE C 140 TYR 0.015 0.001 TYR A1067 ARG 0.003 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 132 time to evaluate : 2.618 Fit side-chains revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7760 (t60) cc_final: 0.7400 (t60) REVERT: A 104 TRP cc_start: 0.7811 (m-90) cc_final: 0.7417 (m-90) REVERT: A 133 PHE cc_start: 0.7804 (m-80) cc_final: 0.6690 (t80) REVERT: A 392 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7680 (m-80) REVERT: A 453 TYR cc_start: 0.7161 (p90) cc_final: 0.6892 (p90) REVERT: A 567 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7511 (mpt90) REVERT: A 985 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.6907 (p0) REVERT: A 988 GLU cc_start: 0.7790 (mp0) cc_final: 0.7133 (mp0) REVERT: B 133 PHE cc_start: 0.7412 (m-80) cc_final: 0.6385 (t80) REVERT: B 453 TYR cc_start: 0.7171 (p90) cc_final: 0.6941 (p90) REVERT: B 574 ASP cc_start: 0.7439 (t0) cc_final: 0.7145 (t0) REVERT: B 902 MET cc_start: 0.8107 (mmm) cc_final: 0.7842 (tpt) REVERT: B 985 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7455 (p0) REVERT: B 1004 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8828 (tt) REVERT: C 100 ILE cc_start: 0.8014 (mm) cc_final: 0.7640 (mm) REVERT: C 133 PHE cc_start: 0.7653 (m-80) cc_final: 0.6579 (t80) REVERT: C 574 ASP cc_start: 0.7465 (t70) cc_final: 0.7185 (t0) outliers start: 81 outliers final: 51 residues processed: 205 average time/residue: 0.3069 time to fit residues: 105.3772 Evaluate side-chains 163 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 107 time to evaluate : 2.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 160 optimal weight: 0.0070 chunk 205 optimal weight: 10.0000 chunk 159 optimal weight: 0.6980 chunk 237 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 chunk 280 optimal weight: 0.6980 chunk 175 optimal weight: 0.1980 chunk 170 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 764 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23304 Z= 0.138 Angle : 0.467 8.167 31704 Z= 0.245 Chirality : 0.042 0.150 3636 Planarity : 0.004 0.039 4095 Dihedral : 5.535 52.324 3147 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.90 % Allowed : 10.02 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.16), residues: 2841 helix: 2.23 (0.21), residues: 660 sheet: -0.24 (0.19), residues: 681 loop : -0.53 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 104 HIS 0.002 0.000 HIS A1048 PHE 0.015 0.001 PHE B 400 TYR 0.015 0.001 TYR C1067 ARG 0.003 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 124 time to evaluate : 2.822 Fit side-chains revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7814 (t60) cc_final: 0.7451 (t60) REVERT: A 104 TRP cc_start: 0.7778 (m-90) cc_final: 0.7429 (m-90) REVERT: A 133 PHE cc_start: 0.7674 (m-80) cc_final: 0.6682 (t80) REVERT: A 392 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7791 (m-80) REVERT: A 453 TYR cc_start: 0.7128 (p90) cc_final: 0.6864 (p90) REVERT: A 567 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7459 (mpt90) REVERT: A 581 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7859 (p) REVERT: A 985 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.6959 (p0) REVERT: A 988 GLU cc_start: 0.7774 (mp0) cc_final: 0.7248 (mp0) REVERT: B 133 PHE cc_start: 0.7299 (m-80) cc_final: 0.6268 (t80) REVERT: B 226 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7742 (tp) REVERT: B 453 TYR cc_start: 0.7237 (p90) cc_final: 0.6999 (p90) REVERT: B 574 ASP cc_start: 0.7442 (t0) cc_final: 0.7134 (t0) REVERT: B 902 MET cc_start: 0.8050 (mmm) cc_final: 0.7647 (tpt) REVERT: B 1004 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8800 (tt) REVERT: C 100 ILE cc_start: 0.7997 (mm) cc_final: 0.7627 (mm) REVERT: C 133 PHE cc_start: 0.7576 (m-80) cc_final: 0.6609 (t80) REVERT: C 574 ASP cc_start: 0.7461 (t70) cc_final: 0.7147 (t0) REVERT: C 990 GLU cc_start: 0.7337 (mp0) cc_final: 0.7135 (mp0) outliers start: 74 outliers final: 53 residues processed: 188 average time/residue: 0.3425 time to fit residues: 107.4715 Evaluate side-chains 170 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 111 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 5.9990 chunk 112 optimal weight: 0.0370 chunk 167 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 220 optimal weight: 7.