Starting phenix.real_space_refine on Mon Feb 19 15:58:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhk_31997/02_2024/7vhk_31997.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhk_31997/02_2024/7vhk_31997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhk_31997/02_2024/7vhk_31997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhk_31997/02_2024/7vhk_31997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhk_31997/02_2024/7vhk_31997.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhk_31997/02_2024/7vhk_31997.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 114 5.16 5 C 16056 2.51 5 N 4203 2.21 5 O 4818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 766": "OE1" <-> "OE2" Residue "B ASP 789": "OD1" <-> "OD2" Residue "B PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 978": "OD1" <-> "OD2" Residue "B GLU 1010": "OE1" <-> "OE2" Residue "B TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1104": "OE1" <-> "OE2" Residue "B ASP 1132": "OD1" <-> "OD2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 766": "OE1" <-> "OE2" Residue "A ASP 789": "OD1" <-> "OD2" Residue "A PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 978": "OD1" <-> "OD2" Residue "A GLU 1010": "OE1" <-> "OE2" Residue "A TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1104": "OE1" <-> "OE2" Residue "A ASP 1132": "OD1" <-> "OD2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 467": "OD1" <-> "OD2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C ASP 614": "OD1" <-> "OD2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 766": "OE1" <-> "OE2" Residue "C ASP 789": "OD1" <-> "OD2" Residue "C PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 978": "OD1" <-> "OD2" Residue "C GLU 1010": "OE1" <-> "OE2" Residue "C TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1104": "OE1" <-> "OE2" Residue "C ASP 1132": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25191 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 8397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8397 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1025} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 8397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8397 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1025} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8397 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1025} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 13.14, per 1000 atoms: 0.52 Number of scatterers: 25191 At special positions: 0 Unit cell: (149.76, 157.04, 174.72, 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 114 16.00 O 4818 8.00 N 4203 7.00 C 16056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 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=2.04 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=2.38 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.13 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=1.97 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 731 " - pdb=" SG CYS B 753 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B1025 " - pdb=" SG CYS B1036 " distance=2.03 Simple disulfide: pdb=" SG CYS B1075 " - pdb=" SG CYS B1119 " distance=2.03 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=2.04 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=2.38 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.13 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=1.97 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 731 " - pdb=" SG CYS A 753 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A1025 " - pdb=" SG CYS A1036 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1119 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 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=2.38 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.13 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=1.97 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 731 " - pdb=" SG CYS C 753 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C1025 " - pdb=" SG CYS C1036 " distance=2.03 Simple disulfide: pdb=" SG CYS C1075 " - pdb=" SG CYS C1119 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.22 Conformation dependent library (CDL) restraints added in 4.7 seconds 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6036 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 54 sheets defined 22.9% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.678A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.963A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.347A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.756A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.675A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 735 Processing helix chain 'B' and resid 740 through 750 removed outlier: 3.684A pdb=" N GLY B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 775 removed outlier: 3.663A pdb=" N PHE B 775 " --> pdb=" O THR B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 814 Processing helix chain 'B' and resid 842 through 849 Processing helix chain 'B' and resid 859 through 876 Processing helix chain 'B' and resid 879 through 884 removed outlier: 4.258A pdb=" N ALA B 883 " --> pdb=" O TRP B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 902 Processing helix chain 'B' and resid 905 through 912 removed outlier: 4.279A pdb=" N LEU B 909 " --> pdb=" O THR B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 932 Processing helix chain 'B' and resid 933 through 939 removed outlier: 6.902A pdb=" N SER B 936 " --> pdb=" O SER B 933 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B 937 " --> pdb=" O THR B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 957 removed outlier: 4.131A pdb=" N ASN B 946 " --> pdb=" O GLN B 942 