Starting phenix.real_space_refine on Fri Apr 12 14:41:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bnm_12229/04_2024/7bnm_12229.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bnm_12229/04_2024/7bnm_12229.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/7bnm_12229/04_2024/7bnm_12229.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bnm_12229/04_2024/7bnm_12229.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bnm_12229/04_2024/7bnm_12229.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bnm_12229/04_2024/7bnm_12229.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= 0.004 sd= 0.050 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 16521 2.51 5 N 4251 2.21 5 O 5085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 298": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 25971 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8363 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 54, 'TRANS': 1014} Chain breaks: 5 Chain: "B" Number of atoms: 8363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8363 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 54, 'TRANS': 1014} Chain breaks: 5 Chain: "C" Number of atoms: 8363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8363 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 54, 'TRANS': 1014} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "BA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 13.27, per 1000 atoms: 0.51 Number of scatterers: 25971 At special positions: 0 Unit cell: (162.35, 153.85, 178.5, 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 5085 8.00 N 4251 7.00 C 16521 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 Links applied BETA1-4 " NAG 3 1 " - " NAG 3 2 " " NAG 7 1 " - " NAG 7 2 " " NAG 9 1 " - " NAG 9 2 " " NAG D 1 " - " NAG D 2 " " NAG N 1 " - " NAG N 2 " " NAG R 1 " - " NAG R 2 " " NAG T 1 " - " NAG T 2 " " NAG V 1 " - " NAG V 2 " " NAG Y 1 " - " NAG Y 2 " " NAG i 1 " - " NAG i 2 " " NAG m 1 " - " NAG m 2 " " NAG o 1 " - " NAG o 2 " " NAG q 1 " - " NAG q 2 " " NAG t 1 " - " NAG t 2 " " NAGBA 1 " - " NAGBA 2 " NAG-ASN " NAG 3 1 " - " ASN C 717 " " NAG 7 1 " - " ASN C1098 " " NAG 9 1 " - " ASN C1134 " " NAG A1201 " - " ASN A 282 " " NAG A1202 " - " ASN A 122 " " NAG A1203 " - " ASN A 165 " " NAG A1204 " - " ASN A 234 " " NAG A1205 " - " ASN A 331 " " NAG A1206 " - " ASN A 343 " " NAG A1207 " - " ASN A 616 " " NAG A1208 " - " ASN A 657 " " NAG A1209 " - " ASN A 709 " " NAG A1210 " - " ASN A 801 " " NAG A1211 " - " ASN A1074 " " NAG B1201 " - " ASN B 282 " " NAG B1202 " - " ASN B 122 " " NAG B1203 " - " ASN B 165 " " NAG B1204 " - " ASN B 234 " " NAG B1205 " - " ASN B 331 " " NAG B1206 " - " ASN B 343 " " NAG B1207 " - " ASN B 616 " " NAG B1208 " - " ASN B 657 " " NAG B1209 " - " ASN B 709 " " NAG B1210 " - " ASN B 801 " " NAG B1211 " - " ASN B1074 " " NAG C1201 " - " ASN C 282 " " NAG C1202 " - " ASN C 122 " " NAG C1203 " - " ASN C 165 " " NAG C1204 " - " ASN C 234 " " NAG C1205 " - " ASN C 331 " " NAG C1206 " - " ASN C 343 " " NAG C1207 " - " ASN C 616 " " NAG C1208 " - " ASN C 657 " " NAG C1209 " - " ASN C 709 " " NAG C1210 " - " ASN C 801 " " NAG C1211 " - " ASN C1074 " " NAG D 1 " - " ASN A 17 " " NAG N 1 " - " ASN A 717 " " NAG R 1 " - " ASN A1098 " " NAG T 1 " - " ASN A1134 " " NAG V 1 " - " ASN A 61 " " NAG Y 1 " - " ASN B 17 " " NAG i 1 " - " ASN B 717 " " NAG m 1 " - " ASN B1098 " " NAG o 1 " - " ASN B1134 " " NAG q 1 " - " ASN B 61 " " NAG t 1 " - " ASN C 17 " " NAGBA 1 " - " ASN C 61 " Time building additional restraints: 10.37 Conformation dependent library (CDL) restraints added in 5.0 seconds 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6000 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 46 sheets defined 23.3% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.553A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.125A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.693A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.596A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.740A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.712A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.503A pdb=" N GLN A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.064A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.669A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.180A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.728A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.608A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1146 removed outlier: 3.529A pdb=" N ASP A1146 