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23304 Z= 0.228 Angle : 0.487 7.872 31704 Z= 0.255 Chirality : 0.043 0.152 3636 Planarity : 0.004 0.042 4095 Dihedral : 5.500 52.600 3145 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.05 % Allowed : 9.90 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.16), residues: 2841 helix: 2.16 (0.21), residues: 660 sheet: -0.24 (0.19), residues: 675 loop : -0.55 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 104 HIS 0.003 0.001 HIS A1048 PHE 0.022 0.001 PHE C 65 TYR 0.017 0.001 TYR C1067 ARG 0.003 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 117 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7773 (t60) cc_final: 0.7381 (t60) REVERT: A 104 TRP cc_start: 0.7816 (m-90) cc_final: 0.7406 (m-90) REVERT: A 133 PHE cc_start: 0.7777 (m-80) cc_final: 0.6815 (t80) REVERT: A 392 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: A 453 TYR cc_start: 0.7150 (p90) cc_final: 0.6860 (p90) REVERT: A 567 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7556 (mpt90) REVERT: A 581 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7844 (p) REVERT: A 985 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.6939 (p0) REVERT: A 988 GLU cc_start: 0.7755 (mp0) cc_final: 0.7187 (mp0) REVERT: B 133 PHE cc_start: 0.7409 (m-80) cc_final: 0.6523 (t80) REVERT: B 453 TYR cc_start: 0.7226 (p90) cc_final: 0.7013 (p90) REVERT: B 574 ASP cc_start: 0.7458 (t0) cc_final: 0.7144 (t0) REVERT: B 990 GLU cc_start: 0.7284 (mp0) cc_final: 0.7043 (mp0) REVERT: B 1004 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8826 (tt) REVERT: C 100 ILE cc_start: 0.8013 (mm) cc_final: 0.7636 (mm) REVERT: C 133 PHE cc_start: 0.7360 (m-80) cc_final: 0.6604 (t80) REVERT: C 574 ASP cc_start: 0.7468 (t70) cc_final: 0.7152 (t0) outliers start: 78 outliers final: 62 residues processed: 184 average time/residue: 0.3152 time to fit residues: 97.6940 Evaluate side-chains 178 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 111 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 3.9990 chunk 268 optimal weight: 0.9980 chunk 245 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 205 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 247 optimal weight: 6.9990 chunk 260 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23304 Z= 0.180 Angle : 0.474 8.209 31704 Z= 0.248 Chirality : 0.043 0.155 3636 Planarity : 0.004 0.041 4095 Dihedral : 5.394 52.698 3145 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.82 % Allowed : 10.05 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2841 helix: 2.22 (0.21), residues: 660 sheet: -0.24 (0.19), residues: 675 loop : -0.55 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 104 HIS 0.003 0.000 HIS A1048 PHE 0.020 0.001 PHE C 65 TYR 0.016 0.001 TYR C1067 ARG 0.003 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 117 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7789 (t60) cc_final: 0.7377 (t60) REVERT: A 104 TRP cc_start: 0.7789 (m-90) cc_final: 0.7376 (m-90) REVERT: A 133 PHE cc_start: 0.7744 (m-80) cc_final: 0.6796 (t80) REVERT: A 392 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: A 453 TYR cc_start: 0.7092 (p90) cc_final: 0.6807 (p90) REVERT: A 567 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7559 (mpt90) REVERT: A 581 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7815 (p) REVERT: A 985 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.6655 (p0) REVERT: A 988 GLU cc_start: 0.7647 (mp0) cc_final: 0.7074 (mp0) REVERT: B 133 PHE cc_start: 0.7397 (m-80) cc_final: 0.6543 (t80) REVERT: B 377 PHE cc_start: 0.8188 (t80) cc_final: 0.7678 (t80) REVERT: B 453 TYR cc_start: 0.7158 (p90) cc_final: 0.6914 (p90) REVERT: B 574 ASP cc_start: 0.7450 (t0) cc_final: 0.7144 (t0) REVERT: B 902 