Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 10:24:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x58_6703/04_2023/5x58_6703.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x58_6703/04_2023/5x58_6703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x58_6703/04_2023/5x58_6703.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x58_6703/04_2023/5x58_6703.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x58_6703/04_2023/5x58_6703.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x58_6703/04_2023/5x58_6703.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.012 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 132 5.16 5 C 16102 2.51 5 N 4127 2.21 5 O 4904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 306": "NH1" <-> "NH2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 761": "NH1" <-> "NH2" Residue "A ARG 797": "NH1" <-> "NH2" Residue "A ARG 965": "NH1" <-> "NH2" Residue "A ARG 977": "NH1" <-> "NH2" Residue "A ARG 1073": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B ARG 441": "NH1" <-> "NH2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 761": "NH1" <-> "NH2" Residue "B ARG 797": "NH1" <-> "NH2" Residue "B ARG 965": "NH1" <-> "NH2" Residue "B ARG 977": "NH1" <-> "NH2" Residue "B ARG 1073": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 441": "NH1" <-> "NH2" Residue "C ARG 544": "NH1" <-> "NH2" Residue "C PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 761": "NH1" <-> "NH2" Residue "C ARG 797": "NH1" <-> "NH2" Residue "C ARG 965": "NH1" <-> "NH2" Residue "C ARG 977": "NH1" <-> "NH2" Residue "C ARG 1073": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 25265 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1054, 8234 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 50, 'TRANS': 1001} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 8226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8226 Classifications: {'peptide': 1053} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 50, 'TRANS': 1000} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 8217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8217 Classifications: {'peptide': 1052} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 50, 'TRANS': 999} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 12.95, per 1000 atoms: 0.51 Number of scatterers: 25265 At special positions: 0 Unit cell: (149.5, 139.1, 159.9, 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 132 16.00 O 4904 8.00 N 4127 7.00 C 16102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.04 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.04 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.01 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.04 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.04 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.04 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.01 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.04 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.04 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.04 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.01 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=3, symmetry=0 Links applied NAG-ASN " NAG A1302 " - " ASN A 691 " " NAG A1303 " - " ASN A 699 " " NAG A1304 " - " ASN A 783 " " NAG A1305 " - " ASN A1056 " " NAG A1306 " - " ASN A 357 " " NAG A1307 " - " ASN A 330 " " NAG A1308 " - " ASN A 318 " " NAG A1309 " - " ASN A 269 " " NAG A1310 " - " ASN A 227 " " NAG A1311 " - " ASN A 158 " " NAG A1312 " - " ASN A 119 " " NAG A1313 " - " ASN A 65 " " NAG B1301 " - " ASN B 602 " " NAG B1302 " - " ASN B 691 " " NAG B1303 " - " ASN B 699 " " NAG B1304 " - " ASN B 783 " " NAG B1305 " - " ASN B1056 " " NAG B1306 " - " ASN B 357 " " NAG B1307 " - " ASN B 330 " " NAG B1308 " - " ASN B 318 " " NAG B1309 " - " ASN B 269 " " NAG B1310 " - " ASN B 227 " " NAG B1311 " - " ASN B 158 " " NAG B1312 " - " ASN B 119 " " NAG B1313 " - " ASN B 65 " " NAG C1301 " - " ASN C 602 " " NAG C1302 " - " ASN C 691 " " NAG C1303 " - " ASN C 699 " " NAG C1304 " - " ASN C 783 " " NAG C1305 " - " ASN C1056 " " NAG C1306 " - " ASN C 357 " " NAG C1307 " - " ASN C 330 " " NAG C1308 " - " ASN C 318 " " NAG C1309 " - " ASN C 269 " " NAG C1310 " - " ASN C 227 " " NAG C1311 " - " ASN C 158 " " NAG C1312 " - " ASN C 119 " " NAG C1313 " - " ASN C 65 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.52 Conformation dependent library (CDL) restraints added in 3.9 seconds 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5934 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 45 sheets defined 22.0% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 327 removed outlier: 3.852A pdb=" N GLU A 327 " --> pdb=" O PRO A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 327' Processing helix chain 'A' and resid 390 through 397 removed outlier: 4.192A pdb=" N ARG A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 603 through 611 removed outlier: 3.964A pdb=" N ALA A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.583A pdb=" N GLY A 726 " --> pdb=" O MET A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 744 through 765 removed outlier: 4.108A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 807 removed outlier: 3.810A pdb=" N LYS A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 866 Processing helix chain 'A' and resid 