Starting phenix.real_space_refine on Tue Mar 19 02:17:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb0_31511/03_2024/7fb0_31511.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb0_31511/03_2024/7fb0_31511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb0_31511/03_2024/7fb0_31511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb0_31511/03_2024/7fb0_31511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb0_31511/03_2024/7fb0_31511.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fb0_31511/03_2024/7fb0_31511.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.079 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 14624 2.51 5 N 3796 2.21 5 O 4357 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A ASP 994": "OD1" <-> "OD2" Residue "A ASP 1146": "OD1" <-> "OD2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 405": "OD1" <-> "OD2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "C GLU 1092": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22876 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7628 Classifications: {'peptide': 976} Link IDs: {'PTRANS': 49, 'TRANS': 926} Chain breaks: 10 Chain: "B" Number of atoms: 7624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 975, 7624 Classifications: {'peptide': 975} Link IDs: {'PTRANS': 49, 'TRANS': 925} Chain breaks: 11 Chain: "C" Number of atoms: 7624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 975, 7624 Classifications: {'peptide': 975} Link IDs: {'PTRANS': 49, 'TRANS': 925} Chain breaks: 11 Time building chain proxies: 11.89, per 1000 atoms: 0.52 Number of scatterers: 22876 At special positions: 0 Unit cell: (138.72, 130.56, 171.36, 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 4357 8.00 N 3796 7.00 C 14624 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 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=2.02 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=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 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: 9.06 Conformation dependent library (CDL) restraints added in 4.0 seconds 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5502 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 62 sheets defined 25.6% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 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 364 through 370 removed outlier: 4.010A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.912A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.313A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.604A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.981A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.662A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.119A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 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 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.668A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.970A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.715A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.661A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 756 through 759 Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.678A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.884A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 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 966 removed outlier: 3.925A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.784A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.889A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.607A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.565A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.006A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.887A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 421 removed outlier: 4.018A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.501A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.527A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.124A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.311A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 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 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.027A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.947A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.674A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.798A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.957A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.957A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.889A pdb=" N LEU A 277 " --> pdb=" O HIS A 49 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.627A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.939A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.105A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA9, first strand: chain 'A' and resid 118 through 121 removed outlier: 3.763A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.789A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.725A pdb=" N ILE A 326 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.610A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.813A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.697A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 