Starting phenix.real_space_refine on Fri Mar 6 06:41:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tht_25904/03_2026/7tht_25904.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tht_25904/03_2026/7tht_25904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tht_25904/03_2026/7tht_25904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tht_25904/03_2026/7tht_25904.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tht_25904/03_2026/7tht_25904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tht_25904/03_2026/7tht_25904.map" } resolution = 3.42 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 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= 0.001 sd= 0.070 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 129 5.16 5 C 18386 2.51 5 N 4730 2.21 5 O 5655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28900 Number of models: 1 Model: "" Number of chains: 25 Chain: "S" Number of atoms: 7620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7620 Classifications: {'peptide': 991} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 48, 'TRANS': 942} Chain breaks: 9 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "V" Number of atoms: 7587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7587 Classifications: {'peptide': 986} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 937} Chain breaks: 10 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "C" Number of atoms: 7606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7606 Classifications: {'peptide': 990} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 48, 'TRANS': 941} Chain breaks: 8 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 9, 'GLN:plan1': 2, 'GLU:plan': 10} Unresolved non-hydrogen planarities: 87 Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 804 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 97} Chain: "a" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "c" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 804 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 97} Chain: "d" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "b" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 804 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 97} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" 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: "G" 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "V" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 6.98, per 1000 atoms: 0.24 Number of scatterers: 28900 At special positions: 0 Unit cell: (130.134, 153.41, 215.832, 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 129 16.00 O 5655 8.00 N 4730 7.00 C 18386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS S 291 " - pdb=" SG CYS S 301 " distance=2.02 Simple disulfide: pdb=" SG CYS S 538 " - pdb=" SG CYS S 590 " distance=2.03 Simple disulfide: pdb=" SG CYS S 617 " - pdb=" SG CYS S 649 " distance=2.03 Simple disulfide: pdb=" SG CYS S 662 " - pdb=" SG CYS S 671 " distance=2.04 Simple disulfide: pdb=" SG CYS S 738 " - pdb=" SG CYS S 760 " distance=2.03 Simple disulfide: pdb=" SG CYS S 743 " - pdb=" SG CYS S 749 " distance=2.03 Simple disulfide: pdb=" SG CYS S1032 " - pdb=" SG CYS S1043 " distance=1.99 Simple disulfide: pdb=" SG CYS S1082 " - pdb=" SG CYS S1126 " distance=2.03 Simple disulfide: pdb=" SG CYS V 131 " - pdb=" SG CYS V 166 " distance=2.04 Simple disulfide: pdb=" SG CYS V 291 " - pdb=" SG CYS V 301 " distance=2.02 Simple disulfide: pdb=" SG CYS V 391 " - pdb=" SG CYS V 525 " distance=2.06 Simple disulfide: pdb=" SG CYS V 538 " - pdb=" SG CYS V 590 " distance=2.03 Simple disulfide: pdb=" SG CYS V 617 " - pdb=" SG CYS V 649 " distance=2.02 Simple disulfide: pdb=" SG CYS V 662 " - pdb=" SG CYS V 671 " distance=2.04 Simple disulfide: pdb=" SG CYS V 738 " - pdb=" SG CYS V 760 " distance=2.02 Simple disulfide: pdb=" SG CYS V 743 " - pdb=" SG CYS V 749 " distance=2.02 Simple disulfide: pdb=" SG CYS V1032 " - pdb=" SG CYS V1043 " distance=2.02 Simple disulfide: pdb=" SG CYS V1082 " - pdb=" SG CYS V1126 " distance=2.02 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=2.01 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.01 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.99 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS d 22 " - pdb=" SG CYS d 92 " distance=2.03 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 A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A 1 " - " ASN S 717 " " NAG B 1 " - " ASN S 234 " " NAG C1201 " - " ASN C 122 " " NAG C1202 " - " ASN C 234 " " NAG C1203 " - " ASN C 282 " " NAG C1204 " - " ASN C 331 " " NAG C1205 " - " ASN C 603 " " NAG C1206 " - " ASN C 616 " " NAG C1207 " - " ASN C 657 " " NAG C1208 " - " ASN C 709 " " NAG C1209 " - " ASN C1074 " " NAG C1210 " - " ASN C 165 " " NAG C1211 " - " ASN C 61 " " NAG D 1 " - " ASN V 717 " " NAG E 1 " - " ASN C 717 " " NAG F 1 " - " ASN S 801 " " NAG G 1 " - " ASN S1098 " " NAG I 1 " - " ASN V 801 " " NAG J 1 " - " ASN V1098 " " NAG K 1 " - " ASN V1134 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " " NAG S1201 " - " ASN S 282 " " NAG S1202 " - " ASN S 603 " " NAG S1203 " - " ASN S 616 " " NAG S1204 " - " ASN S 657 " " NAG S1205 " - " ASN S 709 " " NAG S1206 " - " ASN S1074 " " NAG S1207 " - " ASN S 61 " " NAG S1208 " - " ASN S 122 " " NAG S1209 " - " ASN S 331 " " NAG S1210 " - " ASN S 343 " " NAG V1201 " - " ASN V 122 " " NAG V1202 " - " ASN V 234 " " NAG V1203 " - " ASN V 282 " " NAG V1204 " - " ASN V 331 " " NAG V1205 " - " ASN V 603 " " NAG V1206 " - " ASN V 616 " " NAG V1207 " - " ASN V 657 " " NAG V1208 " - " ASN V 709 " " NAG V1209 " - " ASN V1074 " " NAG V1210 " - " ASN V 165 " " NAG V1211 " - " ASN V 61 " " NAG V1212 " - " ASN V 343 " " NAG W 1 " - " ASN S1134 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.4 seconds 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6814 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 63 sheets defined 22.6% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'S' and resid 294 through 303 Processing helix chain 'S' and resid 338 through 343 Processing helix chain 'S' and resid 349 through 353 removed outlier: 4.208A pdb=" N TRP S 353 " --> pdb=" O VAL S 350 " (cutoff:3.500A) Processing helix chain 'S' and resid 366 through 371 Processing helix chain 'S' and resid 385 through 389 removed outlier: 4.583A pdb=" N ASN S 388 " --> pdb=" O THR S 385 " (cutoff:3.500A) Processing helix chain 'S' and resid 405 through 410 removed outlier: 4.206A pdb=" N ARG S 408 " --> pdb=" O ASP S 405 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE S 410 " --> pdb=" O VAL S 407 " (cutoff:3.500A) Processing helix chain 'S' and resid 416 through 422 Processing helix chain 'S' and resid 438 through 443 Processing helix chain 'S' and resid 616 through 620 Processing helix chain 'S' and resid 737 through 744 Processing helix chain 'S' and resid 746 through 754 removed outlier: 4.049A pdb=" N LEU S 752 " --> pdb=" O GLU S 748 " (cutoff:3.500A) Processing helix chain 'S' and resid 755 through 757 No H-bonds generated for 'chain 'S' and resid 755 through 757' Processing helix chain 'S' and resid 758 through 783 removed outlier: 6.024A pdb=" N ASN S 764 " --> pdb=" O CYS S 760 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP S 775 " --> pdb=" O ALA S 771 " (cutoff:3.500A) Processing helix chain 'S' and resid 816 through 826 removed outlier: 3.721A pdb=" N VAL S 826 " --> pdb=" O LEU S 822 " (cutoff:3.500A) Processing helix chain 'S' and resid 866 through 885 removed outlier: 3.502A pdb=" N GLY S 885 " --> pdb=" O THR S 881 " (cutoff:3.500A) Processing helix chain 'S' and resid 886 through 891 removed outlier: 3.747A pdb=" N ALA S 890 " --> pdb=" O TRP S 886 " (cutoff:3.500A) Processing helix chain 'S' and resid 897 through 909 removed outlier: 3.572A pdb=" N ILE S 909 " --> pdb=" O ARG S 905 " (cutoff:3.500A) Processing helix chain 'S' and resid 913 through 918 Processing helix chain 'S' and resid 919 through 941 Processing helix chain 'S' and resid 942 through 944 No H-bonds generated for 'chain 'S' and resid 942 through 944' Processing helix chain 'S' and resid 945 through 965 removed outlier: 3.837A pdb=" N VAL S 951 " --> pdb=" O LYS S 947 " (cutoff:3.500A) Processing helix chain 'S' and resid 966 through 968 No H-bonds generated for 'chain 'S' and resid 966 through 968' Processing helix chain 'S' and resid 976 through 984 Processing helix chain 'S' and resid 985 through 1033 removed outlier: 4.875A pdb=" N VAL S 991 " --> pdb=" O PRO S 987 " (cutoff:3.500A) Processing helix chain 'S' and resid 1140 through 1146 removed outlier: 4.604A pdb=" N GLU S1144 " --> pdb=" O PRO S1140 " (cutoff:3.500A) Processing helix chain 'V' and resid 294 through 303 Processing helix chain 'V' and resid 339 through 343 Processing helix chain 'V' and resid 383 through 388 removed outlier: 3.898A pdb=" N ASN V 388 " --> pdb=" O PRO V 384 " (cutoff:3.500A) Processing helix chain 'V' and resid 405 through 411 removed outlier: 4.999A pdb=" N ARG V 408 " --> pdb=" O ASP V 405 " (cutoff:3.500A) Processing helix chain 'V' and resid 416 through 422 removed outlier: 3.562A pdb=" N TYR V 421 " --> pdb=" O LYS V 417 " (cutoff:3.500A) Processing helix chain 'V' and resid 438 through 443 Processing helix chain 'V' and resid 616 through 620 Processing helix chain 'V' and resid 737 through 743 Processing helix chain 'V' and resid 746 through 754 removed outlier: 4.580A pdb=" N LEU V 752 " --> pdb=" O GLU V 748 " (cutoff:3.500A) Processing helix chain 'V' and resid 755 through 757 No H-bonds generated for 'chain 'V' and resid 755 through 757' Processing helix chain 'V' and resid 758 through 783 removed outlier: 3.788A pdb=" N ASP V 775 " --> pdb=" O ALA V 771 " (cutoff:3.500A) Processing helix chain 'V' and resid 801 through 805 removed outlier: 4.570A pdb=" N GLN V 804 " --> pdb=" O ASN V 801 " (cutoff:3.500A) Processing helix chain 'V' and resid 816 through 825 removed outlier: 3.877A pdb=" N PHE V 823 " --> pdb=" O GLU V 819 " (cutoff:3.500A) Processing helix chain 'V' and resid 866 through 884 Processing helix chain 'V' and resid 886 through 891 removed outlier: 3.720A pdb=" N ALA V 890 " --> pdb=" O TRP V 886 " (cutoff:3.500A) Processing helix chain 'V' and resid 897 through 909 removed outlier: 3.659A pdb=" N ALA V 903 " --> pdb=" O ALA V 899 " (cutoff:3.500A) Processing helix chain 'V' and resid 913 through 918 Processing helix chain 'V' and resid 919 through 941 Processing helix chain 'V' and resid 942 through 944 No H-bonds generated for 'chain 'V' and resid 942 through 944' Processing helix chain 'V' and resid 945 through 965 Processing helix chain 'V' and resid 976 through 984 removed outlier: 3.740A pdb=" N ILE V 980 " --> pdb=" O VAL V 976 " (cutoff:3.500A) Processing helix chain 'V' and resid 985 through 1022 removed outlier: 4.245A pdb=" N VAL V 991 " --> pdb=" O