868 through 873 removed outlier: 3.547A pdb=" N ALA A 872 " --> pdb=" O TRP A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 892 removed outlier: 3.694A pdb=" N ILE A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.959A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 removed outlier: 4.170A pdb=" N THR A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 947 removed outlier: 3.933A pdb=" N LYS A 929 " --> pdb=" O THR A 925 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 removed outlier: 3.646A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 1014 removed outlier: 3.645A pdb=" N ASP A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 981 " --> pdb=" O ARG A 977 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 988 " --> pdb=" O GLN A 984 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A1003 " --> pdb=" O GLU A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 327 removed outlier: 3.851A pdb=" N GLU B 327 " --> pdb=" O PRO B 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 324 through 327' Processing helix chain 'B' and resid 390 through 397 removed outlier: 4.192A pdb=" N ARG B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 603 through 611 removed outlier: 3.965A pdb=" N ALA B 609 " --> pdb=" O ASP B 605 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS B 611 " --> pdb=" O SER B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 removed outlier: 3.582A pdb=" N GLY B 726 " --> pdb=" O MET B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 736 Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 744 through 765 removed outlier: 4.109A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 807 removed outlier: 3.810A pdb=" N LYS B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 866 Processing helix chain 'B' and resid 868 through 873 removed outlier: 3.547A pdb=" N ALA B 872 " --> pdb=" O TRP B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 892 removed outlier: 3.693A pdb=" N ILE B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 901 removed outlier: 3.959A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 923 removed outlier: 4.171A pdb=" N THR B 921 " --> pdb=" O GLN B 917 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 947 removed outlier: 3.932A pdb=" N LYS B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU B 930 " --> pdb=" O ALA B 926 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 964 removed outlier: 3.646A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 1014 removed outlier: 3.644A pdb=" N ASP B 976 " --> pdb=" O GLU B 972 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 981 " --> pdb=" O ARG B 977 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 988 " --> pdb=" O GLN B 984 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B1003 " --> pdb=" O GLU B 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 324 through 327 removed outlier: 3.851A pdb=" N GLU C 327 " --> pdb=" O PRO C 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 324 through 327' Processing helix chain 'C' and resid 390 through 397 removed outlier: 4.192A pdb=" N ARG C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 396 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 603 through 611 removed outlier: 3.964A pdb=" N ALA C 609 " --> pdb=" O ASP C 605 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 726 removed outlier: 3.584A pdb=" N GLY C 726 " --> pdb=" O MET C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 736 Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 744 through 765 removed outlier: 4.108A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG C 758 " --> pdb=" O ALA C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 807 removed outlier: 3.811A pdb=" N LYS C 807 " --> pdb=" O LEU C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 866 Processing helix chain 'C' and resid 868 through 873 removed outlier: 3.547A pdb=" N ALA C 872 " --> pdb=" O TRP C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 892 removed outlier: 3.693A pdb=" N ILE C 891 " --> pdb=" O ARG C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 901 removed outlier: 3.959A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 923 removed outlier: 4.171A pdb=" N THR C 921 " --> pdb=" O GLN C 917 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 947 removed outlier: 3.933A pdb=" N LYS C 929 " --> pdb=" O THR C 925 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 964 removed outlier: 3.646A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 1014 removed outlier: 3.644A pdb=" N ASP C 976 " --> pdb=" O GLU C 972 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 981 " --> pdb=" O ARG C 977 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 988 " --> pdb=" O GLN C 984 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C1003 " --> pdb=" O GLU C 999 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.523A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR A 71 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA A 250 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 186 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG A 38 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N LEU A 216 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 48 removed outlier: 5.700A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.744A pdb=" N ASP A 