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN B 948 " --> pdb=" O VAL B 944 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 950 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS B 957 " --> pdb=" O ASN B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 1025 removed outlier: 4.780A pdb=" N VAL B 984 " --> pdb=" O PRO B 980 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN B 985 " --> pdb=" O GLU B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1140 removed outlier: 3.895A pdb=" N SER B1140 " --> pdb=" O PRO B1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.678A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.963A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.348A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.756A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.674A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 735 Processing helix chain 'A' and resid 740 through 750 removed outlier: 3.684A pdb=" N GLY A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 775 removed outlier: 3.663A pdb=" N PHE A 775 " --> pdb=" O THR A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 814 Processing helix chain 'A' and resid 842 through 849 Processing helix chain 'A' and resid 859 through 876 Processing helix chain 'A' and resid 879 through 884 removed outlier: 4.258A pdb=" N ALA A 883 " --> pdb=" O TRP A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 902 Processing helix chain 'A' and resid 905 through 912 removed outlier: 4.280A pdb=" N LEU A 909 " --> pdb=" O THR A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 932 Processing helix chain 'A' and resid 933 through 939 removed outlier: 6.903A pdb=" N SER A 936 " --> pdb=" O SER A 933 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 937 " --> pdb=" O THR A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 957 removed outlier: 4.130A pdb=" N ASN A 946 " --> pdb=" O GLN A 942 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN A 948 " --> pdb=" O VAL A 944 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 950 " --> pdb=" O ASN A 946 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS A 957 " --> pdb=" O ASN A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1025 removed outlier: 4.779A pdb=" N VAL A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN A 985 " --> pdb=" O GLU A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1140 removed outlier: 3.895A pdb=" N SER A1140 " --> pdb=" O PRO A1136 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.677A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.964A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.347A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.756A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.674A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 740 through 750 removed outlier: 3.684A pdb=" N GLY C 750 " --> pdb=" O LEU C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 775 removed outlier: 3.664A pdb=" N PHE C 775 " --> pdb=" O THR C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 814 Processing helix chain 'C' and resid 842 through 849 Processing helix chain 'C' and resid 859 through 876 Processing helix chain 'C' and resid 879 through 884 removed outlier: 4.259A pdb=" N ALA C 883 " --> pdb=" O TRP C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 902 Processing helix chain 'C' and resid 905 through 912 removed outlier: 4.280A pdb=" N LEU C 909 " --> pdb=" O THR C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 932 Processing helix chain 'C' and resid 933 through 939 removed outlier: 6.903A pdb=" N SER C 936 " --> pdb=" O SER C 933 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 937 " --> pdb=" O THR C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 957 removed outlier: 4.130A pdb=" N ASN C 946 " --> pdb=" O GLN C 942 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN C 948 " --> pdb=" O VAL C 944 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN C 950 " --> pdb=" O ASN C 946 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS C 957 " --> pdb=" O ASN C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 1025 removed outlier: 4.780A pdb=" N VAL C 984 " --> pdb=" O PRO C 980 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN C 985 " --> pdb=" O GLU C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 1134 through 1140 removed outlier: 3.895A pdb=" N SER C1140 " --> pdb=" O PRO C1136 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.531A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 230 removed outlier: 7.203A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 107 removed outlier: 3.768A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.707A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.529A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 356 through 358 removed outlier: 4.067A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'B' and resid 539 through 540 removed outlier: 3.675A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 654 through 656 removed outlier: 3.765A pdb=" N VAL B 656 " --> pdb=" O ALA B 687 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR B 689 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B 684 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR B 688 " --> pdb=" O CYS B 671 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 704 through 706 Processing sheet with id=AB4, first strand: chain 'B' and resid 710 through 721 removed outlier: 6.514A pdb=" N ASN B 710 " --> pdb=" O ALA B1063 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR B1059 " --> pdb=" O SER B 714 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N TYR B1060 " --> pdb=" O HIS B1041 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N HIS B1041 " --> pdb=" O