Starting phenix.real_space_refine on Mon Sep 23 21:50:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu3_33457/09_2024/7xu3_33457_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu3_33457/09_2024/7xu3_33457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu3_33457/09_2024/7xu3_33457.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu3_33457/09_2024/7xu3_33457.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu3_33457/09_2024/7xu3_33457_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xu3_33457/09_2024/7xu3_33457_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 114 5.16 5 C 15450 2.51 5 N 3951 2.21 5 O 4704 1.98 5 H 22838 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 153 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 47057 Number of models: 1 Model: "" Number of chains: 15 Chain: "B" Number of atoms: 15433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 15433 Classifications: {'peptide': 1002} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 47, 'TRANS': 954} Chain breaks: 9 Chain: "A" Number of atoms: 15433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 15433 Classifications: {'peptide': 1002} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 47, 'TRANS': 954} Chain breaks: 9 Chain: "C" Number of atoms: 15432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 15432 Classifications: {'peptide': 1002} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 47, 'TRANS': 954} Chain breaks: 9 Chain: "K" 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: "P" 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: 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: "c" 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: "f" 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: "s" 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: "B" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 169 Unusual residues: {'BLA': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 169 Unusual residues: {'BLA': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 169 Unusual residues: {'BLA': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 17.21, per 1000 atoms: 0.37 Number of scatterers: 47057 At special positions: 0 Unit cell: (131.564, 140.052, 164.455, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 O 4704 8.00 N 3951 7.00 C 15450 6.00 H 22838 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 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=2.06 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=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 427 " - pdb=" SG CYS C 987 " distance=2.08 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=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 987 " - pdb=" SG CYS A 427 " distance=2.01 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.06 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=2.05 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=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 987 " - pdb=" SG CYS C 427 " distance=2.01 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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=2.06 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=2.06 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=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=3, symmetry=0 Links applied BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG P 1 " - " NAG P 2 " " NAG a 1 " - " NAG a 2 " " NAG c 1 " - " NAG c 2 " " NAG f 1 " - " NAG f 2 " " NAG q 1 " - " NAG q 2 " " NAG s 1 " - " NAG s 2 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A1402 " - " ASN A 61 " " NAG A1403 " - " ASN A 282 " " NAG A1404 " - " ASN A 331 " " NAG A1405 " - " ASN A 343 " " NAG A1406 " - " ASN A 616 " " NAG A1407 " - " ASN A 657 " " NAG A1408 " - " ASN A 709 " " NAG A1409 " - " ASN A1074 " " NAG A1410 " - " ASN A1134 " " NAG B1402 " - " ASN B 61 " " NAG B1403 " - " ASN B 282 " " NAG B1404 " - " ASN B 331 " " NAG B1405 " - " ASN B 343 " " NAG B1406 " - " ASN B 616 " " NAG B1407 " - " ASN B 657 " " NAG B1408 " - " ASN B 709 " " NAG B1409 " - " ASN B1074 " " NAG B1410 " - " ASN B1134 " " NAG C1402 " - " ASN C 61 " " NAG C1403 " - " ASN C 282 " " NAG C1404 " - " ASN C 331 " " NAG C1405 " - " ASN C 343 " " NAG C1406 " - " ASN C 616 " " NAG C1407 " - " ASN C 657 " " NAG C1408 " - " ASN C 709 " " NAG C1409 " - " ASN C1074 " " NAG C1410 " - " ASN C1134 " " NAG K 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG a 1 " - " ASN A 717 " " NAG c 1 " - " ASN