576 through 577 Processing sheet with id=AB7, first strand: chain 'A' and resid 664 through 665 removed outlier: 3.840A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 712 through 713 Processing sheet with id=AB9, first strand: chain 'A' and resid 717 through 720 removed outlier: 6.365A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 725 through 728 removed outlier: 3.534A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC3, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.588A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC5, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AC6, first strand: chain 'A' and resid 1095 through 1097 Processing sheet with id=AC7, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.568A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.779A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.556A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE B 92 " --> pdb=" O PHE B 192 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.779A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.556A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.530A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 277 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AD3, first strand: chain 'B' and resid 65 through 66 removed outlier: 4.040A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AD5, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.346A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.360A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.927A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.927A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.563A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.572A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.149A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AE4, first strand: chain 'B' and resid 717 through 720 removed outlier: 6.397A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 723 through 728 removed outlier: 3.603A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id=AE7, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id=AE8, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.719A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AF1, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AF2, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.643A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.643A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 275 through 279 removed outlier: 3.697A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.600A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.693A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 354 through 356 removed outlier: 3.709A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.654A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 452 through 453 removed outlier: 3.696A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 575 through 577 removed outlier: 3.631A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.185A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 712 through 713 Processing sheet with id=AG4, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AG5, first strand: chain 'C' and resid 725 through 728 Processing sheet with id=AG6, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AG7, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AG8, first strand: chain 'C' and resid 1094 through 1097 803 hydrogen bonds defined for protein. 2187 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.29 Time building geometry restraints manager: 9.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7393 1.34 - 1.47: 5837 1.47 - 1.59: 10031 1.59 - 1.72: 0 1.72 - 1.84: 123 Bond restraints: 23384 Sorted by residual: bond pdb=" C PHE B 565 " pdb=" N GLY B 566 " ideal model delta sigma weight residual 1.336 1.298 0.038 1.01e-02 9.80e+03 1.39e+01 bond pdb=" C LYS A 790 " pdb=" N THR A 791 " ideal model delta sigma weight residual 1.331 1.235 0.095 3.12e-02 1.03e+03 9.34e+00 bond pdb=" C PHE C 565 " pdb=" N GLY C 566 " ideal model delta sigma weight residual 1.333 1.303 0.030 1.11e-02 8.12e+03 7.33e+00 bond pdb=" C ALA C1078 " pdb=" N PRO C1079 " ideal model delta sigma weight residual 1.334 1.312 0.022 8.40e-03 1.42e+04 6.72e+00 bond pdb=" CA ARG A 190 " pdb=" CB ARG A 190 " ideal model delta sigma weight residual 1.527 1.471 0.056 2.48e-02 1.63e+03 5.18e+00 ... (remaining 23379 not shown) Histogram of bond angle deviations from ideal: 98.34 - 105.52: 494 105.52 - 112.69: 12466 112.69 - 119.87: 7664 119.87 - 127.04: 10982 127.04 - 134.22: 208 Bond angle restraints: 31814 Sorted by residual: angle pdb=" N SER A 205 " pdb=" CA SER A 205 " pdb=" C SER A 205 " ideal model delta sigma weight residual 107.88 113.78 -5.90 1.41e+00 5.03e-01 1.75e+01 angle pdb=" C PHE C 92 " pdb=" N ALA C 93 " pdb=" CA ALA C 93 " ideal model delta sigma weight residual 122.32 115.11 7.21 1.76e+00 3.23e-01 1.68e+01 angle pdb=" N CYS B 432 " pdb=" CA CYS B 432 " pdb=" C CYS B 432 " ideal model delta sigma weight residual 108.38 113.52 -5.14 1.35e+00 5.49e-01 1.45e+01 angle pdb=" CA GLY C 416 " pdb=" C GLY C 416 " pdb=" N LYS C 417 " ideal model delta sigma weight residual 