TYR B1060 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 710 through 721 removed outlier: 6.514A pdb=" N ASN B 710 " --> pdb=" O ALA B1063 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR B1059 " --> pdb=" O SER B 714 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY B1052 " --> pdb=" O ALA B1049 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA B1049 " --> pdb=" O GLY B1052 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 727 through 729 removed outlier: 3.576A pdb=" N SER B 728 " --> pdb=" O THR B 852 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1074 through 1075 Processing sheet with id=AB8, first strand: chain 'B' and resid 1079 through 1083 removed outlier: 4.315A pdb=" N ALA B1080 " --> pdb=" O SER B1116 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B1116 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1087 through 1089 Processing sheet with id=AC1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AC2, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.531A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AC4, first strand: chain 'A' and resid 224 through 230 removed outlier: 7.203A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 103 through 107 removed outlier: 3.769A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.706A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.529A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.068A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'A' and resid 539 through 540 removed outlier: 3.675A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 654 through 656 removed outlier: 3.765A pdb=" N VAL A 656 " --> pdb=" O ALA A 687 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR A 689 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 684 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A 688 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 704 through 706 Processing sheet with id=AD4, first strand: chain 'A' and resid 710 through 721 removed outlier: 6.514A pdb=" N ASN A 710 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A1059 " --> pdb=" O SER A 714 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N TYR A1060 " --> pdb=" O HIS A1041 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N HIS A1041 " --> pdb=" O TYR A1060 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 710 through 721 removed outlier: 6.514A pdb=" N ASN A 710 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A1059 " --> pdb=" O SER A 714 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY A1052 " --> pdb=" O ALA A1049 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A1049 " --> pdb=" O GLY A1052 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 727 through 729 removed outlier: 3.576A pdb=" N SER A 728 " --> pdb=" O THR A 852 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 1074 through 1075 Processing sheet with id=AD8, first strand: chain 'A' and resid 1079 through 1083 removed outlier: 4.315A pdb=" N ALA A1080 " --> pdb=" O SER A1116 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER A1116 " --> pdb=" O ALA A1080 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 1087 through 1089 Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.531A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE4, first strand: chain 'C' and resid 224 through 230 removed outlier: 7.202A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 103 through 107 removed outlier: 3.768A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.706A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.529A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.067A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 539 through 540 removed outlier: 3.675A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 656 removed outlier: 3.766A pdb=" N VAL C 656 " --> pdb=" O ALA C 687 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR C 689 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER C 684 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR C 688 " --> pdb=" O CYS C 671 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 704 through 706 Processing sheet with id=AF4, first strand: chain 'C' and resid 710 through 721 removed outlier: 6.513A pdb=" N ASN C 710 " --> pdb=" O ALA C1063 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C1059 " --> pdb=" O SER C 714 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N TYR C1060 " --> pdb=" O HIS C1041 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N HIS C1041 " --> pdb=" O TYR C1060 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 710 through 721 removed outlier: 6.513A pdb=" N ASN C 710 " --> pdb=" O ALA C1063 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C1059 " --> pdb=" O SER C 714 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY C1052 " --> pdb=" O ALA C1049 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA C1049 " --> pdb=" O GLY C1052 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 727 through 729 removed outlier: 3.577A pdb=" N SER C 728 " --> pdb=" O THR C 852 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1074 through 1075 Processing sheet with id=AF8, first strand: chain 'C' and resid 1079 through 1083 removed outlier: 4.316A pdb=" N ALA C1080 " --> pdb=" O SER C1116 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER C1116 " --> pdb=" O ALA C1080 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1087 through 1089 783 hydrogen bonds defined for protein. 2178 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: 9.81 Time building geometry restraints manager: 10.