A 801 " " NAG f 1 " - " ASN A1098 " " NAG q 1 " - " ASN C 717 " " NAG s 1 " - " ASN C 801 " " NAG v 1 " - " ASN C1098 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.08 Conformation dependent library (CDL) restraints added in 2.9 seconds 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5628 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 44 sheets defined 25.0% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 342 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.673A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 5.040A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.882A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.546A 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 891 removed outlier: 3.790A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.687A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.085A pdb=" N VAL B 991 " --> pdb=" O CYS B 987 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.673A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 5.040A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.882A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.547A 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 891 removed outlier: 3.791A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.686A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.086A pdb=" N VAL A 991 " --> pdb=" O CYS A 987 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.673A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 5.039A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.882A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.545A 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 891 removed outlier: 3.791A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.686A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.086A pdb=" N VAL C 991 " --> pdb=" O CYS C 987 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 30 removed outlier: 8.217A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.808A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.801A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 168 through 171 Processing sheet with id=AA5, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.075A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.381A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.990A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.698A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.889A pdb=" N PHE B 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.259A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.553A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.127A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.385A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.800A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.640A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 29 through 30 removed outlier: 8.217A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.802A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 168 through 171 Processing sheet with id=AC2, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.076A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.381A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.990A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.698A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.884A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.260A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AD1, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.553A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.127A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.384A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.640A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 29 through 30 removed outlier: 8.217A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.801A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 168 through 171 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.076A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.381A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.991A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.698A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.259A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.553A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.128A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.384A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.641A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 995 hydrogen bonds defined for protein. 