114.23 117.34 -3.11 8.80e-01 1.29e+00 1.25e+01 angle pdb=" N CYS C 432 " pdb=" CA CYS C 432 " pdb=" C CYS C 432 " ideal model delta sigma weight residual 108.14 113.44 -5.30 1.52e+00 4.33e-01 1.21e+01 ... (remaining 31809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 12372 17.48 - 34.96: 1337 34.96 - 52.44: 190 52.44 - 69.92: 37 69.92 - 87.40: 13 Dihedral angle restraints: 13949 sinusoidal: 5430 harmonic: 8519 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -8.14 -77.86 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 155.26 -62.26 1 1.00e+01 1.00e-02 5.13e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual -86.00 -29.30 -56.70 1 1.00e+01 1.00e-02 4.33e+01 ... (remaining 13946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2225 0.042 - 0.085: 1030 0.085 - 0.127: 338 0.127 - 0.170: 46 0.170 - 0.212: 6 Chirality restraints: 3645 Sorted by residual: chirality pdb=" CB ILE B 312 " pdb=" CA ILE B 312 " pdb=" CG1 ILE B 312 " pdb=" CG2 ILE B 312 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB ILE C 312 " pdb=" CA ILE C 312 " pdb=" CG1 ILE C 312 " pdb=" CG2 ILE C 312 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CA CYS A 291 " pdb=" N CYS A 291 " pdb=" C CYS A 291 " pdb=" CB CYS A 291 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 3642 not shown) Planarity restraints: 4115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 192 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C PHE A 192 " -0.042 2.00e-02 2.50e+03 pdb=" O PHE A 192 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL A 193 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 84 " 0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO A 85 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 329 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A 330 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " -0.031 5.00e-02 4.00e+02 ... (remaining 4112 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 312 2.52 - 3.12: 19238 3.12 - 3.71: 34058 3.71 - 4.31: 47643 4.31 - 4.90: 79360 Nonbonded interactions: 180611 Sorted by model distance: nonbonded pdb=" O ASP B 290 " pdb=" OG SER B 297 " model vdw 1.931 2.440 nonbonded pdb=" O ASP C 290 " pdb=" OG SER C 297 " model vdw 2.004 2.440 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.010 2.440 nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.095 2.440 nonbonded pdb=" OH TYR A 200 " pdb=" ND2 ASN C 394 " model vdw 2.113 2.520 ... (remaining 180606 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' and (resid 27 through 501 or resid 503 through 1147)) 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: 1.110 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: 4.730 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 60.690 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.010 0.103 23384 Z= 0.680 Angle : 0.876 11.883 31814 Z= 0.494 Chirality : 0.052 0.212 3645 Planarity : 0.005 0.056 4115 Dihedral : 14.092 87.398 8339 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 0.47 % Allowed : 10.29 % Favored : 89.24 % 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: -4.69 (0.13), residues: 2856 helix: -1.49 (0.17), residues: 662 sheet: -3.84 (0.16), residues: 657 loop : -3.60 (0.13), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 64 HIS 0.006 0.001 HIS A1064 PHE 0.031 0.003 PHE B 906 TYR 0.029 0.002 TYR C1067 ARG 0.008 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 151 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8221 (tp30) cc_final: 0.8019 (tm-30) REVERT: A 380 TYR cc_start: 0.8335 (m-80) cc_final: 0.7932 (m-80) REVERT: A 759 PHE cc_start: 0.8406 (m-80) cc_final: 0.8045 (m-80) REVERT: A 773 GLU cc_start: 0.8554 (pt0) cc_final: 0.8306 (pt0) REVERT: A 1002 GLN cc_start: 0.9012 (tt0) cc_final: 0.8458 (tp40) REVERT: A 1029 MET cc_start: 0.8426 (tpp) cc_final: 0.7698 (ttm) REVERT: B 1089 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.8018 (m-80) REVERT: C 55 PHE cc_start: 0.8472 (m-80) cc_final: 0.7858 (m-80) REVERT: C 277 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7160 (pp) REVERT: C 900 MET cc_start: 0.8149 (mtp) cc_final: 0.7513 (mtm) REVERT: C 904 TYR cc_start: 0.7982 (m-10) cc_final: 0.7550 (m-10) REVERT: C 964 LYS cc_start: 0.9433 (tmtt) cc_final: 0.9119 (tptp) REVERT: C 1002 GLN cc_start: 0.8970 (tt0) cc_final: 0.8531 (tm-30) outliers start: 12 outliers final: 8 residues processed: 163 average time/residue: 0.3342 time to fit residues: 86.7854 Evaluate side-chains 114 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 1.9990 chunk 220 optimal weight: 30.0000 chunk 122 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 chunk 169 optimal weight: 0.9990 chunk 264 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 388 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 675 GLN A 690 GLN A 926 GLN A 928 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1005 GLN A1011 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN B 354 ASN B 388 ASN B 448 ASN B 501 ASN B 655 HIS B 675 GLN B 690 GLN B 919 ASN B 953 ASN B 954 GLN B 957 GLN B 965 GLN B1002 GLN B1088 HIS C 448 ASN C 655 HIS C 690 GLN C 764 ASN C 965 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23384 Z= 0.212 Angle : 0.576 8.096 31814 Z= 