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.022A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.126A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.692A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.596A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.740A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.712A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.503A pdb=" N GLN B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.063A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.670A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.179A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 977 through 982 removed outlier: 3.728A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.608A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1146 removed outlier: 3.529A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.021A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.126A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.693A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.596A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.740A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.712A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.502A pdb=" N GLN C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.064A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.669A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.181A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 removed outlier: 3.728A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.608A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1146 removed outlier: 3.530A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.392A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.275A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.008A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.421A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.003A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.718A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.664A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.704A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.813A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.421A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.003A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.718A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.885A pdb=" N THR A 645 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.558A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.538A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.790A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.136A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 removed outlier: 4.051A pdb=" N ASN A 703 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.570A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.265A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.977A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A1133 " --> pdb=" O ALA A1080 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.392A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.275A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.008A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.421A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.718A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.664A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.704A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.813A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.421A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.002A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.718A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.885A pdb=" N THR B 645 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.558A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 448 through 454 removed outlier: 5.538A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.789A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.136A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.569A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.264A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.977A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B1133 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.392A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.275A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.008A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.422A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.003A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.718A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.664A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.705A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.813A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.422A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.003A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.718A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.885A pdb=" N THR C 645 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.558A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.538A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 551 through 554 removed outlier: 5.790A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.136A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.570A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.264A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.977A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C1133 " --> pdb=" O ALA C1080 " (cutoff:3.500A) 984 hydrogen bonds defined for protein. 2679 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: 11.47 Time building geometry restraints manager: 11.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8173 1.34 - 1.46: 6000 1.46 - 1.58: 12239 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 26556 Sorted by residual: bond pdb=" N ILE A 358 " pdb=" CA ILE A 358 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.19e-02 7.06e+03 1.05e+01 bond pdb=" N ILE B 358 " pdb=" CA ILE B 358 " ideal model delta sigma weight residual 1.458 1.497 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" N ILE C 358 " pdb=" CA ILE C 358 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" N VAL B 620 " pdb=" CA VAL B 620 " ideal model delta sigma weight residual 1.462 1.493 -0.032 1.01e-02 9.80e+03 9.84e+00 bond pdb=" N VAL A 620 " pdb=" CA VAL A 620 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.01e-02 9.80e+03 9.69e+00 ... (remaining 26551 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.91: 598 105.91 - 112.94: 14708 112.94 - 119.98: 8685 119.98 - 127.01: 11926 127.01 - 134.04: 221 Bond angle restraints: 36138 Sorted by residual: angle pdb=" C TYR A 369 " pdb=" CA TYR A 369 " pdb=" CB TYR A 369 " ideal model delta sigma weight residual 109.03 119.06 -10.03 1.62e+00 3.81e-01 3.84e+01 angle pdb=" CA ALA A 363 " pdb=" C ALA A 363 " pdb=" N ASP A 364 " ideal model delta sigma weight residual 115.96 109.52 6.44 1.31e+00 5.83e-01 2.42e+01 angle pdb=" CA TYR A 369 " pdb=" C TYR A 369 " pdb=" O TYR A 369 " ideal model delta sigma weight residual 119.24 113.84 5.40 1.13e+00 7.83e-01 2.28e+01 angle pdb=" O ALA A 363 " pdb=" C ALA A 363 " pdb=" N ASP A 364 " ideal model delta sigma weight residual 122.84 128.49 -5.65 1.20e+00 6.94e-01 2.22e+01 angle pdb=" N SER A 366 " pdb=" CA SER A 366 " pdb=" C SER A 366 " ideal model delta sigma weight residual 113.20 108.43 4.77 1.21e+00 6.83e-01 1.55e+01 ... (remaining 36133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 15431 17.03 - 34.06: 926 34.06 - 51.08: 203 51.08 - 68.11: 51 68.11 - 85.14: 27 Dihedral angle restraints: 16638 sinusoidal: 7308 harmonic: 9330 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -135.14 49.14 1 1.00e+01 1.00e-02 3.32e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -135.14 49.14 1 1.00e+01 1.00e-02 3.32e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -135.12 49.12 1 1.00e+01 1.00e-02 3.32e+01 ... (remaining 16635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3674 0.079 - 0.159: 543 0.159 - 0.238: 36 0.238 - 0.318: 14 0.318 - 0.397: 2 Chirality restraints: 4269 Sorted by residual: chirality pdb=" CA LEU A 368 " pdb=" N LEU A 368 " pdb=" C LEU A 368 " pdb=" CB LEU A 368 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA TYR A 369 " pdb=" N TYR A 369 " pdb=" C TYR A 369 " pdb=" CB TYR A 369 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 4266 not shown) Planarity restraints: 4650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1201 " 0.031 2.00e-02 2.50e+03 2.57e-02 8.23e+00 pdb=" C7 NAG C1201 " -0.008 2.00e-02 2.50e+03 pdb=" C8 NAG C1201 " 0.024 2.00e-02 2.50e+03 pdb=" N2 NAG C1201 " -0.041 2.00e-02 2.50e+03 pdb=" O7 NAG C1201 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1201 " 0.031 2.00e-02 2.50e+03 2.56e-02 8.19e+00 pdb=" C7 NAG A1201 " -0.008 2.00e-02 2.50e+03 pdb=" C8 NAG A1201 " 0.024 2.00e-02 2.50e+03 pdb=" N2 NAG A1201 " -0.041 2.00e-02 2.50e+03 pdb=" O7 NAG A1201 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1201 " -0.031 2.00e-02 2.50e+03 2.53e-02 8.02e+00 pdb=" C7 NAG B1201 " 0.008 2.00e-02 2.50e+03 pdb=" C8 NAG B1201 " -0.023 2.00e-02 2.50e+03 pdb=" N2 NAG B1201 " 0.040 2.00e-02 2.50e+03 pdb=" O7 NAG B1201 " 0.006 2.00e-02 2.50e+03 ... (remaining 4647 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3790 2.75 - 3.29: 24868 3.29 - 3.83: 40682 3.83 - 4.36: 46553 4.36 - 4.90: 80466 Nonbonded interactions: 196359 Sorted by model