57 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 removed outlier: 5.597A pdb=" N VAL A 123 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN A 129 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N CYS A 159 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 147 through 150 removed outlier: 7.137A pdb=" N ALA A 139 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER A 239 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 140 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 298 through 299 Processing sheet with id=AA7, first strand: chain 'A' and resid 310 through 312 removed outlier: 7.409A pdb=" N SER A 310 " --> pdb=" O ASN A 526 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 321 through 322 removed outlier: 6.242A pdb=" N ASN A 321 " --> pdb=" O VAL A 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.961A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 537 through 540 removed outlier: 5.701A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE A 551 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 640 through 641 removed outlier: 5.596A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 652 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 683 through 685 Processing sheet with id=AB4, first strand: chain 'A' and resid 693 through 697 removed outlier: 3.546A pdb=" N ILE A 696 " --> pdb=" O ARG A1055 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A1083 " --> pdb=" O ASN A1080 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 704 through 710 removed outlier: 6.889A pdb=" N VAL A1047 " --> pdb=" O LEU A1031 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 704 through 710 Processing sheet with id=AB7, first strand: chain 'A' and resid 769 through 771 removed outlier: 6.097A pdb=" N MET A 770 " --> pdb=" O SER C 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1071 through 1072 removed outlier: 3.539A pdb=" N PHE A1071 " --> pdb=" O PHE A1103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 32 through 34 removed outlier: 7.524A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR B 71 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA B 250 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 186 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG B 38 " --> pdb=" O ASN B 214 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N LEU B 216 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.743A pdb=" N ASP B 57 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 82 removed outlier: 5.598A pdb=" N VAL B 123 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 147 through 150 removed outlier: 7.137A pdb=" N ALA B 139 " --> pdb=" O THR B 148 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER B 239 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 298 through 299 Processing sheet with id=AC5, first strand: chain 'B' and resid 310 through 312 removed outlier: 7.409A pdb=" N SER B 310 " --> pdb=" O ASN B 526 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 321 through 322 removed outlier: 6.242A pdb=" N ASN B 321 " --> pdb=" O VAL B 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.961A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 537 through 540 removed outlier: 5.701A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE B 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 640 through 641 removed outlier: 5.596A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 652 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 683 through 685 Processing sheet with id=AD2, first strand: chain 'B' and resid 693 through 697 removed outlier: 3.545A pdb=" N ILE B 696 " --> pdb=" O ARG B1055 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B1083 " --> pdb=" O ASN B1080 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 704 through 710 removed outlier: 6.889A pdb=" N VAL B1047 " --> pdb=" O LEU B1031 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 704 through 710 Processing sheet with id=AD5, first strand: chain 'B' and resid 1071 through 1072 removed outlier: 3.539A pdb=" N PHE B1071 " --> pdb=" O PHE B1103 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.523A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR C 71 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA C 250 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 186 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG C 38 " --> pdb=" O ASN C 214 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N LEU C 216 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.744A pdb=" N ASP C 57 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 81 through 82 removed outlier: 5.597A pdb=" N VAL C 123 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN C 129 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N CYS C 159 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 147 through 150 removed outlier: 7.137A pdb=" N ALA C 139 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER C 239 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL C 140 " --> pdb=" O SER C 239 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 298 through 299 Processing sheet with id=AE2, first strand: chain 'C' and resid 310 through 312 removed outlier: 7.409A pdb=" N SER C 310 " --> pdb=" O ASN C 526 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 321 through 322 removed outlier: 6.242A