0.305 Chirality : 0.045 0.165 3645 Planarity : 0.005 0.051 4115 Dihedral : 5.418 44.347 3128 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.68 % Allowed : 13.57 % Favored : 84.76 % 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: -3.11 (0.14), residues: 2856 helix: 0.64 (0.20), residues: 653 sheet: -3.13 (0.17), residues: 622 loop : -2.90 (0.13), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 436 HIS 0.004 0.001 HIS B1048 PHE 0.015 0.001 PHE B 906 TYR 0.019 0.001 TYR C1067 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 149 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8233 (tp30) cc_final: 0.7962 (tm-30) REVERT: A 329 PHE cc_start: 0.7466 (m-80) cc_final: 0.7121 (m-80) REVERT: A 380 TYR cc_start: 0.8420 (m-80) cc_final: 0.7887 (m-80) REVERT: A 436 TRP cc_start: 0.7838 (p90) cc_final: 0.7529 (p90) REVERT: A 759 PHE cc_start: 0.8091 (m-80) cc_final: 0.7849 (m-80) REVERT: A 773 GLU cc_start: 0.8438 (pt0) cc_final: 0.8198 (pt0) REVERT: A 954 GLN cc_start: 0.8774 (mt0) cc_final: 0.8424 (mt0) REVERT: A 988 GLU cc_start: 0.7532 (mp0) cc_final: 0.7141 (mp0) REVERT: A 1002 GLN cc_start: 0.8848 (tt0) cc_final: 0.8550 (tp40) REVERT: A 1029 MET cc_start: 0.8221 (tpp) cc_final: 0.7928 (ttm) REVERT: B 95 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8463 (t) REVERT: B 436 TRP cc_start: 0.8050 (p90) cc_final: 0.6183 (p90) REVERT: B 437 ASN cc_start: 0.8733 (p0) cc_final: 0.8521 (t0) REVERT: B 740 MET cc_start: 0.8140 (tpt) cc_final: 0.7863 (tpt) REVERT: B 759 PHE cc_start: 0.8579 (m-80) cc_final: 0.8296 (m-80) REVERT: B 873 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.8539 (m-10) REVERT: B 902 MET cc_start: 0.8317 (tpp) cc_final: 0.7977 (tpt) REVERT: B 1002 GLN cc_start: 0.8851 (tp40) cc_final: 0.8539 (tp40) REVERT: C 55 PHE cc_start: 0.8460 (m-80) cc_final: 0.7744 (m-80) REVERT: C 277 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6535 (pp) REVERT: C 332 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7904 (tp) REVERT: C 436 TRP cc_start: 0.7730 (p90) cc_final: 0.6710 (p90) REVERT: C 759 PHE cc_start: 0.8653 (m-80) cc_final: 0.8234 (m-80) REVERT: C 904 TYR cc_start: 0.7829 (m-10) cc_final: 0.7515 (m-10) REVERT: C 964 LYS cc_start: 0.9384 (tmtt) cc_final: 0.9059 (tptp) outliers start: 43 outliers final: 20 residues processed: 186 average time/residue: 0.2816 time to fit residues: 88.4023 Evaluate side-chains 140 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 873 TYR 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: 2.9990 chunk 82 optimal weight: 3.9990 chunk 219 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 264 optimal weight: 2.9990 chunk 285 optimal weight: 0.9990 chunk 235 optimal weight: 7.9990 chunk 262 optimal weight: 0.0980 chunk 90 optimal weight: 2.9990 chunk 212 optimal weight: 0.0970 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 331 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23384 Z= 0.182 Angle : 0.533 7.244 31814 Z= 0.278 Chirality : 0.043 0.158 3645 Planarity : 0.004 0.049 4115 Dihedral : 4.779 38.031 3117 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.42 % Allowed : 15.28 % Favored : 82.30 % 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: -2.32 (0.15), residues: 2856 helix: 1.40 (0.21), residues: 664 sheet: -2.52 (0.19), residues: 604 loop : -2.54 (0.13), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.005 0.001 HIS B 655 PHE 0.027 0.001 PHE C 201 TYR 0.017 0.001 TYR C1067 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 137 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ARG cc_start: 0.9218 (mmt90) cc_final: 0.8829 (mmm-85) REVERT: A 309 GLU cc_start: 0.8260 (tp30) cc_final: 0.7933 (tm-30) REVERT: A 380 TYR cc_start: 0.8318 (m-80) cc_final: 0.7795 (m-80) REVERT: A 436 TRP cc_start: 0.7754 (p90) cc_final: 0.7196 (p90) REVERT: A 759 PHE cc_start: 0.8155 (m-80) cc_final: 0.7918 (m-80) REVERT: A 773 GLU cc_start: 0.8419 (pt0) cc_final: 0.8120 (pt0) REVERT: A 913 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7613 (pm20) REVERT: A 954 GLN cc_start: 0.8874 (mt0) cc_final: 0.8652 (mt0) REVERT: A 988 GLU cc_start: 0.7712 (mp0) cc_final: 0.7349 (mp0) REVERT: A 1002 GLN cc_start: 0.8806 (tt0) cc_final: 0.8547 (tp40) REVERT: A 1029 MET cc_start: 0.8198 (tpp) cc_final: 0.7966 (ttm) REVERT: B 95 THR cc_start: 0.8487 (OUTLIER) cc_final: 0.8144 (t) REVERT: B 297 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.8258 (t) REVERT: B 356 LYS cc_start: 0.8262 (pttt) cc_final: 0.7857 (ptmt) REVERT: B 436 TRP cc_start: 0.7920 (p90) cc_final: 0.6400 (p90) REVERT: B 873 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.8474 (m-10) REVERT: B 988 GLU cc_start: 0.8052 (mp0) cc_final: 0.7699 (mp0) REVERT: B 1031 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7719 (mt-10) REVERT: B 1130 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8136 (tp) REVERT: C 55 PHE cc_start: 0.8382 (m-80) cc_final: 0.7780 (m-80) REVERT: C 277 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7034 (pp) REVERT: C 332 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7837 (tp) REVERT: C 436 TRP cc_start: 0.7904 (p90) cc_final: 0.6262 (p90) REVERT: C 759 PHE cc_start: 0.8517 (m-80) cc_final: 0.8109 (m-80) REVERT: C 900 MET cc_start: 