distance: nonbonded pdb=" OG SER B1097 " pdb=" O HIS B1101 " model vdw 2.213 2.440 nonbonded pdb=" OG SER A1097 " pdb=" O HIS A1101 " model vdw 2.213 2.440 nonbonded pdb=" OG SER C1097 " pdb=" O HIS C1101 " model vdw 2.213 2.440 nonbonded pdb=" O GLN B 804 " pdb=" OG SER B 816 " model vdw 2.221 2.440 nonbonded pdb=" O GLN C 804 " pdb=" OG SER C 816 " model vdw 2.221 2.440 ... (remaining 196354 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 '3' selection = chain '7' selection = chain '9' selection = chain 'BA' selection = chain 'D' selection = chain 'N' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'Y' selection = chain 'i' selection = chain 'm' selection = chain 'o' selection = chain 'q' selection = chain 't' } 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: 9.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 28.070 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 68.830 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 26556 Z= 0.534 Angle : 0.835 10.033 36138 Z= 0.463 Chirality : 0.056 0.397 4269 Planarity : 0.005 0.053 4602 Dihedral : 12.004 85.139 10512 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.61 % Allowed : 1.96 % Favored : 97.43 % Cbeta Deviations : 0.07 % 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 (0.14), residues: 3171 helix: 0.78 (0.21), residues: 603 sheet: -0.88 (0.19), residues: 639 loop : -2.36 (0.12), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 353 HIS 0.007 0.001 HIS C 49 PHE 0.035 0.003 PHE C 906 TYR 0.037 0.002 TYR A 369 ARG 0.005 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 265 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5639 (pmm) cc_final: 0.4052 (pmm) REVERT: A 285 ILE cc_start: 0.8941 (mt) cc_final: 0.8741 (mt) REVERT: A 398 ASP cc_start: 0.8753 (m-30) cc_final: 0.8471 (m-30) REVERT: B 177 MET cc_start: 0.5344 (pmm) cc_final: 0.3386 (pmm) REVERT: B 957 GLN cc_start: 0.8571 (tp40) cc_final: 0.8147 (tp40) REVERT: B 985 ASP cc_start: 0.7496 (p0) cc_final: 0.7039 (p0) REVERT: C 177 MET cc_start: 0.5619 (pmm) cc_final: 0.3814 (pmm) REVERT: C 285 ILE cc_start: 0.9003 (mt) cc_final: 0.8536 (mt) REVERT: C 398 ASP cc_start: 0.8719 (m-30) cc_final: 0.8403 (m-30) outliers start: 17 outliers final: 6 residues processed: 279 average time/residue: 0.4151 time to fit residues: 178.7023 Evaluate side-chains 148 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 142 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain C residue 102 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.0770 chunk 241 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 249 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 151 optimal weight: 20.0000 chunk 185 optimal weight: 1.9990 chunk 288 optimal weight: 0.0000 overall best weight: 0.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 164 ASN A 474 GLN A 563 GLN A 641 ASN A 901 GLN A 978 ASN B 146 HIS B 164 ASN B 474 GLN B 563 GLN B 641 ASN B 901 GLN C 146 HIS C 164 ASN C 474 GLN C 563 GLN C 641 ASN C 901 GLN C 978 ASN C1071 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26556 Z= 0.176 Angle : 0.603 11.176 36138 Z= 0.313 Chirality : 0.044 0.191 4269 Planarity : 0.004 0.043 4602 Dihedral : 7.047 58.165 4777 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.89 % Allowed : 7.00 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.14), residues: 3171 helix: 1.68 (0.21), residues: 633 sheet: -0.58 (0.20), residues: 657 loop : -1.92 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C1102 HIS 0.005 0.001 HIS A 66 PHE 0.019 0.001 PHE C 400 TYR 0.024 0.001 TYR A1138 ARG 0.009 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 178 time to evaluate : 3.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5450 (pmm) cc_final: 0.3908 (pmm) REVERT: A 226 LEU cc_start: 0.7682 (tp) cc_final: 0.7469 (tt) REVERT: A 780 GLU cc_start: 0.8688 (tp30) cc_final: 0.8430 (tp30) REVERT: A 957 GLN cc_start: 0.8590 (tp40) cc_final: 0.8195 (tp40) REVERT: B 177 MET cc_start: 0.5158 (pmm) cc_final: 0.3310 (pmm) REVERT: B 456 PHE cc_start: 0.9241 (m-80) cc_final: 0.8934 (t80) REVERT: B 780 GLU cc_start: 0.8526 (tp30) cc_final: 0.7986 (tp30) REVERT: B 957 GLN cc_start: 0.8490 (tp40) cc_final: 0.8093 (tp40) REVERT: C 177 MET cc_start: 0.5411 (pmm) cc_final: 0.3705 (pmm) REVERT: C 456 PHE cc_start: 0.9256 (m-80) cc_final: 0.9009 (t80) REVERT: C 780 GLU cc_start: 0.8639 (tp30) cc_final: 0.8253 (tp30) REVERT: C 957 GLN cc_start: 0.8561 (tp40) cc_final: 0.8333 (tp40) outliers start: 25 outliers final: 11 residues processed: 199 average time/residue: 0.3657 time to fit residues: 119.6998 Evaluate side-chains 135 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 978 