pdb=" N ASN C 321 " --> pdb=" O VAL C 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.962A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 640 through 641 removed outlier: 5.596A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 652 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 693 through 697 removed outlier: 3.545A pdb=" N ILE C 696 " --> pdb=" O ARG C1055 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C1083 " --> pdb=" O ASN C1080 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 704 through 710 removed outlier: 6.889A pdb=" N VAL C1047 " --> pdb=" O LEU C1031 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 704 through 710 Processing sheet with id=AE9, first strand: chain 'C' and resid 1071 through 1072 removed outlier: 3.539A pdb=" N PHE C1071 " --> pdb=" O PHE C1103 " (cutoff:3.500A) 811 hydrogen bonds defined for protein. 2244 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: 11.30 Time building geometry restraints manager: 11.29 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: 7870 1.34 - 1.46: 5722 1.46 - 1.58: 12087 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 25859 Sorted by residual: bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C ASP B 790 " pdb=" N PRO B 791 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.66e+01 bond pdb=" C ASP A 790 " pdb=" N PRO A 791 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.64e+01 ... (remaining 25854 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.80: 598 105.80 - 112.96: 13629 112.96 - 120.11: 9098 120.11 - 127.27: 11599 127.27 - 134.42: 266 Bond angle restraints: 35190 Sorted by residual: angle pdb=" N ARG A 306 " pdb=" CA ARG A 306 " pdb=" C ARG A 306 " ideal model delta sigma weight residual 110.91 120.17 -9.26 1.17e+00 7.31e-01 6.27e+01 angle pdb=" N ARG C 306 " pdb=" CA ARG C 306 " pdb=" C ARG C 306 " ideal model delta sigma weight residual 110.91 120.13 -9.22 1.17e+00 7.31e-01 6.21e+01 angle pdb=" N ARG B 306 " pdb=" CA ARG B 306 " pdb=" C ARG B 306 " ideal model delta sigma weight residual 110.91 120.12 -9.21 1.17e+00 7.31e-01 6.20e+01 angle pdb=" N VAL B 354 " pdb=" CA VAL B 354 " pdb=" C VAL B 354 " ideal model delta sigma weight residual 110.72 103.92 6.80 1.01e+00 9.80e-01 4.53e+01 angle pdb=" N VAL C 354 " pdb=" CA VAL C 354 " pdb=" C VAL C 354 " ideal model delta sigma weight residual 110.72 103.94 6.78 1.01e+00 9.80e-01 4.51e+01 ... (remaining 35185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 14245 16.57 - 33.13: 575 33.13 - 49.70: 106 49.70 - 66.27: 12 66.27 - 82.83: 33 Dihedral angle restraints: 14971 sinusoidal: 5749 harmonic: 9222 Sorted by residual: dihedral pdb=" CA THR B 616 " pdb=" C THR B 616 " pdb=" N PRO B 617 " pdb=" CA PRO B 617 " ideal model delta harmonic sigma weight residual 180.00 132.11 47.89 0 5.00e+00 4.00e-02 9.17e+01 dihedral pdb=" CA THR C 616 " pdb=" C THR C 616 " pdb=" N PRO C 617 " pdb=" CA PRO C 617 " ideal model delta harmonic sigma weight residual 180.00 132.17 47.83 0 5.00e+00 4.00e-02 9.15e+01 dihedral pdb=" CA THR A 616 " pdb=" C THR A 616 " pdb=" N PRO A 617 " pdb=" CA PRO A 617 " ideal model delta harmonic sigma weight residual 180.00 132.18 47.82 0 5.00e+00 4.00e-02 9.15e+01 ... (remaining 14968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3462 0.084 - 0.168: 551 0.168 - 0.252: 48 0.252 - 0.336: 17 0.336 - 0.420: 10 Chirality restraints: 4088 Sorted by residual: chirality pdb=" CB ILE B 787 " pdb=" CA ILE B 787 " pdb=" CG1 ILE B 787 " pdb=" CG2 ILE B 787 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CB ILE A 787 " pdb=" CA ILE A 787 " pdb=" CG1 ILE A 787 " pdb=" CG2 ILE A 787 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CB ILE C 787 " pdb=" CA ILE C 787 " pdb=" CG1 ILE C 787 " pdb=" CG2 ILE C 787 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.34e+00 ... (remaining 4085 not shown) Planarity restraints: 4536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 616 " 0.049 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO C 617 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO C 617 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 617 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 616 " -0.049 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO A 617 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 617 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 617 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 616 " -0.049 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO B 617 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 617 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 617 " -0.042 5.00e-02 4.00e+02 ... (remaining 4533 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6567 2.80 - 3.32: 22850 3.32 - 3.85: 42174 3.85 - 4.37: 49285 4.37 - 4.90: 82893 Nonbonded interactions: 203769 Sorted by model distance: nonbonded pdb=" O GLU A 647 " pdb=" OH TYR A 677 " model vdw 2.272 2.440 nonbonded pdb=" O GLU C 647 " pdb=" OH TYR C 677 " model vdw 2.273 2.440 nonbonded pdb=" O GLU B 647 " pdb=" OH TYR B 677 " model vdw 2.273 2.440 nonbonded pdb=" OH TYR A 738 " pdb=" OD1 ASP A 976 " model vdw 2.313 2.440 nonbonded pdb=" OH TYR B 738 " pdb=" OD1 ASP B 976 " model vdw 2.314 2.440 ... (remaining 203764 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 662 or resid 673 through 809 or resid 831 throu \ gh 1104 