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8184 1.35 - 1.48: 6623 1.48 - 1.60: 10825 1.60 - 1.73: 0 1.73 - 1.85: 144 Bond restraints: 25776 Sorted by residual: bond pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 1.808 1.852 -0.044 3.30e-02 9.18e+02 1.80e+00 bond pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 1.808 1.852 -0.044 3.30e-02 9.18e+02 1.79e+00 bond pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 1.808 1.852 -0.044 3.30e-02 9.18e+02 1.79e+00 bond pdb=" CA SER B 596 " pdb=" C SER B 596 " ideal model delta sigma weight residual 1.529 1.515 0.014 1.04e-02 9.25e+03 1.78e+00 bond pdb=" CB CYS C 731 " pdb=" SG CYS C 731 " ideal model delta sigma weight residual 1.808 1.764 0.044 3.30e-02 9.18e+02 1.76e+00 ... (remaining 25771 not shown) Histogram of bond angle deviations from ideal: 99.93 - 106.75: 694 106.75 - 113.56: 14171 113.56 - 120.38: 9274 120.38 - 127.19: 10726 127.19 - 134.01: 220 Bond angle restraints: 35085 Sorted by residual: angle pdb=" N GLY B 750 " pdb=" CA GLY B 750 " pdb=" C GLY B 750 " ideal model delta sigma weight residual 110.20 117.39 -7.19 1.32e+00 5.74e-01 2.97e+01 angle pdb=" N GLY C 750 " pdb=" CA GLY C 750 " pdb=" C GLY C 750 " ideal model delta sigma weight residual 110.20 117.38 -7.18 1.32e+00 5.74e-01 2.96e+01 angle pdb=" N GLY A 750 " pdb=" CA GLY A 750 " pdb=" C GLY A 750 " ideal model delta sigma weight residual 110.20 117.36 -7.16 1.32e+00 5.74e-01 2.94e+01 angle pdb=" C PHE B 562 " pdb=" N GLN B 563 " pdb=" CA GLN B 563 " ideal model delta sigma weight residual 121.54 127.91 -6.37 1.91e+00 2.74e-01 1.11e+01 angle pdb=" C PHE C 562 " pdb=" N GLN C 563 " pdb=" CA GLN C 563 " ideal model delta sigma weight residual 121.54 127.83 -6.29 1.91e+00 2.74e-01 1.09e+01 ... (remaining 35080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 13755 17.63 - 35.27: 1293 35.27 - 52.90: 249 52.90 - 70.53: 28 70.53 - 88.17: 29 Dihedral angle restraints: 15354 sinusoidal: 5955 harmonic: 9399 Sorted by residual: dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual -86.00 -173.80 87.80 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual -86.00 -173.79 87.79 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -173.78 87.78 1 1.00e+01 1.00e-02 9.23e+01 ... (remaining 15351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2407 0.035 - 0.070: 1090 0.070 - 0.105: 364 0.105 - 0.141: 96 0.141 - 0.176: 15 Chirality restraints: 3972 Sorted by residual: chirality pdb=" CA PRO C 463 " pdb=" N PRO C 463 " pdb=" C PRO C 463 " pdb=" CB PRO C 463 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA PRO A 463 " pdb=" N PRO A 463 " pdb=" C PRO A 463 " pdb=" CB PRO A 463 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CA PRO B 463 " pdb=" N PRO B 463 " pdb=" C PRO B 463 " pdb=" CB PRO B 463 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 3969 not shown) Planarity restraints: 4563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 173 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO B 174 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 174 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 174 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 173 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO A 174 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 173 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO C 174 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 174 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 174 " 0.023 5.00e-02 4.00e+02 ... (remaining 4560 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 382 2.63 - 3.20: 23919 3.20 - 3.76: 36930 3.76 - 4.33: 53435 4.33 - 4.90: 87074 Nonbonded interactions: 201740 Sorted by model distance: nonbonded pdb=" OG1 THR B 385 " pdb=" OG1 THR A 415 " model vdw 2.059 2.440 nonbonded pdb=" OG1 THR A 385 " pdb=" OG1 THR C 415 " model vdw 2.117 2.440 nonbonded pdb=" OE2 GLU C 654 " pdb=" OG SER C 684 " model vdw 2.137 2.440 nonbonded pdb=" OE2 GLU B 654 " pdb=" OG SER B 684 " model vdw 2.138 2.440 nonbonded pdb=" OE2 GLU A 654 " pdb=" OG SER A 684 " model vdw 2.138 2.440 ... (remaining 201735 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.630 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 66.880 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25776 Z= 0.345 Angle : 0.731 7.613 35085 Z= 0.426 Chirality : 0.045 0.176 3972 Planarity : 0.004 0.041 4563 Dihedral : 14.124 88.168 9201 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.15 % Favored : 90.76 % Rotamer: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % 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: -4.61 (0.12), residues: 3213 helix: -1.90 (0.16), residues: 702 sheet: -3.42 (0.18), residues: 606 loop : -3.56 (0.12), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 436 HIS 0.008 0.001 HIS B 245 PHE 0.011 0.001 PHE B 541 TYR 0.012 0.001 TYR B 749 ARG 0.003 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 2.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 TRP cc_start: 0.7707 (t60) cc_final: 0.7357 (t60) REVERT: B 655 HIS cc_start: 0.8254 (t70) cc_final: 0.8019 (t70) REVERT: B 847 LYS cc_start: 0.7911 (tmtt) cc_final: 0.7575 (tttm) REVERT: B 1043 MET cc_start: 0.8174 (ptp) cc_final: 0.7963 (ptm) REVERT: A 65 PHE cc_start: 0.7213 (m-80) cc_final: 0.6770 (m-10) REVERT: A 104 TRP cc_start: 0.7420 (m-90) cc_final: 0.6988 (m-90) REVERT: A 191 GLU cc_start: 0.7148 (mp0) cc_final: 0.6241 (mt-10) REVERT: A 206 LYS cc_start: 0.8602 (tptt) cc_final: 0.8221 (tptt) REVERT: A 505 TYR cc_start: 0.6494 (m-80) cc_final: 0.6148 (m-80) REVERT: A 927 ILE cc_start: 0.8849 (tp) cc_final: 0.8595 (tp) REVERT: C 190 ARG cc_start: 0.6678 (mtm180) cc_final: 0.5300 (mtt180) REVERT: C 297 SER cc_start: 0.7953 (m) cc_final: 0.7708 (t) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.3581 time to fit residues: 223.0408 Evaluate side-chains 235 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 3.