2670 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: 17.64 Time building geometry restraints manager: 11.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 22833 1.05 - 1.26: 3926 1.26 - 1.48: 10390 1.48 - 1.70: 10301 1.70 - 1.91: 141 Bond restraints: 47591 Sorted by residual: bond pdb=" NB BLA B1401 " pdb=" C4B BLA B1401 " ideal model delta sigma weight residual 1.371 1.534 -0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" C1C BLA C1401 " pdb=" NC BLA C1401 " ideal model delta sigma weight residual 1.368 1.531 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" C1C BLA A1401 " pdb=" NC BLA A1401 " ideal model delta sigma weight residual 1.368 1.530 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" NB BLA A1401 " pdb=" C4B BLA A1401 " ideal model delta sigma weight residual 1.371 1.533 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" NB BLA C1401 " pdb=" C4B BLA C1401 " ideal model delta sigma weight residual 1.371 1.533 -0.162 2.00e-02 2.50e+03 6.56e+01 ... (remaining 47586 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.90: 85304 7.90 - 15.79: 56 15.79 - 23.69: 12 23.69 - 31.58: 1 31.58 - 39.48: 3 Bond angle restraints: 85376 Sorted by residual: angle pdb=" CG ASN B 907 " pdb=" ND2 ASN B 907 " pdb="HD22 ASN B 907 " ideal model delta sigma weight residual 120.00 159.48 -39.48 3.00e+00 1.11e-01 1.73e+02 angle pdb="HD21 ASN B 907 " pdb=" ND2 ASN B 907 " pdb="HD22 ASN B 907 " ideal model delta sigma weight residual 120.00 82.10 37.90 3.00e+00 1.11e-01 1.60e+02 angle pdb=" CG ASN B 907 " pdb=" ND2 ASN B 907 " pdb="HD21 ASN B 907 " ideal model delta sigma weight residual 120.00 87.75 32.25 3.00e+00 1.11e-01 1.16e+02 angle pdb=" CG PHE B 86 " pdb=" CB PHE B 86 " pdb=" HB3 PHE B 86 " ideal model delta sigma weight residual 108.00 83.54 24.46 3.00e+00 1.11e-01 6.65e+01 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 132.39 -17.99 2.30e+00 1.89e-01 6.12e+01 ... (remaining 85371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 21084 17.86 - 35.71: 1806 35.71 - 53.57: 432 53.57 - 71.43: 160 71.43 - 89.28: 19 Dihedral angle restraints: 23501 sinusoidal: 12977 harmonic: 10524 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -22.06 -63.94 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -22.08 -63.92 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -22.09 -63.91 1 1.00e+01 1.00e-02 5.38e+01 ... (remaining 23498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3539 0.083 - 0.167: 373 0.167 - 0.250: 21 0.250 - 0.334: 3 0.334 - 0.417: 6 Chirality restraints: 3942 Sorted by residual: chirality pdb=" C1 NAG C1404 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1404 " pdb=" O5 NAG C1404 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" C1 NAG B1404 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1404 " pdb=" O5 NAG B1404 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" C1 NAG A1404 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1404 " pdb=" O5 NAG A1404 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 3939 not shown) Planarity restraints: 7158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA A1401 " -0.059 2.00e-02 2.50e+03 7.32e-02 1.34e+02 pdb=" C1A BLA A1401 " 0.166 2.00e-02 2.50e+03 pdb=" C1D BLA A1401 " -0.009 2.00e-02 2.50e+03 pdb=" C2D BLA A1401 " 0.013 2.00e-02 2.50e+03 pdb=" C3D BLA A1401 " -0.017 2.00e-02 2.50e+03 pdb=" C4D BLA A1401 " -0.062 2.00e-02 2.50e+03 pdb=" CAD BLA A1401 " 0.008 2.00e-02 2.50e+03 pdb=" CHA BLA A1401 " -0.111 2.00e-02 2.50e+03 pdb=" CHD BLA A1401 " -0.005 2.00e-02 2.50e+03 pdb=" CMD BLA A1401 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA B1401 " -0.059 2.00e-02 2.50e+03 7.32e-02 1.34e+02 pdb=" C1A BLA B1401 " 0.166 2.00e-02 2.50e+03 pdb=" C1D BLA B1401 " -0.009 2.00e-02 2.50e+03 pdb=" C2D BLA B1401 " 0.014 2.00e-02 2.50e+03 pdb=" C3D BLA B1401 " -0.018 2.00e-02 2.50e+03 pdb=" C4D BLA B1401 " -0.062 2.00e-02 2.50e+03 pdb=" CAD BLA B1401 " 0.008 2.00e-02 2.50e+03 pdb=" CHA BLA B1401 " -0.110 2.00e-02 2.50e+03 pdb=" CHD BLA B1401 " -0.005 2.00e-02 2.50e+03 pdb=" CMD BLA B1401 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA C1401 " -0.059 2.00e-02 2.50e+03 7.31e-02 1.33e+02 pdb=" C1A BLA C1401 " 0.166 2.00e-02 2.50e+03 pdb=" C1D BLA C1401 " -0.009 2.00e-02 2.50e+03 pdb=" C2D BLA C1401 " 0.014 2.00e-02 2.50e+03 pdb=" C3D BLA C1401 " -0.018 2.00e-02 2.50e+03 pdb=" C4D BLA C1401 " -0.061 2.00e-02 2.50e+03 pdb=" CAD BLA C1401 " 0.008 2.00e-02 2.50e+03 pdb=" CHA