or resid 1302 through 1301)) selection = (chain 'B' and (resid 18 through 662 or resid 673 through 1104 or resid 1301 thr \ ough 1314)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 4.330 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 66.710 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.150 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 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 : 0.007 0.090 25859 Z= 0.476 Angle : 1.173 18.125 35190 Z= 0.657 Chirality : 0.066 0.420 4088 Planarity : 0.006 0.075 4498 Dihedral : 10.447 76.935 8983 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 5.88 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.64 (0.12), residues: 3135 helix: -4.02 (0.11), residues: 609 sheet: -2.43 (0.18), residues: 614 loop : -3.11 (0.12), residues: 1912 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 692 time to evaluate : 2.938 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 outliers start: 12 outliers final: 4 residues processed: 704 average time/residue: 0.4157 time to fit residues: 456.6219 Evaluate side-chains 359 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 355 time to evaluate : 3.035 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2272 time to fit residues: 5.8868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 127 optimal weight: 50.0000 chunk 246 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 150 optimal weight: 0.0870 chunk 183 optimal weight: 0.8980 chunk 286 optimal weight: 10.0000 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 112 GLN A 135 ASN A 409 ASN A 522 ASN ** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 GLN A 614 GLN A 632 GLN A 766 GLN A 917 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN A 937 ASN ** A 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1090 ASN A1101 ASN B 70 HIS B 135 ASN B 280 GLN B 409 ASN B 522 ASN ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN B 614 GLN B 632 GLN B 692 ASN B 733 ASN B 766 GLN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 889 ASN B 904 GLN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 936 GLN B 937 ASN ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1053 GLN B1090 ASN B1101 ASN C 135 ASN C 201 GLN C 409 ASN C 522 ASN ** C 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN ** C 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 GLN C 632 GLN C 766 GLN C 835 GLN C 896 ASN C 904 GLN C 917 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 936 GLN C 937 ASN ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 25859 Z= 0.221 Angle : 0.701 13.945 35190 Z= 0.362 Chirality : 0.049 0.348 4088 Planarity : 0.005 0.072 4498 Dihedral : 6.853 41.105 3396 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer Outliers : 2.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 3.92 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.13), residues: 3135 helix: -1.55 (0.18), residues: 609 sheet: -1.79 (0.18), residues: 669 loop : -2.78 (0.13), residues: 1857 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 429 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 44 residues processed: 479 average time/residue: 0.3677 time to fit residues: 278.7197 Evaluate side-chains 381 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 337 time to evaluate : 3.214 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.2295 time to fit residues: 22.9583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 158 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 238 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 286 optimal weight: 0.0870 chunk 309 optimal weight: 4.9990 chunk 255 optimal weight: 0.9990 chunk 284 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 ASN ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 733 ASN A 766 GLN A 904 GLN A 917 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN B 526 ASN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 936 GLN B 987 GLN C 492 GLN ** C 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 GLN C 599 GLN C 766 GLN C 917 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 25859 Z= 0.217 Angle : 0.668 14.423 35190 Z= 0.339 Chirality : 0.048 0.331 4088 Planarity : 0.004 0.069 4498 Dihedral : 6.408 39.981 3396 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 3.92 % 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: -2.62 (0.14), residues: 3135 helix: -0.06 (0.21), residues: 608 sheet: -1.42 (0.19), residues: 658 loop : -2.57 (0.13), residues: 1869 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 368 time to evaluate : 3.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 35 residues processed: 418 average time/residue: 0.3771 time to fit residues: 251.6996 Evaluate side-chains 339 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 304 time to evaluate : 3.111 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 35 outliers final: 1 residues processed: 35 average time/residue: 0.2330 time to fit residues: 19.6145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 283 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 287 optimal weight: 9.9990 chunk 304 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 272 optimal weight: 0.0000 chunk 82 optimal weight: 10.0000 overall best weight: 4.