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 0.0670 chunk 243 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 164 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 251 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 152 optimal weight: 0.8980 chunk 187 optimal weight: 0.9990 chunk 291 optimal weight: 3.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 207 HIS B 239 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1081 HIS A 165 ASN A 448 ASN A 460 ASN A 544 ASN ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1081 HIS A1101 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN C 207 HIS C 448 ASN C 460 ASN C 544 ASN ** C 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1081 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25776 Z= 0.183 Angle : 0.569 7.681 35085 Z= 0.298 Chirality : 0.043 0.172 3972 Planarity : 0.004 0.060 4563 Dihedral : 4.914 25.066 3468 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.42 % Allowed : 10.81 % Favored : 87.76 % 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: -3.38 (0.14), residues: 3213 helix: -0.48 (0.19), residues: 711 sheet: -2.84 (0.18), residues: 657 loop : -2.83 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 436 HIS 0.003 0.001 HIS A 245 PHE 0.021 0.001 PHE C 429 TYR 0.023 0.001 TYR A1060 ARG 0.006 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 320 time to evaluate : 2.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 TYR cc_start: 0.4850 (t80) cc_final: 0.4440 (t80) REVERT: B 165 ASN cc_start: 0.4891 (OUTLIER) cc_final: 0.4395 (t0) REVERT: B 514 SER cc_start: 0.7957 (m) cc_final: 0.7620 (p) REVERT: B 655 HIS cc_start: 0.8044 (t70) cc_final: 0.7797 (t70) REVERT: B 987 ASP cc_start: 0.6475 (m-30) cc_final: 0.6189 (m-30) REVERT: B 1010 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7955 (tm-30) REVERT: B 1022 MET cc_start: 0.8074 (tpp) cc_final: 0.7621 (ttm) REVERT: B 1043 MET cc_start: 0.7534 (ptp) cc_final: 0.7222 (ptm) REVERT: A 65 PHE cc_start: 0.7187 (m-80) cc_final: 0.6800 (m-10) REVERT: A 165 ASN cc_start: 0.5014 (OUTLIER) cc_final: 0.4634 (t0) REVERT: A 177 MET cc_start: 0.5140 (tmm) cc_final: 0.4863 (tmm) REVERT: A 774 VAL cc_start: 0.9018 (t) cc_final: 0.8696 (t) REVERT: A 927 ILE cc_start: 0.8626 (tp) cc_final: 0.8360 (tp) REVERT: A 1022 MET cc_start: 0.8495 (tpp) cc_final: 0.7615 (ttm) REVERT: C 190 ARG cc_start: 0.7117 (mtm180) cc_final: 0.5477 (mtt180) REVERT: C 297 SER cc_start: 0.7817 (m) cc_final: 0.7582 (t) REVERT: C 598 ILE cc_start: 0.8726 (mt) cc_final: 0.8366 (mt) outliers start: 40 outliers final: 27 residues processed: 346 average time/residue: 0.3225 time to fit residues: 185.6596 Evaluate side-chains 272 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 243 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 852 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 162 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 242 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 292 optimal weight: 5.9990 chunk 315 optimal weight: 2.9990 chunk 260 optimal weight: 5.9990 chunk 289 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 234 optimal weight: 0.4980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 770 ASN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 519 HIS C 658 ASN ** C 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25776 Z= 0.208 Angle : 0.549 7.525 35085 Z= 0.284 Chirality : 0.043 0.249 3972 Planarity : 0.004 0.062 4563 Dihedral : 4.682 23.844 3468 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.81 % Allowed : 13.48 % Favored : 83.71 % 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: -2.89 (0.14), residues: 3213 helix: 0.13 (0.19), residues: 711 sheet: -2.41 (0.19), residues: 645 loop : -2.68 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 436 HIS 0.006 0.001 HIS B 69 PHE 0.028 0.001 PHE B 140 TYR 0.021 0.001 TYR A1060 ARG 0.004 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 267 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 TYR cc_start: 0.4861 (t80) cc_final: 0.4467 (t80) REVERT: B 514 SER cc_start: 0.7923 (m) cc_final: 0.7593 (p) REVERT: B 987 ASP cc_start: 0.6560 (m-30) cc_final: 0.6068 (m-30) REVERT: B 1022 MET cc_start: 0.8102 (tpp) cc_final: 0.7604 (ttm) REVERT: B 1043 MET cc_start: 0.7558 (ptp) cc_final: 0.7297 (ptm) REVERT: A 206 LYS cc_start: 0.8306 (tptm) cc_final: 0.7715 (tptm) REVERT: A 927 ILE cc_start: 0.8596 (tp) cc_final: 0.8332 (tp) REVERT: C 190 ARG cc_start: 0.7204 (mtm180) cc_final: 0.5532 (mtt180) REVERT: C 297 SER cc_start: 0.7809 (m) cc_final: 0.7605 (t) REVERT: C 658 ASN cc_start: 0.7314 (OUTLIER) cc_final: 0.6688 (p0) outliers start: 79 outliers final: 59 residues processed: 322 average time/residue: 0.3071 time to fit residues: 167.1435 Evaluate side-chains 292 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 232 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 724 MET Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 1054 VAL Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 852 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1054 VAL Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 151 optimal weight: 0.2980 chunk 32 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 196 optimal weight: 0.5980 chunk 293 optimal weight: 4.9990 chunk 310 optimal weight: 0.8980 chunk 153 optimal weight: 8.9990 chunk 277 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 544 ASN B 767 GLN ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 519 HIS A 658 ASN A 770 ASN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN C 703 ASN ** C 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 ASN C1112 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25776 Z= 0.223 Angle : 0.552 9.246 35085 Z= 0.282 Chirality : 0.043 0.213 3972 Planarity : 0.004 