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 289 optimal weight: 2.9990 chunk 312 optimal weight: 1.9990 chunk 257 optimal weight: 6.9990 chunk 286 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 232 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 644 GLN A 965 GLN ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 965 GLN B 978 ASN C 474 GLN C 644 GLN C 901 GLN C 978 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26556 Z= 0.263 Angle : 0.593 12.711 36138 Z= 0.307 Chirality : 0.044 0.179 4269 Planarity : 0.004 0.050 4602 Dihedral : 6.707 57.410 4773 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.96 % Allowed : 8.67 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.14), residues: 3171 helix: 1.78 (0.21), residues: 630 sheet: -0.52 (0.20), residues: 660 loop : -1.88 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 353 HIS 0.004 0.001 HIS A1088 PHE 0.020 0.001 PHE A 135 TYR 0.021 0.001 TYR B1067 ARG 0.003 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 3.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5519 (pmm) cc_final: 0.3884 (pmm) REVERT: A 226 LEU cc_start: 0.7676 (tp) cc_final: 0.7457 (tt) REVERT: A 780 GLU cc_start: 0.8721 (tp30) cc_final: 0.8488 (tp30) REVERT: A 957 GLN cc_start: 0.8656 (tp40) cc_final: 0.8249 (tp40) REVERT: A 985 ASP cc_start: 0.8098 (t0) cc_final: 0.7746 (t0) REVERT: B 177 MET cc_start: 0.5146 (pmm) cc_final: 0.3193 (pmm) REVERT: B 456 PHE cc_start: 0.9225 (m-80) cc_final: 0.8931 (t80) REVERT: B 780 GLU cc_start: 0.8624 (tp30) cc_final: 0.8040 (tp30) REVERT: B 957 GLN cc_start: 0.8568 (tp40) cc_final: 0.8179 (tp40) REVERT: B 985 ASP cc_start: 0.8320 (t0) cc_final: 0.7885 (t0) REVERT: C 177 MET cc_start: 0.5403 (pmm) cc_final: 0.3573 (pmm) REVERT: C 456 PHE cc_start: 0.9257 (m-80) cc_final: 0.9010 (t80) REVERT: C 780 GLU cc_start: 0.8693 (tp30) cc_final: 0.8319 (tp30) REVERT: C 957 GLN cc_start: 0.8593 (tp40) cc_final: 0.8327 (tp40) outliers start: 27 outliers final: 21 residues processed: 153 average time/residue: 0.3724 time to fit residues: 95.0567 Evaluate side-chains 140 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 981 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 290 optimal weight: 3.9990 chunk 307 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 275 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN B 613 GLN B1071 GLN C 613 GLN C 901 GLN C 965 GLN C 978 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 26556 Z= 0.329 Angle : 0.615 11.036 36138 Z= 0.315 Chirality : 0.044 0.233 4269 Planarity : 0.004 0.049 4602 Dihedral : 6.542 56.329 4773 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.61 % Allowed : 9.85 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.15), residues: 3171 helix: 1.73 (0.21), residues: 630 sheet: -0.58 (0.19), residues: 672 loop : -1.81 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 353 HIS 0.005 0.001 HIS C 49 PHE 0.018 0.002 PHE C 135 TYR 0.022 0.002 TYR A1067 ARG 0.003 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 118 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5583 (pmm) cc_final: 0.3942 (pmm) REVERT: A 226 LEU cc_start: 0.7719 (tp) cc_final: 0.7470 (tt) REVERT: A 248 TYR cc_start: 0.7954 (m-80) cc_final: 0.7752 (m-80) REVERT: A 780 GLU cc_start: 0.8732 (tp30) cc_final: 0.8462 (tp30) REVERT: A 957 GLN cc_start: 0.8683 (tp40) cc_final: 0.8294 (tp40) REVERT: A 985 ASP cc_start: 0.7801 (t0) cc_final: 0.7390 (t0) REVERT: B 177 MET cc_start: 0.5251 (pmm) cc_final: 0.5023 (pmm) REVERT: B 456 PHE cc_start: 0.9213 (m-80) cc_final: 0.8939 (t80) REVERT: B 780 GLU cc_start: 0.8645 (tp30) cc_final: 0.8034 (tp30) REVERT: B 957 GLN cc_start: 0.8596 (tp40) cc_final: 0.8236 (tp40) REVERT: B 985 ASP cc_start: 0.7874 (t0) cc_final: 0.7364 (t0) REVERT: C 177 MET cc_start: 0.5540 (pmm) cc_final: 0.3687 (pmm) REVERT: C 456 PHE cc_start: 0.9234 (m-80) cc_final: 0.8993 (t80) REVERT: C 780 GLU cc_start: 0.8721 (tp30) cc_final: 0.8361 (tp30) REVERT: C 957 GLN cc_start: 0.8593 (tp40) cc_final: 0.8332 (tp40) REVERT: C 985 ASP cc_start: 0.8074 (t0) cc_final: 0.7694 (t0) outliers start: 45 outliers final: 35 residues processed: 155 average time/residue: 0.3607 time to fit residues: 93.1224 Evaluate side-chains 153 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 118 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1027 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 228 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 262 optimal weight: 3.9990 chunk 212 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 156 optimal weight: 7.9990 chunk 275 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN C 901 GLN C 926 