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1090 ASN A1101 ASN ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN C 280 GLN ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 HIS ** C 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN C1101 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.126 25859 Z= 0.466 Angle : 0.785 16.255 35190 Z= 0.400 Chirality : 0.053 0.353 4088 Planarity : 0.005 0.065 4498 Dihedral : 6.643 38.866 3396 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer Outliers : 3.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 2.61 % Twisted General : 0.07 % 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: -2.65 (0.14), residues: 3135 helix: -0.07 (0.21), residues: 628 sheet: -1.40 (0.19), residues: 661 loop : -2.63 (0.13), residues: 1846 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 361 time to evaluate : 2.879 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 outliers start: 105 outliers final: 68 residues processed: 425 average time/residue: 0.3771 time to fit residues: 254.0370 Evaluate side-chains 374 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 306 time to evaluate : 2.983 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.2350 time to fit residues: 34.1142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 253 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 226 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 259 optimal weight: 8.9990 chunk 210 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 155 optimal weight: 1.9990 chunk 273 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 GLN A 835 GLN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS B 614 GLN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1090 ASN C 280 GLN C 614 GLN C 766 GLN C 835 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 987 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 25859 Z= 0.228 Angle : 0.653 11.965 35190 Z= 0.331 Chirality : 0.049 0.324 4088 Planarity : 0.004 0.064 4498 Dihedral : 6.212 37.347 3396 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 3.27 % Twisted General : 0.10 % 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: -2.21 (0.14), residues: 3135 helix: 0.51 (0.21), residues: 649 sheet: -1.08 (0.20), residues: 634 loop : -2.48 (0.14), residues: 1852 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 366 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 22 residues processed: 405 average time/residue: 0.3788 time to fit residues: 241.8738 Evaluate side-chains 342 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 320 time to evaluate : 3.082 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3016 time to fit residues: 15.8795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 102 optimal weight: 2.9990 chunk 274 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 178 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 304 optimal weight: 0.8980 chunk 253 optimal weight: 20.0000 chunk 141 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 GLN A 766 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 931 GLN ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.091 25859 Z= 0.352 Angle : 0.702 14.996 35190 Z= 0.353 Chirality : 0.050 0.336 4088 Planarity : 0.005 0.061 4498 Dihedral : 6.245 37.751 3396 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 3.27 % Twisted General : 0.10 % 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: -2.25 (0.14), residues: 3135 helix: 0.53 (0.21), residues: 640 sheet: -1.18 (0.19), residues: 667 loop : -2.49 (0.13), residues: 1828 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 331 time to evaluate : 3.000 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 outliers start: 75 outliers final: 52 residues processed: 379 average time/residue: 0.3877 time to fit residues: 232.4053 Evaluate side-chains 358 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 306 time to evaluate : 2.957 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 52 outliers final: 1 residues processed: 52 average time/residue: 0.2503 time to fit residues: 27.8745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 293 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 chunk 222 optimal weight: 0.9980 chunk 172 optimal weight: 7.9990 chunk 256 optimal weight: 0.8980 chunk 170 optimal weight: 0.0670 chunk 303 optimal weight: 0.9980 chunk 190 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 GLN A 766 GLN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN B 936 GLN B 987 GLN C 280 GLN C 492 GLN ** C 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 987 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 25859 Z= 0.177 Angle : 0.621 14.354 35190 Z= 0.314 Chirality : 0.047 0.314 4088 Planarity : 0.004 0.060 4498 Dihedral : 5.840 36.179 3396 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 3.27 % Twisted General : 0.10 % 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: -1.89 (0.15), residues: 3135 helix: 1.03 (0.21), residues: 646 sheet: -0.97 (0.20), residues: 634 loop : -2.33 (0.14), residues: 1855 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 369 time to evaluate : 3.