BLA C1401 " -0.110 2.00e-02 2.50e+03 pdb=" CHD BLA C1401 " -0.005 2.00e-02 2.50e+03 pdb=" CMD BLA C1401 " 0.076 2.00e-02 2.50e+03 ... (remaining 7155 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 2621 2.19 - 2.79: 95366 2.79 - 3.40: 124401 3.40 - 4.00: 172188 4.00 - 4.60: 260687 Nonbonded interactions: 655263 Sorted by model distance: nonbonded pdb="HH12 ARG A 403 " pdb=" OD1 ASP A 405 " model vdw 1.591 2.450 nonbonded pdb="HH12 ARG C 403 " pdb=" OD1 ASP C 405 " model vdw 1.622 2.450 nonbonded pdb="HH12 ARG B 403 " pdb=" OD1 ASP B 405 " model vdw 1.622 2.450 nonbonded pdb=" O THR B 124 " pdb=" H PHE B 175 " model vdw 1.640 2.450 nonbonded pdb=" O THR A 124 " pdb=" H PHE A 175 " model vdw 1.640 2.450 ... (remaining 655258 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 426 or (resid 427 and (name N or name CA or nam \ e C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3 \ )) or resid 428 through 1140 or resid 1401 through 1410)) selection = (chain 'B' and (resid 27 through 986 or (resid 987 and (name N or name CA or nam \ e C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3 \ )) or resid 988 through 1140 or resid 1401 through 1410)) selection = chain 'C' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'P' selection = chain 'a' selection = chain 'c' selection = chain 'f' selection = chain 'q' selection = chain 's' selection = chain 'v' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 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: 0.620 Extract box with map and model: 1.260 Check model and map are aligned: 0.260 Set scattering table: 0.340 Process input model: 77.210 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.009 0.163 24753 Z= 0.573 Angle : 0.884 17.995 33675 Z= 0.446 Chirality : 0.052 0.417 3942 Planarity : 0.005 0.073 4287 Dihedral : 13.993 89.283 9555 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.34 % Allowed : 0.46 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.15), residues: 2946 helix: -0.25 (0.20), residues: 639 sheet: -0.68 (0.17), residues: 732 loop : -1.36 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 886 HIS 0.004 0.001 HIS A1048 PHE 0.064 0.002 PHE A 86 TYR 0.056 0.002 TYR B 756 ARG 0.031 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 182 time to evaluate : 2.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 505 TYR cc_start: 0.6571 (t80) cc_final: 0.6330 (t80) REVERT: B 574 ASP cc_start: 0.8172 (t70) cc_final: 0.7880 (t0) REVERT: A 360 ASN cc_start: 0.8536 (m-40) cc_final: 0.8194 (p0) REVERT: A 574 ASP cc_start: 0.8129 (t70) cc_final: 0.7807 (t0) REVERT: A 646 ARG cc_start: 0.7980 (tpt90) cc_final: 0.7779 (mmm160) REVERT: C 360 ASN cc_start: 0.8615 (m-40) cc_final: 0.8157 (p0) REVERT: C 574 ASP cc_start: 0.8058 (t70) cc_final: 0.7730 (t0) outliers start: 9 outliers final: 5 residues processed: 187 average time/residue: 2.7155 time to fit residues: 578.2587 Evaluate side-chains 140 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain C residue 403 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 0.0010 chunk 227 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 153 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 235 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 142 optimal weight: 0.9980 chunk 175 optimal weight: 0.0870 chunk 272 optimal weight: 0.9990 overall best weight: 0.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 24753 Z= 0.196 Angle : 0.595 12.765 33675 Z= 0.313 Chirality : 0.047 0.329 3942 Planarity : 0.004 0.050 4287 Dihedral : 8.523 60.635 4249 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.34 % Allowed : 4.62 % Favored : 95.04 % 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: -1.01 (0.15), residues: 2946 helix: 0.58 (0.21), residues: 672 sheet: -0.47 (0.18), residues: 720 loop : -1.33 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.002 0.001 HIS B1048 PHE 0.015 0.001 PHE A 106 TYR 0.010 0.001 TYR B1067 ARG 0.005 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 ARG cc_start: 0.7666 (ptm-80) cc_final: 0.7304 (ptm-80) REVERT: B 360 ASN cc_start: 0.8424 (m-40) cc_final: 0.8178 (p0) REVERT: B 505 TYR cc_start: 0.6720 (t80) cc_final: 0.6388 (t80) REVERT: B 574 ASP cc_start: 0.8311 (t70) cc_final: 0.7972 (t0) REVERT: A 360 ASN cc_start: 0.8455 (m-40) cc_final: 0.8218 (p0) REVERT: A 574 ASP cc_start: 0.8278 (t70) cc_final: 0.7939 (t0) REVERT: C 360 ASN cc_start: 0.8530 (m-40) cc_final: 0.8146 (p0) REVERT: C 574 ASP cc_start: 0.8172 (t70) cc_final: 0.7870 (t0) REVERT: C 646 ARG cc_start: 0.7907 (mmm160) cc_final: 0.7490 (tpt-90) REVERT: C 900 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7859 (mtt) outliers start: 9 outliers final: 4 residues processed: 139 average time/residue: 2.8822 time to fit residues: 455.4084 Evaluate side-chains 132 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 226 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 272 optimal weight: 0.0870 chunk 294 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 chunk 270 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 218 optimal weight: 5.