PRO V 987 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN V 992 " --> pdb=" O GLU V 988 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG V 995 " --> pdb=" O VAL V 991 " (cutoff:3.500A) Processing helix chain 'V' and resid 1023 through 1033 Processing helix chain 'V' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.707A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.706A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.298A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.060A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.126A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.457A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.690A pdb=" N PHE C 823 " --> pdb=" O GLU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 4.183A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.555A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.616A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.510A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.066A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'a' and resid 73 through 75 No H-bonds generated for 'chain 'a' and resid 73 through 75' Processing helix chain 'c' and resid 79 through 83 Processing helix chain 'b' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'S' and resid 28 through 31 removed outlier: 3.540A pdb=" N SER S 60 " --> pdb=" O SER S 31 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ASN S 61 " --> pdb=" O TYR S 269 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N TYR S 269 " --> pdb=" O ASN S 61 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA S 264 " --> pdb=" O THR S 95 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR S 95 " --> pdb=" O ALA S 264 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N SER S 205 " --> pdb=" O PRO S 225 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N HIS S 207 " --> pdb=" O LEU S 223 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N LEU S 223 " --> pdb=" O HIS S 207 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL S 36 " --> pdb=" O LEU S 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 42 through 43 removed outlier: 6.573A pdb=" N PHE S 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 47 through 55 removed outlier: 7.221A pdb=" N THR S 274 " --> pdb=" O ASP S 290 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP S 290 " --> pdb=" O THR S 274 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU S 276 " --> pdb=" O ALA S 288 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA S 288 " --> pdb=" O LEU S 276 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS S 278 " --> pdb=" O THR S 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'S' and resid 311 through 319 removed outlier: 5.346A pdb=" N ILE S 312 " --> pdb=" O THR S 599 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR S 599 " --> pdb=" O ILE S 312 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLN S 314 " --> pdb=" O VAL S 597 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL S 597 " --> pdb=" O GLN S 314 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER S 316 " --> pdb=" O VAL S 595 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLY S 594 " --> pdb=" O GLN S 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'S' and resid 361 through 362 removed outlier: 7.031A pdb=" N CYS S 361 " --> pdb=" O CYS S 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'S' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'S' and resid 538 through 543 removed outlier: 5.425A pdb=" N GLU S 583 " --> pdb=" O ASP S 578 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ASP S 574 " --> pdb=" O ILE S 587 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY S 566 " --> pdb=" O ASP S 574 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE S 565 " --> pdb=" O PHE V 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 654 through 655 removed outlier: 6.659A pdb=" N ILE S 670 " --> pdb=" O ILE S 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'S' and resid 711 through 728 removed outlier: 6.489A pdb=" N SER S 711 " --> pdb=" O THR S1076 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR S1076 " --> pdb=" O SER S 711 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA S 713 " --> pdb=" O ASN S1074 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN S1074 " --> pdb=" O ALA S 713 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLU S1072 " --> pdb=" O PRO S 715 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA S1056 " --> pdb=" O GLY S1059 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TYR S1067 " --> pdb=" O HIS S1048 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N HIS S1048 " --> pdb=" O TYR S1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'S' and resid 788 through 790 removed outlier: 6.308A pdb=" N ILE S 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 'S' and resid 1120 through 1125 removed outlier: 4.717A pdb=" N ALA S1087 " --> pdb=" O SER S1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'V' and resid 47 through 55 removed outlier: 3.791A pdb=" N ASP V 287 " --> pdb=" O LYS V 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'V' and resid 63 through 65 removed outlier: 6.082A pdb=" N PHE V 201 " --> pdb=" O ASP V 228 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP V 228 " --> pdb=" O PHE V 201 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE V 203 " --> pdb=" O LEU V 