0.7736 (mtp) cc_final: 0.7454 (mtm) REVERT: C 964 LYS cc_start: 0.9378 (tmtt) cc_final: 0.9036 (tptp) REVERT: C 988 GLU cc_start: 0.7768 (mp0) cc_final: 0.7409 (mp0) outliers start: 62 outliers final: 32 residues processed: 188 average time/residue: 0.2835 time to fit residues: 91.8645 Evaluate side-chains 147 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 108 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 873 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 4.9990 chunk 199 optimal weight: 8.9990 chunk 137 optimal weight: 40.0000 chunk 29 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 177 optimal weight: 0.8980 chunk 265 optimal weight: 3.9990 chunk 281 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 251 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23384 Z= 0.182 Angle : 0.520 8.431 31814 Z= 0.269 Chirality : 0.043 0.159 3645 Planarity : 0.004 0.047 4115 Dihedral : 4.564 39.293 3116 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.73 % Allowed : 16.06 % Favored : 81.21 % 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: -1.88 (0.15), residues: 2856 helix: 1.75 (0.21), residues: 642 sheet: -2.22 (0.19), residues: 626 loop : -2.20 (0.14), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.005 0.001 HIS B1048 PHE 0.020 0.001 PHE C 201 TYR 0.017 0.001 TYR C1067 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 121 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8278 (tp30) cc_final: 0.7945 (tm-30) REVERT: A 329 PHE cc_start: 0.7524 (m-80) cc_final: 0.7314 (m-80) REVERT: A 436 TRP cc_start: 0.7852 (p90) cc_final: 0.7499 (p90) REVERT: A 759 PHE cc_start: 0.8125 (m-80) cc_final: 0.7891 (m-80) REVERT: A 913 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7542 (pm20) REVERT: A 954 GLN cc_start: 0.8882 (mt0) cc_final: 0.8664 (mt0) REVERT: A 988 GLU cc_start: 0.7878 (mp0) cc_final: 0.7515 (mp0) REVERT: A 994 ASP cc_start: 0.9001 (t0) cc_final: 0.8756 (t0) REVERT: A 1002 GLN cc_start: 0.8778 (tt0) cc_final: 0.8510 (tp40) REVERT: A 1029 MET cc_start: 0.8194 (tpp) cc_final: 0.7956 (ttm) REVERT: B 95 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.7859 (t) REVERT: B 297 SER cc_start: 0.8498 (OUTLIER) cc_final: 0.8283 (t) REVERT: B 356 LYS cc_start: 0.8398 (pttt) cc_final: 0.7906 (ptmt) REVERT: B 436 TRP cc_start: 0.7788 (p90) cc_final: 0.6239 (p90) REVERT: B 873 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.8466 (m-10) REVERT: B 988 GLU cc_start: 0.8006 (mp0) cc_final: 0.7659 (mp0) REVERT: B 1031 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7446 (mt-10) REVERT: B 1130 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8219 (tp) REVERT: C 55 PHE cc_start: 0.8374 (m-80) cc_final: 0.7795 (m-80) REVERT: C 277 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7288 (pp) REVERT: C 421 TYR cc_start: 0.5514 (OUTLIER) cc_final: 0.4964 (t80) REVERT: C 436 TRP cc_start: 0.7958 (p90) cc_final: 0.6370 (p90) REVERT: C 577 ARG cc_start: 0.7905 (ttp-170) cc_final: 0.7424 (ttm-80) REVERT: C 759 PHE cc_start: 0.8446 (m-80) cc_final: 0.8042 (m-10) REVERT: C 964 LYS cc_start: 0.9362 (tmtt) cc_final: 0.9015 (tptp) REVERT: C 988 GLU cc_start: 0.7820 (mp0) cc_final: 0.7470 (mp0) outliers start: 70 outliers final: 41 residues processed: 183 average time/residue: 0.2771 time to fit residues: 86.9463 Evaluate side-chains 163 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 115 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 209 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 240 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 252 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A1002 GLN A1011 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 317 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 23384 Z= 0.297 Angle : 0.562 8.044 31814 Z= 0.293 Chirality : 0.044 0.151 3645 Planarity : 0.004 0.047 4115 Dihedral : 4.768 41.685 3116 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.39 % Allowed : 16.80 % Favored : 79.81 % 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: -1.87 (0.15), residues: 2856 helix: 1.60 (0.21), residues: 643 sheet: -2.26 (0.19), residues: 658 loop : -2.07 (0.14), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 64 HIS 0.004 0.001 HIS B 655 PHE 0.021 0.001 PHE B1121 TYR 0.023 0.001 TYR B 91 ARG 0.003 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 116 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8716 (mt) REVERT: A 309 GLU cc_start: 0.8266 (tp30) cc_final: 0.7967 (tm-30) REVERT: A 436 TRP cc_start: 0.7875 (p90) cc_final: 0.7372 (p90) REVERT: A 759 PHE cc_start: 0.8250 (m-80) cc_final: 0.7968 (m-80) REVERT: A 913 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7600 (pm20) REVERT: A 954 GLN cc_start: 0.8889 (mt0) cc_final: 0.8685 (mt0) REVERT: A 988 GLU cc_start: 0.7837 (mp0) cc_final: 0.7396 (mp0) REVERT: A 1029 MET cc_start: 0.8334 (tpp) cc_final: 0.7983 (ttm) REVERT: B 95 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7583 (t) REVERT: B 297 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.8217 (t) REVERT: B 356 LYS cc_start: 0.8365 (pttt) cc_final: 0.7882 (ptmt) REVERT: B 436 TRP cc_start: 0.7903 (p90) cc_final: 0.6049 (p90) REVERT: B 873 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.8538 (m-10) REVERT: B 988 GLU cc_start: 0.7990 (mp0) cc_final: 0.7655 (mp0) REVERT: B 1031 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7484 (mt-10) REVERT: C 55 PHE cc_start: 0.8453 (m-80) cc_final: 0.7852 (m-80) REVERT: C 277 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7107 (pp) REVERT: C 332 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7736 (tp) REVERT: C 436 TRP cc_start: 0.7968 (p90) cc_final: 0.7123 (p90) REVERT: C 759 PHE cc_start: 0.8540 (m-80) cc_final: 0.8165 (m-10) REVERT: C 904 TYR cc_start: 0.7631 (m-10) cc_final: 0.7331 (m-10) REVERT: C 964 LYS cc_start: 0.9371 (tmtt) cc_final: 0.9033 (tptp) REVERT: C 988 GLU cc_start: 0.7951 (mp0) cc_final: 0.7613 (mp0) outliers start: 87 outliers final: 57 residues processed: 195 average time/residue: 0.2828 time to fit residues: 95.7299 Evaluate side-chains 169 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 105 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 5.9990 chunk 253 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 281 optimal weight: 0.5980 chunk 233 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A1011 GLN B 655 HIS ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23384 Z= 0.162 Angle : 0.501 6.955 31814 Z= 0.258 Chirality : 0.042 0.141 3645 Planarity : 0.004 0.045 4115 Dihedral : 4.391 41.004 3116 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.96 % Allowed : 17.70 % Favored : 79.34 % 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: -1.47 (0.15), residues: 2856 helix: 2.01 (0.22), residues: 632 sheet: -1.92 (0.19), residues: 632 loop : -1.88 (0.14), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 104 HIS 0.005 0.001 HIS C1048 PHE 0.019 0.001 PHE C 201 TYR 0.016 0.001 TYR C1067 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 127 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8287 (tp30) cc_final: 0.7943 (tm-30) REVERT: A 436 TRP cc_start: 0.8022 (p90) cc_final: 0.7543 (p90) REVERT: A 759 PHE cc_start: 0.8112 (m-80) cc_final: 0.7848 (m-80) REVERT: A 913 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7526 (pm20) REVERT: A 988 GLU cc_start: 0.7726 (mp0) cc_final: 0.7387 (mp0) REVERT: A 1029 MET cc_start: 0.8171 (tpp) cc_final: 0.7958 (ttm) REVERT: B 297 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8228 (t) REVERT: B 329 PHE cc_start: 0.7252 (m-10) cc_final: 0.7022 (m-10) REVERT: B 356 LYS cc_start: 0.8367 (pttt) cc_final: 0.7885 (ptmt) REVERT: B 436 TRP cc_start: 0.7898 (p90) cc_final: 0.6076 (p90) REVERT: B 902 MET cc_start: 0.8582 (tpt) cc_final: 0.7943 (tpt) REVERT: B 988 GLU cc_start: 0.8024 (mp0) cc_final: 0.7684 (mp0) REVERT: B 1031 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7393 (mt-10) REVERT: C 55 PHE cc_start: 0.8341 (m-80) cc_final: 0.7780 (m-80) REVERT: C 277 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7269 (pp) REVERT: C 303 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7760 (tp) REVERT: C 332 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7832 (tp) REVERT: C 436 TRP cc_start: 0.7949 (p90) cc_final: 0.6851 (p90) REVERT: C 759 PHE cc_start: 0.8582 (m-80) cc_final: 0.7974 (m-10) REVERT: C 916 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8343 (tt) REVERT: C 964 LYS cc_start: 0.9383 (tmtt) cc_final: 0.9045 (tptp) REVERT: C 988 GLU cc_start: 0.7947 (mp0) cc_final: 0.7601 (mp0) outliers start: 76 outliers final: 46 residues processed: 192 average time/residue: 0.2799 time to fit residues: 91.6643 Evaluate side-chains 167 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 115 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 4.9990 chunk 31 optimal weight: 30.0000 chunk 160 optimal weight: 3.9990 chunk 205 optimal weight: 20.0000 chunk 159 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 280 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A1011 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23384 Z= 0.328 Angle : 0.574 8.195 31814 Z= 0.300 Chirality : 0.045 0.262 3645 Planarity : 0.004 0.046 4115 Dihedral : 4.737 43.192 3116 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.39 % Allowed : 18.09 % Favored : 78.52 % 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: -1.61 (0.15), residues: 2856 helix: 1.65 (0.21), residues: 643 sheet: -2.01 (0.19), residues: 636 loop : -1.88 (0.14), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 64 HIS 0.004 0.001 HIS A1064 PHE 0.022 0.002 PHE B1121 TYR 0.026 0.001 TYR B 91 ARG 0.002 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 111 time to evaluate : 2.686 Fit side-chains revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8271 (tp30) cc_final: 0.7972 (tm-30) REVERT: A 436 TRP cc_start: 0.7939 (p90) cc_final: 0.7524 (p90) REVERT: A 740 MET cc_start: 0.8474 (tpt) cc_final: 0.7919 (tpt) REVERT: A 759 PHE cc_start: 0.8191 (m-80) cc_final: 0.7942 (m-80) REVERT: A 913 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: A 988 GLU cc_start: 0.7805 (mp0) cc_final: 0.7424 (mp0) REVERT: A 1029 MET cc_start: 0.8376 (tpp) cc_final: 0.7993 (ttm) REVERT: A 1122 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8369 (p) REVERT: B 297 SER cc_start: 0.8449 (OUTLIER) cc_final: 0.8164 (t) REVERT: B 436 TRP cc_start: 0.7883 (p90) cc_final: 0.6097 (p90) REVERT: B 516 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6289 (pm20) REVERT: B 873 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.8557 (m-10) REVERT: B 988 GLU cc_start: 0.7986 (mp0) cc_final: 0.7622 (mp0) REVERT: B 1017 GLU cc_start: 0.8042 (tp30) cc_final: 0.7764 (tp30) REVERT: C 55 PHE cc_start: 0.8457 (m-80) cc_final: 0.7843 (m-80) REVERT: C 277 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7134 (pp) REVERT: C 332 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7847 (tp) REVERT: C 436 TRP cc_start: 0.7962 (p90) cc_final: 0.6928 (p90) REVERT: C 904 TYR cc_start: 0.7654 (m-10) cc_final: 0.7315 (m-10) REVERT: C 964 LYS cc_start: 0.9371 (tmtt) cc_final: 0.9033 (tptp) REVERT: C 988 GLU cc_start: 0.7997 (mp0) cc_final: 0.7645 (mp0) outliers start: 87 outliers final: 64 residues processed: 190 average time/residue: 0.2672 time to fit residues: 87.6740 Evaluate side-chains 174 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 103 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 178 optimal weight: 0.9990 chunk 191 optimal weight: 0.2980 chunk 138 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 220 optimal weight: 20.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A1011 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23384 Z= 0.200 Angle : 0.519 7.342 31814 Z= 0.269 Chirality : 0.043 0.255 3645 Planarity : 0.004 0.052 4115 Dihedral : 4.460 42.768 3116 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.16 % Allowed : 18.48 % Favored : 78.36 % 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: -1.43 (0.16), residues: 2856 helix: 1.84 (0.21), residues: 642 sheet: -1.83 (0.19), residues: 660 loop : -1.80 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 104 HIS 0.005 0.001 HIS C1048 PHE 0.026 0.001 PHE A 565 TYR 0.017 0.001 TYR C1067 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 113 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7258 (m-90) cc_final: 0.6582 (m-90) REVERT: A 309 GLU cc_start: 0.8253 (tp30) cc_final: 0.7964 (tm-30) REVERT: A 759 PHE cc_start: 0.8117 (m-80) cc_final: 0.7876 (m-80) REVERT: A 913 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: A 988 GLU cc_start: 0.7725 (mp0) cc_final: 0.7404 (mp0) REVERT: A 1029 MET cc_start: 0.8236 (tpp) cc_final: 0.7981 (ttm) REVERT: A 1122 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8394 (p) REVERT: B 55 PHE cc_start: 0.8210 (m-80) cc_final: 0.7891 (m-80) REVERT: B 297 SER cc_start: 0.8543 (OUTLIER) cc_final: 0.8323 (t) REVERT: B 356 LYS cc_start: 0.8330 (pttt) cc_final: 0.7716 (ptmt) REVERT: B 436 TRP cc_start: 0.7840 (p90) cc_final: 0.6654 (p90) REVERT: B 516 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6307 (pm20) REVERT: B 873 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.8463 (m-10) REVERT: B 902 MET cc_start: 0.8506 (tpt) cc_final: 0.7936 (tpt) REVERT: B 988 GLU cc_start: 0.8078 (mp0) cc_final: 0.7738 (mp0) REVERT: B 1130 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8207 (tp) REVERT: C 55 PHE cc_start: 0.8369 (m-80) cc_final: 0.7787 (m-80) REVERT: C 277 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7322 (pp) REVERT: C 329 PHE cc_start: 0.6709 (m-80) cc_final: 0.6404 (m-10) REVERT: C 332 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7846 (tp) REVERT: C 436 TRP cc_start: 0.8001 (p90) cc_final: 0.6903 (p90) REVERT: C 900 MET cc_start: 0.7785 (mtp) cc_final: 0.7539 (mtm) REVERT: C 964 LYS cc_start: 0.9371 (tmtt) cc_final: 0.9027 (tptp) REVERT: C 988 GLU cc_start: 0.7960 (mp0) cc_final: 0.7611 (mp0) outliers start: 81 outliers final: 59 residues processed: 187 average time/residue: 0.2800 time to fit residues: 89.0202 Evaluate side-chains 173 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 106 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 chunk 260 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B1142 GLN C 437 ASN C 755 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23384 Z= 0.187 Angle : 0.511 7.540 31814 Z= 0.264 Chirality : 0.043 0.198 3645 Planarity : 0.004 0.055 4115 Dihedral : 4.374 42.276 3116 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.96 % Allowed : 18.87 % Favored : 78.17 % 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: -1.29 (0.16), residues: 2856 helix: 1.94 (0.21), residues: 648 sheet: -1.73 (0.19), residues: 652 loop : -1.73 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.005 0.001 HIS C1048 PHE 0.029 0.001 PHE A 565 TYR 0.016 0.001 TYR C1067 ARG 0.002 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 118 time to evaluate : 2.