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1005 GLN C 957 GLN C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 24753 Z= 0.209 Angle : 0.548 12.409 33675 Z= 0.288 Chirality : 0.045 0.309 3942 Planarity : 0.003 0.075 4287 Dihedral : 7.497 60.539 4237 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.46 % Allowed : 5.12 % Favored : 94.43 % 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: -0.89 (0.15), residues: 2946 helix: 1.00 (0.21), residues: 669 sheet: -0.53 (0.17), residues: 723 loop : -1.35 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.002 0.000 HIS B1064 PHE 0.014 0.001 PHE C 238 TYR 0.027 0.001 TYR A 170 ARG 0.009 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 2.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.6925 (mmm) cc_final: 0.6642 (mmm) REVERT: B 346 ARG cc_start: 0.7731 (ptm-80) cc_final: 0.7441 (ptm-80) REVERT: B 505 TYR cc_start: 0.6799 (t80) cc_final: 0.6464 (t80) REVERT: B 574 ASP cc_start: 0.8315 (t70) cc_final: 0.7980 (t0) REVERT: A 360 ASN cc_start: 0.8460 (m-40) cc_final: 0.8251 (p0) REVERT: A 574 ASP cc_start: 0.8303 (t70) cc_final: 0.7933 (t0) REVERT: A 646 ARG cc_start: 0.7939 (mmm160) cc_final: 0.7560 (tpt170) REVERT: A 900 MET cc_start: 0.8623 (mmm) cc_final: 0.8319 (mtp) REVERT: C 360 ASN cc_start: 0.8472 (m-40) cc_final: 0.8121 (p0) REVERT: C 574 ASP cc_start: 0.8199 (t70) cc_final: 0.7887 (t0) REVERT: C 646 ARG cc_start: 0.7970 (mmm160) cc_final: 0.7507 (tpt-90) REVERT: C 957 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7778 (tt0) outliers start: 12 outliers final: 5 residues processed: 136 average time/residue: 2.5917 time to fit residues: 407.1405 Evaluate side-chains 125 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 119 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 0.6980 chunk 205 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 30 optimal weight: 0.0980 chunk 130 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 273 optimal weight: 0.9990 chunk 289 optimal weight: 0.5980 chunk 143 optimal weight: 0.5980 chunk 259 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1005 GLN C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24753 Z= 0.183 Angle : 0.524 12.426 33675 Z= 0.276 Chirality : 0.045 0.305 3942 Planarity : 0.003 0.048 4287 Dihedral : 6.971 60.183 4237 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.46 % Allowed : 6.30 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 2946 helix: 1.20 (0.21), residues: 669 sheet: -0.48 (0.18), residues: 726 loop : -1.27 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.002 0.000 HIS C1088 PHE 0.024 0.001 PHE B 168 TYR 0.017 0.001 TYR C1138 ARG 0.005 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7121 (mmm) cc_final: 0.6867 (mmm) REVERT: B 346 ARG cc_start: 0.7805 (ptm-80) cc_final: 0.7514 (ptm-80) REVERT: B 505 TYR cc_start: 0.6783 (t80) cc_final: 0.6397 (t80) REVERT: B 574 ASP cc_start: 0.8346 (t70) cc_final: 0.7980 (t0) REVERT: A 574 ASP cc_start: 0.8306 (t70) cc_final: 0.7944 (t0) REVERT: A 900 MET cc_start: 0.8598 (mmm) cc_final: 0.8334 (mtp) REVERT: C 360 ASN cc_start: 0.8466 (m-40) cc_final: 0.8151 (p0) REVERT: C 574 ASP cc_start: 0.8164 (t70) cc_final: 0.7854 (t0) REVERT: C 646 ARG cc_start: 0.8034 (mmm160) cc_final: 0.7551 (tpt-90) REVERT: C 900 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7980 (mtt) outliers start: 12 outliers final: 5 residues processed: 130 average time/residue: 2.5161 time to fit residues: 378.2441 Evaluate side-chains 124 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN B1005 GLN A1002 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 24753 Z= 0.313 Angle : 0.550 12.791 33675 Z= 0.290 Chirality : 0.045 0.298 3942 Planarity : 0.003 0.044 4287 Dihedral : 6.621 58.447 4237 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.65 % Allowed : 7.14 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.15), residues: 2946 helix: 