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 26556 Z= 0.445 Angle : 0.680 9.401 36138 Z= 0.350 Chirality : 0.046 0.226 4269 Planarity : 0.005 0.048 4602 Dihedral : 6.673 56.842 4773 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.25 % Allowed : 10.96 % Favored : 86.80 % 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: -1.37 (0.14), residues: 3171 helix: 1.45 (0.21), residues: 630 sheet: -0.72 (0.19), residues: 723 loop : -1.94 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 353 HIS 0.007 0.001 HIS B 49 PHE 0.018 0.002 PHE A 906 TYR 0.025 0.002 TYR A1067 ARG 0.003 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 119 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5641 (pmm) cc_final: 0.4011 (pmm) REVERT: A 226 LEU cc_start: 0.7787 (tp) cc_final: 0.7545 (tt) REVERT: A 985 ASP cc_start: 0.7899 (t0) cc_final: 0.7451 (t0) REVERT: B 177 MET cc_start: 0.5363 (pmm) cc_final: 0.5136 (pmm) REVERT: B 456 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8918 (t80) REVERT: B 780 GLU cc_start: 0.8680 (tp30) cc_final: 0.8091 (tp30) REVERT: B 957 GLN cc_start: 0.8662 (tp40) cc_final: 0.8357 (tp40) REVERT: B 985 ASP cc_start: 0.7807 (t0) cc_final: 0.7327 (t0) REVERT: C 177 MET cc_start: 0.5622 (pmm) cc_final: 0.3840 (pmm) REVERT: C 456 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.9009 (t80) REVERT: C 985 ASP cc_start: 0.8005 (t0) cc_final: 0.7560 (t0) REVERT: C 1029 MET cc_start: 0.9330 (tpp) cc_final: 0.9060 (tpp) outliers start: 63 outliers final: 46 residues processed: 168 average time/residue: 0.3452 time to fit residues: 97.7127 Evaluate side-chains 161 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 113 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 1.9990 chunk 276 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 180 optimal weight: 0.0470 chunk 75 optimal weight: 0.5980 chunk 307 optimal weight: 0.7980 chunk 255 optimal weight: 10.0000 chunk 142 optimal weight: 0.0010 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 overall best weight: 0.4284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 978 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26556 Z= 0.163 Angle : 0.565 11.356 36138 Z= 0.287 Chirality : 0.043 0.189 4269 Planarity : 0.004 0.048 4602 Dihedral : 6.192 56.266 4773 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.03 % Allowed : 12.53 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 3171 helix: 1.98 (0.22), residues: 630 sheet: -0.37 (0.19), residues: 690 loop : -1.74 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 104 HIS 0.004 0.001 HIS C1088 PHE 0.014 0.001 PHE C 400 TYR 0.023 0.001 TYR B1138 ARG 0.004 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5604 (pmm) cc_final: 0.4080 (pmm) REVERT: A 226 LEU cc_start: 0.7494 (tp) cc_final: 0.7214 (tt) REVERT: A 780 GLU cc_start: 0.8677 (tp30) cc_final: 0.8416 (tp30) REVERT: A 957 GLN cc_start: 0.8603 (tp40) cc_final: 0.8238 (tp40) REVERT: A 985 ASP cc_start: 0.7836 (t0) cc_final: 0.7442 (t0) REVERT: B 177 MET cc_start: 0.5294 (pmm) cc_final: 0.3392 (pmm) REVERT: B 456 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8880 (t80) REVERT: B 780 GLU cc_start: 0.8681 (tp30) cc_final: 0.8117 (tp30) REVERT: B 957 GLN cc_start: 0.8513 (tp40) cc_final: 0.8251 (tp40) REVERT: B 985 ASP cc_start: 0.7771 (t0) cc_final: 0.7346 (t0) REVERT: C 177 MET cc_start: 0.5582 (pmm) cc_final: 0.3939 (pmm) REVERT: C 456 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.9005 (t80) REVERT: C 780 GLU cc_start: 0.8665 (tp30) cc_final: 0.8310 (tp30) REVERT: C 957 GLN cc_start: 0.8503 (tp40) cc_final: 0.8296 (tp40) REVERT: C 985 ASP cc_start: 0.7860 (t0) cc_final: 0.7414 (t0) outliers start: 29 outliers final: 21 residues processed: 151 average time/residue: 0.3749 time to fit residues: 93.5422 Evaluate side-chains 143 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 259 optimal weight: 0.2980 chunk 171 optimal weight: 1.9990 chunk 306 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26556 Z= 0.275 Angle : 0.588 11.363 36138 Z= 0.300 Chirality : 0.043 0.195 4269 Planarity : 0.004 0.048 4602 Dihedral : 6.191 56.120 4773 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.57 % Allowed : 12.99 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.15), residues: 3171 helix: 2.12 (0.22), residues: 612 sheet: -0.35 (0.19), residues: 684 loop : -1.70 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 353 HIS 0.004 0.001 HIS B 49 PHE 0.018 0.001 PHE B 392 TYR 0.022 0.001 TYR A1067 ARG 0.006 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 122 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5542 (pmm) cc_final: 0.3949 (pmm) REVERT: A 226 LEU cc_start: 