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 390 average time/residue: 0.3872 time to fit residues: 241.7140 Evaluate side-chains 335 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 323 time to evaluate : 3.193 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.2345 time to fit residues: 9.2392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 187 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 181 optimal weight: 0.1980 chunk 91 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 193 optimal weight: 4.9990 chunk 206 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 238 optimal weight: 6.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 GLN A 626 ASN A 766 GLN A 901 ASN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 GLN B 661 HIS B 883 GLN ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 931 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.103 25859 Z= 0.373 Angle : 0.712 19.020 35190 Z= 0.357 Chirality : 0.051 0.333 4088 Planarity : 0.005 0.078 4498 Dihedral : 6.016 36.242 3396 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 1.96 % Twisted General : 0.10 % 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: -2.00 (0.15), residues: 3135 helix: 0.86 (0.21), residues: 638 sheet: -0.97 (0.20), residues: 645 loop : -2.39 (0.14), residues: 1852 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 329 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 32 residues processed: 358 average time/residue: 0.3786 time to fit residues: 218.2294 Evaluate side-chains 339 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 307 time to evaluate : 3.032 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 32 outliers final: 1 residues processed: 32 average time/residue: 0.2587 time to fit residues: 19.4753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 276 optimal weight: 5.9990 chunk 290 optimal weight: 0.7980 chunk 265 optimal weight: 4.9990 chunk 282 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 222 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 255 optimal weight: 0.0970 chunk 267 optimal weight: 0.7980 chunk 281 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN A 733 ASN A 766 GLN A 835 GLN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 987 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 25859 Z= 0.179 Angle : 0.634 15.829 35190 Z= 0.319 Chirality : 0.047 0.312 4088 Planarity : 0.004 0.058 4498 Dihedral : 5.755 34.842 3396 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 2.61 % Twisted General : 0.10 % 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: -1.76 (0.15), residues: 3135 helix: 1.18 (0.21), residues: 647 sheet: -0.86 (0.20), residues: 624 loop : -2.27 (0.14), residues: 1864 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 337 time to evaluate : 2.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 349 average time/residue: 0.3878 time to fit residues: 216.8435 Evaluate side-chains 318 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 309 time to evaluate : 3.138 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.2431 time to fit residues: 8.4777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 185 optimal weight: 3.9990 chunk 299 optimal weight: 0.1980 chunk 182 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 313 optimal weight: 8.9990 chunk 288 optimal weight: 6.9990 chunk 249 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 193 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** C 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 896 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 25859 Z= 0.246 Angle : 0.661 17.318 35190 Z= 0.330 Chirality : 0.049 0.322 4088 Planarity : 0.004 0.057 4498 Dihedral : 5.746 36.351 3396 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 1.96 % Twisted General : 0.10 % 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: -1.71 (0.15), residues: 3135 helix: 1.31 (0.21), residues: 640 sheet: -0.83 (0.20), residues: 633 loop : -2.27 (0.14), residues: 1862 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 314 time to evaluate : 3.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 323 average time/residue: 0.3863 time to fit residues: 200.8889 Evaluate side-chains 315 residues out of total 2742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 306 time to evaluate : 2.912 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.2491 time to fit residues: 8.1712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 198 optimal weight: 0.9990 chunk 266 optimal weight: 4.9990 chunk 76 optimal weight: 0.0870 chunk 230 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 250 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 257 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 896 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.181295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.147362 restraints weight = 38807.080| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.83 r_work: 0.3620 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.092 25859 Z= 0.268 Angle : 0.669 17.082 35190 Z= 0.335 Chirality : 0.049 0.326 4088 Planarity : 0.004 0.057 4498 Dihedral : 5.790 35.541 3396 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.10 % Twisted Proline : 1.96 % Twisted General : 0.10 % 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: -1.76 (0.15), residues: 3135 helix: 1.22 (0.21), residues: 641 sheet: -0.83 (0.20), residues: 625 loop : -2.29 (0.14), residues: 1869 =============================================================================== Job complete usr+sys time: 5711.71 seconds wall clock time: 104 minutes 54.01 seconds (6294.01 seconds total)