1.25 (0.21), residues: 666 sheet: -0.58 (0.17), residues: 729 loop : -1.27 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.003 0.001 HIS B1064 PHE 0.016 0.001 PHE A 377 TYR 0.010 0.001 TYR C1067 ARG 0.009 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7155 (mmm) cc_final: 0.6929 (mmm) REVERT: B 346 ARG cc_start: 0.7887 (ptm-80) cc_final: 0.7105 (ptm-80) REVERT: B 574 ASP cc_start: 0.8322 (t70) cc_final: 0.7956 (t0) REVERT: A 574 ASP cc_start: 0.8328 (t70) cc_final: 0.7950 (t0) REVERT: A 646 ARG cc_start: 0.7991 (mmm160) cc_final: 0.7471 (tpt170) REVERT: A 900 MET cc_start: 0.8662 (mmm) cc_final: 0.8415 (mtp) REVERT: C 360 ASN cc_start: 0.8511 (m-40) cc_final: 0.8187 (p0) REVERT: C 574 ASP cc_start: 0.8196 (t70) cc_final: 0.7881 (t0) outliers start: 17 outliers final: 8 residues processed: 133 average time/residue: 2.3668 time to fit residues: 367.1828 Evaluate side-chains 123 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 170 optimal weight: 0.0370 chunk 71 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 152 optimal weight: 0.9980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1002 GLN A1002 GLN A1005 GLN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 24753 Z= 0.200 Angle : 0.524 12.591 33675 Z= 0.275 Chirality : 0.045 0.293 3942 Planarity : 0.003 0.041 4287 Dihedral : 6.293 58.482 4233 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.65 % Allowed : 7.37 % Favored : 91.98 % 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: -0.65 (0.15), residues: 2946 helix: 1.43 (0.21), residues: 666 sheet: -0.55 (0.18), residues: 729 loop : -1.21 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.002 0.000 HIS A1088 PHE 0.013 0.001 PHE A 898 TYR 0.016 0.001 TYR B1138 ARG 0.009 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 ARG cc_start: 0.7883 (ptm-80) cc_final: 0.7095 (ptm-80) REVERT: B 574 ASP cc_start: 0.8249 (t70) cc_final: 0.7915 (t0) REVERT: A 574 ASP cc_start: 0.8321 (t70) cc_final: 0.7938 (t0) REVERT: A 900 MET cc_start: 0.8612 (mmm) cc_final: 0.8389 (mtp) REVERT: C 360 ASN cc_start: 0.8477 (m-40) cc_final: 0.8214 (p0) REVERT: C 574 ASP cc_start: 0.8182 (t70) cc_final: 0.7846 (t0) REVERT: C 646 ARG cc_start: 0.7999 (mmm160) cc_final: 0.7482 (tpt-90) outliers start: 17 outliers final: 10 residues processed: 134 average time/residue: 2.2585 time to fit residues: 355.7347 Evaluate side-chains 132 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 165 optimal weight: 0.9990 chunk 211 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1002 GLN A1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 24753 Z= 0.307 Angle : 0.546 12.784 33675 Z= 0.287 Chirality : 0.045 0.288 3942 Planarity : 0.003 0.038 4287 Dihedral : 6.201 57.921 4233 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.73 % Allowed : 8.25 % Favored : 91.03 % 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: -0.63 (0.15), residues: 2946 helix: 1.43 (0.21), residues: 666 sheet: -0.49 (0.18), residues: 732 loop : -1.22 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 886 HIS 0.003 0.001 HIS A1088 PHE 0.016 0.001 PHE B 220 TYR 0.010 0.001 TYR B1067 ARG 0.006 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 ARG cc_start: 0.7939 (ptm-80) cc_final: 0.7166 (ptm-80) REVERT: B 574 ASP cc_start: 0.8240 (t70) cc_final: 0.7903 (t0) REVERT: A 574 ASP cc_start: 0.8300 (t70) cc_final: 0.7916 (t0) REVERT: A 646 ARG cc_start: 0.8056 (mmm160) cc_final: 0.7823 (mmm-85) REVERT: C 360 ASN cc_start: 0.8502 (m-40) cc_final: 0.8284 (p0) REVERT: C 574 ASP cc_start: 0.8182 (t70) cc_final: 0.7845 (t0) REVERT: C 646 ARG cc_start: 0.8048 (mmm160) cc_final: 0.7536 (tpt-90) outliers start: 19 outliers final: 11 residues processed: 132 average time/residue: 2.2423 time to fit residues: 348.0088 Evaluate side-chains 127 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 227 optimal weight: 0.9980 chunk 263 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 24753 Z= 0.204 Angle : 0.525 12.623 33675 Z= 0.275 Chirality : 0.045 0.282 3942 Planarity : 0.003 0.033 4287 Dihedral : 6.058 58.375 4233 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.53 % Allowed : 9.09 % Favored : 90.38 % 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: -0.55 (0.15), residues: 2946 helix: 1.52 (0.21), residues: 666 sheet: -0.49 (0.18), residues: 735 loop : -1.14 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 104 HIS 0.002 0.000 HIS C1088 PHE 0.014 0.001 PHE B 106 TYR 0.019 0.001 TYR B1138 ARG 0.006 