0.7566 (tp) cc_final: 0.7282 (tt) REVERT: A 780 GLU cc_start: 0.8724 (tp30) cc_final: 0.8444 (tp30) REVERT: A 957 GLN cc_start: 0.8669 (tp40) cc_final: 0.8293 (tp40) REVERT: A 985 ASP cc_start: 0.7760 (t0) cc_final: 0.7400 (t0) REVERT: B 177 MET cc_start: 0.5279 (pmm) cc_final: 0.5048 (pmm) REVERT: B 456 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8882 (t80) REVERT: B 780 GLU cc_start: 0.8718 (tp30) cc_final: 0.8173 (tp30) REVERT: B 957 GLN cc_start: 0.8564 (tp40) cc_final: 0.8313 (tp40) REVERT: B 985 ASP cc_start: 0.7749 (t0) cc_final: 0.7361 (t0) REVERT: C 177 MET cc_start: 0.5630 (pmm) cc_final: 0.3956 (pmm) REVERT: C 456 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8973 (t80) REVERT: C 957 GLN cc_start: 0.8568 (tp40) cc_final: 0.8335 (tp40) REVERT: C 985 ASP cc_start: 0.7820 (t0) cc_final: 0.7367 (t0) outliers start: 44 outliers final: 31 residues processed: 157 average time/residue: 0.3671 time to fit residues: 96.0095 Evaluate side-chains 148 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 3.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 0.7980 chunk 122 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 194 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 151 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 240 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26556 Z= 0.205 Angle : 0.566 11.024 36138 Z= 0.289 Chirality : 0.043 0.227 4269 Planarity : 0.004 0.050 4602 Dihedral : 6.031 55.695 4773 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.46 % Allowed : 13.35 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.15), residues: 3171 helix: 2.24 (0.22), residues: 612 sheet: -0.27 (0.20), residues: 681 loop : -1.64 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 353 HIS 0.003 0.001 HIS C1088 PHE 0.020 0.001 PHE B 392 TYR 0.021 0.001 TYR A1067 ARG 0.004 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 122 time to evaluate : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5575 (pmm) cc_final: 0.4022 (pmm) REVERT: A 226 LEU cc_start: 0.7459 (tp) cc_final: 0.7173 (tt) REVERT: A 780 GLU cc_start: 0.8702 (tp30) cc_final: 0.8433 (tp30) REVERT: A 957 GLN cc_start: 0.8613 (tp40) cc_final: 0.8214 (tp40) REVERT: A 985 ASP cc_start: 0.7704 (t0) cc_final: 0.7318 (t0) REVERT: B 177 MET cc_start: 0.5363 (pmm) cc_final: 0.3372 (pmm) REVERT: B 456 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.8879 (t80) REVERT: B 780 GLU cc_start: 0.8678 (tp30) cc_final: 0.8160 (tp30) REVERT: B 957 GLN cc_start: 0.8524 (tp40) cc_final: 0.8283 (tp40) REVERT: B 985 ASP cc_start: 0.7630 (t0) cc_final: 0.7278 (t0) REVERT: C 177 MET cc_start: 0.5592 (pmm) cc_final: 0.3928 (pmm) REVERT: C 421 TYR cc_start: 0.8814 (m-10) cc_final: 0.8324 (m-10) REVERT: C 456 PHE cc_start: 0.9217 (m-80) cc_final: 0.9006 (t80) REVERT: C 780 GLU cc_start: 0.8682 (tp30) cc_final: 0.8307 (tp30) REVERT: C 957 GLN cc_start: 0.8502 (tp40) cc_final: 0.8291 (tp40) REVERT: C 985 ASP cc_start: 0.7771 (t0) cc_final: 0.7345 (t0) outliers start: 41 outliers final: 29 residues processed: 153 average time/residue: 0.3690 time to fit residues: 94.3034 Evaluate side-chains 148 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 118 time to evaluate : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.5980 chunk 293 optimal weight: 0.7980 chunk 267 optimal weight: 6.9990 chunk 285 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 chunk 87 optimal weight: 0.5980 chunk 258 optimal weight: 30.0000 chunk 270 optimal weight: 0.0060 chunk 284 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 901 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 26556 Z= 0.165 Angle : 0.550 11.195 36138 Z= 0.276 Chirality : 0.042 0.183 4269 Planarity : 0.004 0.051 4602 Dihedral : 5.781 55.516 4773 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.18 % Allowed : 13.74 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.15), residues: 3171 helix: 2.15 (0.23), residues: 633 sheet: -0.23 (0.19), residues: 696 loop : -1.62 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 258 HIS 0.003 0.001 HIS C 66 PHE 0.014 0.001 PHE C 400 TYR 0.020 0.001 TYR A1067 ARG 0.004 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 132 time to evaluate : 3.