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7324 (m-90) cc_final: 0.6672 (m-90) REVERT: A 309 GLU cc_start: 0.8260 (tp30) cc_final: 0.7957 (tm-30) REVERT: A 436 TRP cc_start: 0.7571 (p90) cc_final: 0.7256 (p90) REVERT: A 759 PHE cc_start: 0.8094 (m-80) cc_final: 0.7857 (m-80) REVERT: A 913 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7613 (pm20) REVERT: A 988 GLU cc_start: 0.7820 (mp0) cc_final: 0.7449 (mp0) REVERT: A 1029 MET cc_start: 0.8247 (tpp) cc_final: 0.7968 (ttm) REVERT: B 55 PHE cc_start: 0.8038 (m-80) cc_final: 0.7751 (m-80) REVERT: B 297 SER cc_start: 0.8505 (OUTLIER) cc_final: 0.8231 (t) REVERT: B 329 PHE cc_start: 0.6994 (m-10) cc_final: 0.6762 (m-10) REVERT: B 356 LYS cc_start: 0.8360 (pttt) cc_final: 0.7729 (ptmt) REVERT: B 436 TRP cc_start: 0.7841 (p90) cc_final: 0.6729 (p90) REVERT: B 516 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6302 (pm20) REVERT: B 873 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.8456 (m-10) REVERT: B 902 MET cc_start: 0.8500 (tpt) cc_final: 0.7913 (tpt) REVERT: B 988 GLU cc_start: 0.8053 (mp0) cc_final: 0.7719 (mp0) REVERT: B 1130 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8243 (tp) REVERT: C 55 PHE cc_start: 0.8350 (m-80) cc_final: 0.7760 (m-80) REVERT: C 277 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7298 (pp) REVERT: C 332 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7714 (tp) REVERT: C 334 ASN cc_start: 0.8519 (m110) cc_final: 0.8276 (t0) REVERT: C 436 TRP cc_start: 0.7986 (p90) cc_final: 0.6916 (p90) REVERT: C 964 LYS cc_start: 0.9367 (tmtt) cc_final: 0.9021 (tptp) REVERT: C 988 GLU cc_start: 0.7959 (mp0) cc_final: 0.7592 (mp0) outliers start: 76 outliers final: 60 residues processed: 186 average time/residue: 0.2693 time to fit residues: 86.0264 Evaluate side-chains 172 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 105 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 192 optimal weight: 0.9980 chunk 289 optimal weight: 8.9990 chunk 266 optimal weight: 2.9990 chunk 230 optimal weight: 40.0000 chunk 23 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN C 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23384 Z= 0.172 Angle : 0.510 8.941 31814 Z= 0.262 Chirality : 0.043 0.168 3645 Planarity : 0.004 0.050 4115 Dihedral : 4.286 42.524 3116 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.85 % Allowed : 19.10 % Favored : 78.05 % 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: -1.17 (0.16), residues: 2856 helix: 1.99 (0.21), residues: 650 sheet: -1.58 (0.20), residues: 637 loop : -1.67 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 104 HIS 0.004 0.001 HIS C1048 PHE 0.026 0.001 PHE A 565 TYR 0.016 0.001 TYR C1067 ARG 0.002 0.000 ARG A 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 120 time to evaluate : 2.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7222 (m-90) cc_final: 0.6604 (m-90) REVERT: A 309 GLU cc_start: 0.8289 (tp30) cc_final: 0.7942 (tm-30) REVERT: A 759 PHE cc_start: 0.8023 (m-80) cc_final: 0.7787 (m-80) REVERT: A 777 ASN cc_start: 0.8345 (m-40) cc_final: 0.8132 (m110) REVERT: A 988 GLU cc_start: 0.7830 (mp0) cc_final: 0.7432 (mp0) REVERT: A 1029 MET cc_start: 0.8228 (tpp) cc_final: 0.7975 (ttm) REVERT: B 238 PHE cc_start: 0.6021 (p90) cc_final: 0.5761 (p90) REVERT: B 297 SER cc_start: 0.8563 (OUTLIER) cc_final: 0.8349 (t) REVERT: B 329 PHE cc_start: 0.6915 (m-10) cc_final: 0.6588 (m-10) REVERT: B 356 LYS cc_start: 0.8388 (pttt) cc_final: 0.7663 (ptmt) REVERT: B 436 TRP cc_start: 0.7941 (p90) cc_final: 0.6868 (p90) REVERT: B 516 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6310 (pm20) REVERT: B 873 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.8449 (m-10) REVERT: B 902 MET cc_start: 0.8513 (tpt) cc_final: 0.7928 (tpt) REVERT: B 988 GLU cc_start: 0.8146 (mp0) cc_final: 0.7853 (mp0) REVERT: B 1130 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8224 (tp) REVERT: C 55 PHE cc_start: 0.8314 (m-80) cc_final: 0.7751 (m-80) REVERT: C 277 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7272 (pp) REVERT: C 303 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7689 (tp) REVERT: C 332 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7647 (tp) REVERT: C 334 ASN cc_start: 0.8506 (m110) cc_final: 0.8280 (t0) REVERT: C 436 TRP cc_start: 0.7904 (p90) cc_final: 0.6949 (p90) REVERT: C 964 LYS cc_start: 0.9382 (tmtt) cc_final: 0.9042 (tptp) REVERT: C 988 GLU cc_start: 0.7939 (mp0) cc_final: 0.7581 (mp0) outliers start: 73 outliers final: 58 residues processed: 186 average time/residue: 0.2775 time to fit residues: 89.8487 Evaluate side-chains 173 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 108 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 0.3980 chunk 245 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 231 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 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 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A1011 GLN C 354 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.128130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.082348 restraints weight = 47350.510| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 4.05 r_work: 0.3072 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23384 Z= 0.245 Angle : 0.541 8.240 31814 Z= 0.280 Chirality : 0.043 0.217 3645 Planarity : 0.004 0.052 4115 Dihedral : 4.462 42.703 3116 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.73 % Allowed : 19.65 % Favored : 77.62 % 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: -1.24 (0.16), residues: 2856 helix: 1.91 (0.21), residues: 646 sheet: -1.64 (0.19), residues: 651 loop : -1.69 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.005 0.001 HIS C1048 PHE 0.028 0.001 PHE C 201 TYR 0.018 0.001 TYR C 91 ARG 0.002 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4146.25 seconds wall clock time: 76 minutes 24.18 seconds (4584.18 seconds total)