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 ASP cc_start: 0.8197 (t70) cc_final: 0.7848 (t0) REVERT: A 346 ARG cc_start: 0.7811 (ptm-80) cc_final: 0.7478 (ptm-80) REVERT: A 574 ASP cc_start: 0.8291 (t70) cc_final: 0.7905 (t0) REVERT: C 574 ASP cc_start: 0.8179 (t70) cc_final: 0.7870 (t0) REVERT: C 646 ARG cc_start: 0.8049 (mmm160) cc_final: 0.7518 (tpt-90) outliers start: 14 outliers final: 10 residues processed: 131 average time/residue: 2.3117 time to fit residues: 353.7346 Evaluate side-chains 127 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 0.5980 chunk 252 optimal weight: 0.0980 chunk 269 optimal weight: 0.0270 chunk 276 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 211 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 chunk 254 optimal weight: 4.9990 chunk 268 optimal weight: 0.9980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1002 GLN A1002 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 24753 Z= 0.172 Angle : 0.516 12.389 33675 Z= 0.270 Chirality : 0.045 0.276 3942 Planarity : 0.003 0.033 4287 Dihedral : 5.887 58.387 4233 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.65 % Allowed : 9.32 % Favored : 90.03 % 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: -0.42 (0.15), residues: 2946 helix: 1.63 (0.22), residues: 666 sheet: -0.40 (0.18), residues: 729 loop : -1.07 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 104 HIS 0.002 0.000 HIS A1088 PHE 0.018 0.001 PHE A 106 TYR 0.010 0.001 TYR A 489 ARG 0.007 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 505 TYR cc_start: 0.6935 (t80) cc_final: 0.6471 (t80) REVERT: B 574 ASP cc_start: 0.8187 (t70) cc_final: 0.7836 (t0) REVERT: A 346 ARG cc_start: 0.7870 (ptm-80) cc_final: 0.7536 (ptm-80) REVERT: A 574 ASP cc_start: 0.8254 (t70) cc_final: 0.7892 (t0) REVERT: A 646 ARG cc_start: 0.8099 (mmm160) cc_final: 0.7835 (mmm-85) REVERT: C 574 ASP cc_start: 0.8175 (t70) cc_final: 0.7843 (t0) REVERT: C 646 ARG cc_start: 0.8035 (mmm160) cc_final: 0.7507 (tpt-90) outliers start: 17 outliers final: 11 residues processed: 137 average time/residue: 2.3993 time to fit residues: 385.7639 Evaluate side-chains 133 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 chunk 275 optimal weight: 0.9980 chunk 237 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24753 Z= 0.284 Angle : 0.544 12.629 33675 Z= 0.284 Chirality : 0.045 0.272 3942 Planarity : 0.003 0.037 4287 Dihedral : 5.922 57.984 4233 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.46 % Allowed : 9.85 % Favored : 89.69 % 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: -0.45 (0.15), residues: 2946 helix: 1.56 (0.21), residues: 666 sheet: -0.42 (0.18), residues: 732 loop : -1.07 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.003 0.001 HIS A1088 PHE 0.014 0.001 PHE A 898 TYR 0.020 0.001 TYR B1138 ARG 0.007 0.000 ARG B 646 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 505 TYR cc_start: 0.7037 (t80) cc_final: 0.6589 (t80) REVERT: B 574 ASP cc_start: 0.8185 (t70) cc_final: 0.7834 (t0) REVERT: A 346 ARG cc_start: 0.7877 (ptm-80) cc_final: 0.7570 (ptm-80) REVERT: A 574 ASP cc_start: 0.8288 (t70) cc_final: 0.7906 (t0) REVERT: C 574 ASP cc_start: 0.8178 (t70) cc_final: 0.7852 (t0) REVERT: C 646 ARG cc_start: 0.8023 (mmm160) cc_final: 0.7471 (tpt-90) outliers start: 12 outliers final: 10 residues processed: 132 average time/residue: 2.3295 time to fit residues: 358.1879 Evaluate side-chains 131 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 219 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 238 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.126047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.087765 restraints weight = 132726.446| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.06 r_work: 0.2918 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24753 Z= 0.196 Angle : 0.525 12.456 33675 Z= 0.274 Chirality : 0.044 0.267 3942 Planarity : 0.003 0.036 4287 Dihedral : 5.805 58.343 4233 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.50 % Allowed : 9.81 % Favored : 89.69 % 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: -0.35 (0.15), residues: 2946 helix: 1.68 (0.22), residues: 663 sheet: -0.38 (0.18), residues: 729 loop : -0.99 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 104 HIS 0.002 0.000 HIS C1088 PHE 0.017 0.001 PHE A 106 TYR 0.010 0.001 TYR A 489 ARG 0.008 0.000 ARG B 646 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9411.82 seconds wall clock time: 163 minutes 20.42 seconds (9800.42 seconds total)