0.063 4563 Dihedral : 4.612 24.163 3468 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.34 % Allowed : 14.98 % Favored : 81.68 % 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: -2.63 (0.14), residues: 3213 helix: 0.35 (0.20), residues: 711 sheet: -2.18 (0.20), residues: 645 loop : -2.54 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 436 HIS 0.004 0.001 HIS B 69 PHE 0.024 0.001 PHE C 168 TYR 0.021 0.001 TYR B1060 ARG 0.004 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 247 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 TYR cc_start: 0.4859 (t80) cc_final: 0.4582 (t80) REVERT: B 177 MET cc_start: 0.3814 (mmm) cc_final: 0.1171 (tmm) REVERT: B 430 THR cc_start: 0.7559 (OUTLIER) cc_final: 0.7344 (t) REVERT: B 997 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8341 (tt) REVERT: B 1043 MET cc_start: 0.7559 (ptp) cc_final: 0.7279 (ptm) REVERT: A 749 TYR cc_start: 0.8033 (m-80) cc_final: 0.7463 (t80) REVERT: A 927 ILE cc_start: 0.8605 (tp) cc_final: 0.8330 (tp) REVERT: A 1022 MET cc_start: 0.8525 (tpp) cc_final: 0.7593 (ttm) REVERT: A 1104 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7704 (tm-30) outliers start: 94 outliers final: 77 residues processed: 309 average time/residue: 0.2904 time to fit residues: 155.2834 Evaluate side-chains 305 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 226 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 724 MET Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 730 ASP Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain B residue 1054 VAL Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 852 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1054 VAL Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 258 optimal weight: 20.0000 chunk 176 optimal weight: 0.6980 chunk 4 optimal weight: 30.0000 chunk 231 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 264 optimal weight: 8.9990 chunk 214 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 158 optimal weight: 0.9990 chunk 278 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 25776 Z= 0.395 Angle : 0.649 8.773 35085 Z= 0.333 Chirality : 0.046 0.219 3972 Planarity : 0.004 0.066 4563 Dihedral : 5.126 25.874 3468 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 3.84 % Allowed : 16.40 % Favored : 79.76 % 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: -2.79 (0.14), residues: 3213 helix: 0.08 (0.19), residues: 711 sheet: -2.26 (0.20), residues: 663 loop : -2.58 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 436 HIS 0.005 0.001 HIS A1041 PHE 0.026 0.002 PHE A 643 TYR 0.026 0.002 TYR A1060 ARG 0.003 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 234 time to evaluate : 3.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 TYR cc_start: 0.5200 (t80) cc_final: 0.4852 (t80) REVERT: B 153 MET cc_start: 0.5253 (mmm) cc_final: 0.4791 (mmm) REVERT: B 177 MET cc_start: 0.3963 (mmm) cc_final: 0.1444 (tmm) REVERT: B 392 PHE cc_start: 0.6950 (OUTLIER) cc_final: 0.6698 (m-10) REVERT: B 430 THR cc_start: 0.7535 (OUTLIER) cc_final: 0.7307 (t) REVERT: B 436 TRP cc_start: 0.6305 (OUTLIER) cc_final: 0.5421 (p-90) REVERT: B 514 SER cc_start: 0.8018 (m) cc_final: 0.7723 (p) REVERT: B 987 ASP cc_start: 0.6465 (m-30) cc_final: 0.6037 (m-30) REVERT: B 1043 MET cc_start: 0.7742 (ptp) cc_final: 0.7482 (ptm) REVERT: A 65 PHE cc_start: 0.7155 (m-80) cc_final: 0.6844 (m-10) REVERT: A 927 ILE cc_start: 0.8638 (tp) cc_final: 0.8321 (tp) REVERT: C 436 TRP cc_start: 0.6170 (OUTLIER) cc_final: 0.4281 (p-90) REVERT: C 660 TYR cc_start: 0.7591 (OUTLIER) cc_final: 0.6801 (m-80) REVERT: C 895 MET cc_start: 0.8539 (tpp) cc_final: 0.8219 (tpt) REVERT: C 950 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8142 (tm-30) outliers start: 108 outliers final: 84 residues processed: 306 average time/residue: 0.3064 time to fit residues: 161.0261 Evaluate side-chains 307 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 218 time to evaluate : 3.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain B residue 1054 VAL Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 749 TYR Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 852 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1054 VAL Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 104 optimal weight: 0.9990 chunk 279 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 182 optimal weight: 0.7980 chunk 76 optimal weight: 0.4980 chunk 310 optimal weight: 0.8980 chunk 257 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25776 Z= 0.175 Angle : 0.535 8.161 35085 Z= 0.275 Chirality : 0.042 0.188 3972 Planarity : 0.004 0.070 4563 Dihedral : 4.516 23.820 3468 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.95 % Allowed : 18.25 % Favored : 78.80 % 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: 3213 helix: 0.58 (0.20), residues: 711 sheet: -1.96 (0.20), residues: 642 loop : -2.33 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 436 HIS 0.004 0.000 HIS B 69 PHE 0.030 0.001 PHE C 168 TYR 0.020 0.001 TYR A1060 ARG 0.003 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 259 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 TYR cc_start: 0.5068 (t80) cc_final: 0.4656 (t80) REVERT: B 177 MET cc_start: 0.3978 (mmm) cc_final: 0.1396 (tmm) REVERT: B 436 TRP cc_start: 0.6288 (OUTLIER) cc_final: 0.5263 (p-90) REVERT: B 514 SER cc_start: 0.7866 (m) cc_final: 0.7644 (p) REVERT: B 946 ASN cc_start: 0.8285 (t0) cc_final: 0.8017 (t0) REVERT: B 1022 MET cc_start: 0.7980 (tpp) cc_final: 0.7599 (ttm) REVERT: B 1043 MET cc_start: 0.7532 (ptp) cc_final: 0.7264 (ptm) REVERT: A 655 HIS cc_start: 0.7878 (t70) cc_final: 0.7532 (t70) REVERT: A 749 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7585 (t80) REVERT: A 927 ILE cc_start: 0.8456 (tp) cc_final: 0.8157 (tp) REVERT: A 1022 MET cc_start: 0.8440 (tpp) cc_final: 0.7558 (ttm) REVERT: A 1104 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7764 (tm-30) REVERT: C 88 ASP cc_start: 0.7169 (p0) cc_final: 0.6832 (p0) REVERT: C 190 ARG cc_start: 0.7019 (mtm180) cc_final: 0.5473 (mtt180) REVERT: C 436 TRP cc_start: 0.6038 (OUTLIER) cc_final: 0.3975 (p-90) REVERT: C 950 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8007 (tm-30) outliers start: 83 outliers final: 69 residues processed: 319 average time/residue: 0.3032 time to fit residues: 164.5734 Evaluate side-chains 303 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 231 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 1054 VAL Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 749 TYR Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 852 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 299 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 226 optimal weight: 20.0000 chunk 175 optimal weight: 0.4980 chunk 261 optimal weight: 4.9990 chunk 173 optimal weight: 0.3980 chunk 309 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 658 ASN B 767 GLN ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25776 Z= 0.332 Angle : 0.614 12.309 35085 Z= 0.312 Chirality : 0.045 0.181 3972 Planarity : 0.004 0.067 4563 Dihedral : 4.878 25.629 3468 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 3.88 % Allowed : 18.36 % Favored : 77.77 % 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: -2.44 (0.15), residues: 3213 helix: 0.38 (0.20), residues: 711 sheet: -2.01 (0.20), residues: 657 loop : -2.37 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 436 HIS 0.005 0.001 HIS B1041 PHE 0.032 0.002 PHE A 65 TYR 0.024 0.001 TYR B1060 ARG 0.003 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 228 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 TYR cc_start: 0.5096 (t80) cc_final: 0.4696 (t80) REVERT: B 177 MET cc_start: 0.3986 (mmm) cc_final: 0.1579 (tmm) REVERT: B 392 PHE cc_start: 0.6580 (OUTLIER) cc_final: 0.6325 (m-10) REVERT: B 436 TRP cc_start: 0.6351 (OUTLIER) cc_final: 0.5251 (p-90) REVERT: B 514 SER cc_start: 0.7950 (m) cc_final: 0.7722 (p) REVERT: B 946 ASN cc_start: 0.8351 (t0) cc_final: 0.8079 (t0) REVERT: B 987 ASP cc_start: 0.6426 (m-30) cc_final: 0.5996 (m-30) REVERT: B 1043 MET cc_start: 0.7688 (ptp) cc_final: 0.7399 (ptm) REVERT: A 143 VAL cc_start: 0.6691 (OUTLIER) cc_final: 0.6233 (t) REVERT: A 927 ILE cc_start: 0.8588 (tp) cc_final: 0.8252 (tp) REVERT: C 190 ARG cc_start: 0.7074 (mtm180) cc_final: 0.5494 (mtt180) REVERT: C 436 TRP cc_start: 0.6327 (OUTLIER) cc_final: 0.4304 (p-90) REVERT: C 895 MET cc_start: 0.8468 (tpp) cc_final: 0.8123 (tpt) REVERT: C 950 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8045 (tm-30) outliers start: 109 outliers final: 90 residues processed: 303 average time/residue: 0.3036 time to fit residues: 157.5539 Evaluate side-chains 316 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 222 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 1054 VAL Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 749 TYR Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 852 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 191 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 196 optimal weight: 0.8980 chunk 210 optimal weight: 3.9990 chunk 152 optimal weight: 0.0270 chunk 28 optimal weight: 1.9990 chunk 243 optimal weight: 0.0980 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25776 Z= 0.158 Angle : 0.529 10.689 35085 Z= 0.269 Chirality : 0.042 0.161 3972 Planarity : 0.004 0.066 4563 Dihedral : 4.361 23.623 3468 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.17 % Allowed : 19.35 % Favored : 77.48 % 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: -2.04 (0.15), residues: 3213 helix: 0.91 (0.21), residues: 693 sheet: -1.75 (0.21), residues: 645 loop : -2.18 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 436 HIS 0.003 0.000 HIS B 69 PHE 0.030 0.001 PHE A 168 TYR 0.019 0.001 TYR A1060 ARG 0.007 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 268 time to evaluate : 3.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.4412 (mmm) cc_final: 0.1840 (tmm) REVERT: B 355 ARG cc_start: 0.8161 (mmm160) cc_final: 0.7890 (mmm160) REVERT: B 436 TRP cc_start: 0.6356 (OUTLIER) cc_final: 0.5255 (p-90) REVERT: B 465 GLU cc_start: 0.4315 (pm20) cc_final: 0.3853 (pt0) REVERT: B 946 ASN cc_start: 0.8173 (t0) cc_final: 0.7904 (t0) REVERT: B 1022 MET cc_start: 0.8015 (tpp) cc_final: 0.7633 (ttm) REVERT: B 1043 MET cc_start: 0.7484 (ptp) cc_final: 0.7168 (ptm) REVERT: A 143 VAL cc_start: 0.6530 (OUTLIER) cc_final: 0.6072 (t) REVERT: A 655 HIS cc_start: 0.7712 (t70) cc_final: 0.7404 (t70) REVERT: A 749 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7637 (t80) REVERT: A 927 ILE cc_start: 0.8434 (tp) cc_final: 0.8177 (tp) REVERT: A 1022 MET cc_start: 0.8455 (tpp) cc_final: 0.7542 (ttm) REVERT: C 190 ARG cc_start: 0.6980 (mtm180) cc_final: 0.5488 (mtt180) REVERT: C 436 TRP cc_start: 0.6011 (OUTLIER) cc_final: 0.3999 (p-90) REVERT: C 950 GLN cc_start: 0.8425 (tm-30) cc_final: 0.7963 (tm-30) outliers start: 89 outliers final: 74 residues processed: 330 average time/residue: 0.3266 time to fit residues: 182.0024 Evaluate side-chains 315 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 237 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 749 TYR Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 852 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 281 optimal weight: 0.7980 chunk 296 optimal weight: 4.9990 chunk 270 optimal weight: 7.9990 chunk 288 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 226 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 260 optimal weight: 8.9990 chunk 272 optimal weight: 0.9980 chunk 287 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25776 Z= 0.264 Angle : 0.579 12.587 35085 Z= 0.292 Chirality : 0.043 0.174 3972 Planarity : 0.004 0.074 4563 Dihedral : 4.590 24.912 3468 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.49 % Allowed : 19.71 % Favored : 76.81 % 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: -2.12 (0.15), residues: 3213 helix: 0.65 (0.20), residues: 708 sheet: -1.81 (0.20), residues: 678 loop : -2.16 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 353 HIS 0.005 0.001 HIS B 69 PHE 0.024 0.001 PHE A 643 TYR 0.022 0.001 TYR A1060 ARG 0.005 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 230 time to evaluate : 3.