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5508 (pmm) cc_final: 0.3912 (pmm) REVERT: A 421 TYR cc_start: 0.8945 (m-10) cc_final: 0.8546 (m-10) REVERT: A 780 GLU cc_start: 0.8655 (tp30) cc_final: 0.8433 (tp30) REVERT: A 957 GLN cc_start: 0.8579 (tp40) cc_final: 0.8190 (tp40) REVERT: A 1039 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.7804 (ptm-80) REVERT: B 177 MET cc_start: 0.5479 (pmm) cc_final: 0.3561 (pmm) REVERT: B 389 ASP cc_start: 0.8744 (t0) cc_final: 0.8503 (p0) REVERT: B 421 TYR cc_start: 0.8884 (m-10) cc_final: 0.8447 (m-10) REVERT: B 456 PHE cc_start: 0.9180 (m-80) cc_final: 0.8918 (t80) REVERT: B 780 GLU cc_start: 0.8655 (tp30) cc_final: 0.8187 (tp30) REVERT: B 957 GLN cc_start: 0.8502 (tp40) cc_final: 0.8276 (tp40) REVERT: B 978 ASN cc_start: 0.7757 (m110) cc_final: 0.7471 (m-40) REVERT: B 1029 MET cc_start: 0.9275 (tpp) cc_final: 0.9050 (tpp) REVERT: C 177 MET cc_start: 0.5501 (pmm) cc_final: 0.3844 (pmm) REVERT: C 421 TYR cc_start: 0.8849 (m-10) cc_final: 0.8393 (m-10) REVERT: C 456 PHE cc_start: 0.9233 (m-80) cc_final: 0.9025 (t80) REVERT: C 780 GLU cc_start: 0.8647 (tp30) cc_final: 0.8289 (tp30) REVERT: C 985 ASP cc_start: 0.7651 (t0) cc_final: 0.7242 (t0) outliers start: 33 outliers final: 30 residues processed: 159 average time/residue: 0.4043 time to fit residues: 105.3605 Evaluate side-chains 152 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 992 GLN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 1.9990 chunk 302 optimal weight: 0.7980 chunk 184 optimal weight: 0.5980 chunk 143 optimal weight: 0.9990 chunk 209 optimal weight: 0.9980 chunk 316 optimal weight: 4.9990 chunk 291 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B1010 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26556 Z= 0.199 Angle : 0.562 10.131 36138 Z= 0.282 Chirality : 0.042 0.192 4269 Planarity : 0.004 0.051 4602 Dihedral : 5.740 54.965 4773 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.14 % Allowed : 13.95 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.15), residues: 3171 helix: 2.53 (0.23), residues: 591 sheet: -0.23 (0.20), residues: 666 loop : -1.52 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 258 HIS 0.003 0.001 HIS C 66 PHE 0.020 0.001 PHE B 392 TYR 0.020 0.001 TYR A1067 ARG 0.005 0.000 ARG A 765 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 125 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5510 (pmm) cc_final: 0.3803 (pmm) REVERT: A 226 LEU cc_start: 0.7455 (tp) cc_final: 0.7159 (tt) REVERT: A 421 TYR cc_start: 0.8943 (m-10) cc_final: 0.8567 (m-10) REVERT: A 780 GLU cc_start: 0.8706 (tp30) cc_final: 0.8474 (tp30) REVERT: A 957 GLN cc_start: 0.8623 (tp40) cc_final: 0.8246 (tp40) REVERT: A 1039 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.7751 (ptm-80) REVERT: B 177 MET cc_start: 0.5566 (pmm) cc_final: 0.5231 (pmm) REVERT: B 389 ASP cc_start: 0.8716 (t0) cc_final: 0.8482 (p0) REVERT: B 390 LEU cc_start: 0.8800 (tp) cc_final: 0.8204 (tp) REVERT: B 421 TYR cc_start: 0.8896 (m-10) cc_final: 0.8455 (m-10) REVERT: B 456 PHE cc_start: 0.9192 (m-80) cc_final: 0.8932 (t80) REVERT: B 780 GLU cc_start: 0.8674 (tp30) cc_final: 0.8215 (tp30) REVERT: B 957 GLN cc_start: 0.8521 (tp40) cc_final: 0.8275 (tp40) REVERT: B 978 ASN cc_start: 0.7758 (m110) cc_final: 0.7457 (m-40) REVERT: B 1029 MET cc_start: 0.9297 (tpp) cc_final: 0.9078 (tpp) REVERT: C 177 MET cc_start: 0.5663 (pmm) cc_final: 0.4012 (pmm) REVERT: C 265 TYR cc_start: 0.8400 (p90) cc_final: 0.8183 (p90) REVERT: C 421 TYR cc_start: 0.8852 (m-10) cc_final: 0.8399 (m-10) REVERT: C 456 PHE cc_start: 0.9225 (m-80) cc_final: 0.9021 (t80) REVERT: C 957 GLN cc_start: 0.8226 (tp40) cc_final: 0.7824 (tp40) outliers start: 32 outliers final: 29 residues processed: 151 average time/residue: 0.4030 time to fit residues: 99.4072 Evaluate side-chains 151 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 1.9990 chunk 268 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 252 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 259 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 30.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.109355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.070026 restraints weight = 76256.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.072662 restraints weight = 37710.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.074323 restraints weight = 24544.092| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 26556 Z= 0.326 Angle : 0.620 10.261 36138 Z= 0.314 Chirality : 0.044 0.199 4269 Planarity : 0.004 0.051 4602 Dihedral : 5.920 55.360 4769 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.21 % Allowed : 14.06 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.15), residues: 3171 helix: 2.20 (0.22), residues: 591 sheet: -0.27 (0.19), residues: 684 loop : -1.65 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 104 HIS 0.004 0.001 HIS B 49 PHE 0.021 0.002 PHE B 392 TYR 0.022 0.001 TYR A1067 ARG 0.005 0.000 ARG A 765 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4845.47 seconds wall clock time: 90 minutes 36.07 seconds (5436.07 seconds total)