MET cc_start: 0.8095 (mmm) cc_final: 0.7853 (tpt) REVERT: B 1004 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8807 (tt) REVERT: C 100 ILE cc_start: 0.7996 (mm) cc_final: 0.7617 (mm) REVERT: C 133 PHE cc_start: 0.7373 (m-80) cc_final: 0.6669 (t80) REVERT: C 346 ARG cc_start: 0.7321 (tpt170) cc_final: 0.7084 (tpt170) REVERT: C 574 ASP cc_start: 0.7467 (t70) cc_final: 0.7146 (t0) REVERT: C 985 ASP cc_start: 0.7799 (p0) cc_final: 0.6724 (p0) outliers start: 72 outliers final: 58 residues processed: 179 average time/residue: 0.3111 time to fit residues: 92.0299 Evaluate side-chains 170 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 107 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 0.7980 chunk 276 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 289 optimal weight: 0.9990 chunk 266 optimal weight: 0.5980 chunk 230 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23304 Z= 0.265 Angle : 0.509 8.070 31704 Z= 0.267 Chirality : 0.044 0.204 3636 Planarity : 0.004 0.042 4095 Dihedral : 5.498 52.734 3145 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.62 % Allowed : 10.45 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2841 helix: 2.13 (0.21), residues: 657 sheet: -0.28 (0.19), residues: 675 loop : -0.61 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 104 HIS 0.003 0.001 HIS B1064 PHE 0.019 0.001 PHE C 65 TYR 0.017 0.001 TYR C1067 ARG 0.014 0.000 ARG C 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 116 time to evaluate : 2.833 Fit side-chains revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7783 (t60) cc_final: 0.7391 (t60) REVERT: A 104 TRP cc_start: 0.7829 (m-90) cc_final: 0.7427 (m-90) REVERT: A 133 PHE cc_start: 0.7744 (m-80) cc_final: 0.6842 (t80) REVERT: A 392 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7772 (m-80) REVERT: A 453 TYR cc_start: 0.7104 (p90) cc_final: 0.6800 (p90) REVERT: A 567 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7561 (mpt90) REVERT: A 581 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7852 (p) REVERT: A 985 ASP cc_start: 0.7806 (p0) cc_final: 0.6710 (p0) REVERT: A 988 GLU cc_start: 0.7701 (mp0) cc_final: 0.7167 (mp0) REVERT: B 133 PHE cc_start: 0.7420 (m-80) cc_final: 0.6600 (t80) REVERT: B 453 TYR cc_start: 0.7148 (p90) cc_final: 0.6911 (p90) REVERT: B 574 ASP cc_start: 0.7463 (t0) cc_final: 0.7145 (t0) REVERT: B 1004 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8872 (tt) REVERT: C 100 ILE cc_start: 0.8017 (mm) cc_final: 0.7640 (mm) REVERT: C 133 PHE cc_start: 0.7445 (m-80) cc_final: 0.6729 (t80) REVERT: C 346 ARG cc_start: 0.7363 (tpt170) cc_final: 0.7125 (tpt170) REVERT: C 574 ASP cc_start: 0.7480 (t70) cc_final: 0.7159 (t0) REVERT: C 985 ASP cc_start: 0.7848 (p0) cc_final: 0.7423 (p0) outliers start: 67 outliers final: 62 residues processed: 174 average time/residue: 0.3219 time to fit residues: 92.6335 Evaluate side-chains 176 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 110 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 212 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 64 optimal weight: 0.4980 chunk 231 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.126700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.094739 restraints weight = 39499.140| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.65 r_work: 0.3246 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23304 Z= 0.202 Angle : 0.485 8.536 31704 Z= 0.254 Chirality : 0.043 0.184 3636 Planarity : 0.004 0.042 4095 Dihedral : 5.412 52.624 3145 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.70 % Allowed : 10.29 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 2841 helix: 2.15 (0.21), residues: 663 sheet: -0.21 (0.20), residues: 645 loop : -0.55 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 104 HIS 0.003 0.000 HIS A1048 PHE 0.019 0.001 PHE C 65 TYR 0.016 0.001 TYR C1067 ARG 0.006 0.000 ARG C 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4109.75 seconds wall clock time: 76 minutes 27.88 seconds (4587.88 seconds total)