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.4526 (mmm) cc_final: 0.1852 (tmm) REVERT: B 392 PHE cc_start: 0.6302 (OUTLIER) cc_final: 0.5674 (m-80) REVERT: B 436 TRP cc_start: 0.6301 (OUTLIER) cc_final: 0.5103 (p-90) REVERT: B 465 GLU cc_start: 0.4508 (pm20) cc_final: 0.4248 (pt0) REVERT: B 946 ASN cc_start: 0.8267 (t0) cc_final: 0.8002 (t0) REVERT: B 987 ASP cc_start: 0.6392 (m-30) cc_final: 0.5957 (m-30) REVERT: B 1043 MET cc_start: 0.7623 (ptp) cc_final: 0.7309 (ptm) REVERT: A 143 VAL cc_start: 0.6469 (OUTLIER) cc_final: 0.6081 (t) REVERT: A 927 ILE cc_start: 0.8507 (tp) cc_final: 0.8201 (tp) REVERT: C 190 ARG cc_start: 0.7018 (mtm180) cc_final: 0.5462 (mtt180) REVERT: C 436 TRP cc_start: 0.6150 (OUTLIER) cc_final: 0.4065 (p-90) REVERT: C 950 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8023 (tm-30) outliers start: 98 outliers final: 89 residues processed: 297 average time/residue: 0.3133 time to fit residues: 157.9491 Evaluate side-chains 316 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 223 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 749 TYR Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 852 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1054 VAL Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 189 optimal weight: 0.9980 chunk 304 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 319 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 254 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 196 optimal weight: 0.9980 chunk 156 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 ASN ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25776 Z= 0.222 Angle : 0.562 12.361 35085 Z= 0.283 Chirality : 0.043 0.163 3972 Planarity : 0.004 0.068 4563 Dihedral : 4.526 24.991 3468 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.38 % Allowed : 19.89 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.15), residues: 3213 helix: 0.83 (0.20), residues: 693 sheet: -1.84 (0.20), residues: 684 loop : -2.09 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 353 HIS 0.004 0.000 HIS B 69 PHE 0.022 0.001 PHE A 643 TYR 0.021 0.001 TYR A1060 ARG 0.004 0.000 ARG B 567 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 235 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.4380 (mmm) cc_final: 0.1850 (tmm) REVERT: B 436 TRP cc_start: 0.6328 (OUTLIER) cc_final: 0.5120 (p-90) REVERT: B 946 ASN cc_start: 0.8187 (t0) cc_final: 0.7937 (t0) REVERT: B 987 ASP cc_start: 0.6404 (m-30) cc_final: 0.5960 (m-30) REVERT: B 1022 MET cc_start: 0.7999 (tpp) cc_final: 0.7620 (ttm) REVERT: B 1043 MET cc_start: 0.7589 (ptp) cc_final: 0.7288 (ptm) REVERT: A 143 VAL cc_start: 0.6452 (OUTLIER) cc_final: 0.6048 (t) REVERT: A 495 TYR cc_start: 0.6194 (m-80) cc_final: 0.5897 (t80) REVERT: A 927 ILE cc_start: 0.8492 (tp) cc_final: 0.8199 (tp) REVERT: A 1022 MET cc_start: 0.8505 (tpp) cc_final: 0.7556 (ttm) REVERT: C 190 ARG cc_start: 0.7019 (mtm180) cc_final: 0.5447 (mtt180) REVERT: C 436 TRP cc_start: 0.6324 (OUTLIER) cc_final: 0.4157 (p-90) REVERT: C 950 GLN cc_start: 0.8432 (tm-30) cc_final: 0.7963 (tm-30) outliers start: 95 outliers final: 88 residues processed: 302 average time/residue: 0.3317 time to fit residues: 172.0812 Evaluate side-chains 316 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 225 time to evaluate : 3.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 852 THR Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain B residue 1054 VAL Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 749 TYR Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 1054 VAL Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 784 THR Chi-restraints excluded: chain C residue 852 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1054 VAL Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1106 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 202 optimal weight: 2.9990 chunk 271 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 255 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 767 GLN ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.166258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.135785 restraints weight = 39404.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.135210 restraints weight = 48822.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.137071 restraints weight = 46368.224| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25776 Z= 0.243 Angle : 0.573 13.808 35085 Z= 0.288 Chirality : 0.043 0.156 3972 Planarity : 0.004 0.066 4563 Dihedral : 4.572 25.085 3468 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.42 % Allowed : 20.10 % Favored : 76.49 % 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: -2.01 (0.15), residues: 3213 helix: 0.82 (0.20), residues: 693 sheet: -1.83 (0.19), residues: 699 loop : -2.05 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 353 HIS 0.004 0.001 HIS B 69 PHE 0.034 0.001 PHE B 643 TYR 0.021 0.001 TYR A1060 ARG 0.005 0.000 ARG B 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4484.55 seconds wall clock time: 83 minutes 27.09 seconds (5007.09 seconds total)