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'V' and resid 84 through 85 removed outlier: 3.699A pdb=" N PHE V 168 " --> pdb=" O VAL V 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'V' and resid 311 through 319 removed outlier: 5.394A pdb=" N ILE V 312 " --> pdb=" O THR V 599 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N THR V 599 " --> pdb=" O ILE V 312 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLN V 314 " --> pdb=" O VAL V 597 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL V 597 " --> pdb=" O GLN V 314 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER V 316 " --> pdb=" O VAL V 595 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY V 594 " --> pdb=" O GLN V 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 325 through 328 removed outlier: 5.263A pdb=" N ASP V 574 " --> pdb=" O ILE V 587 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA V 575 " --> pdb=" O GLY V 566 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE V 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'V' and resid 348 through 349 removed outlier: 7.168A pdb=" N ALA V 348 " --> pdb=" O VAL V 401 " (cutoff:3.500A) removed outlier: 9.509A pdb=" N ARG V 403 " --> pdb=" O ALA V 348 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'V' and resid 391 through 392 removed outlier: 3.509A pdb=" N VAL V 524 " --> pdb=" O PHE V 392 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'V' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'V' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'V' and resid 654 through 655 removed outlier: 6.144A pdb=" N GLU V 654 " --> pdb=" O ALA V 694 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N THR V 696 " --> pdb=" O GLU V 654 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE V 670 " --> pdb=" O ILE V 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'V' and resid 702 through 704 Processing sheet with id=AD2, first strand: chain 'V' and resid 711 through 715 Processing sheet with id=AD3, first strand: chain 'V' and resid 718 through 728 removed outlier: 3.578A pdb=" N ALA V1056 " --> pdb=" O GLY V1059 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N TYR V1067 " --> pdb=" O HIS V1048 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N HIS V1048 " --> pdb=" O TYR V1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'V' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'V' and resid 1120 through 1123 removed outlier: 4.066A pdb=" N ALA V1087 " --> pdb=" O SER V1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'V' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.063A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.661A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.674A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.943A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.522A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.274A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.714A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.068A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.690A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.820A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 10 through 11 removed outlier: 4.071A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.749A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.749A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 3 through 6 Processing sheet with id=AG1, first strand: chain 'a' and resid 10 through 12 removed outlier: 6.933A pdb=" N ILE a 34 " --> pdb=" O ARG a 50 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ARG a 50 " --> pdb=" O ILE a 34 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TRP a 36 " --> pdb=" O MET a 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 10 through 12 removed outlier: 4.452A pdb=" N VAL a 102 " --> pdb=" O ARG a 94 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'c' and resid 4 through 7 Processing sheet with id=AG4, first strand: chain 'c' and resid 10 through 12 removed outlier: 6.863A pdb=" N LEU c 11 " --> pdb=" O GLU c 105 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP c 35 " --> pdb=" O LEU c 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'd' and resid 3 through 6 removed outlier: 3.826A pdb=" N THR d 77 " --> pdb=" O ASP d 72 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP d 72 " --> pdb=" O THR d 77 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'd' and resid 10 through 12 removed outlier: 6.905A pdb=" N ILE d 34 " --> pdb=" O ARG d 50 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG d 50 " --> pdb=" O ILE d 34 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP d 36 " --> pdb=" O MET d 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'b' and resid 4 through 7 Processing sheet with id=AG8, first strand: chain 'b' and resid 10 through 12 removed outlier: 6.730A pdb=" N LEU b 11 " --> pdb=" O GLU b 105 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLN b 37 " --> pdb=" O LEU b 46 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU b 46 " --> pdb=" O GLN b 37 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 10 through 12 removed outlier: 6.730A pdb=" N LEU b 11 " --> pdb=" O GLU b 105 " (cutoff:3.500A) 1194 hydrogen bonds defined for protein. 3165 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: 6.91 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 4624 1.27 - 1.41: 7535 1.41 - 1.55: 16962 1.55 - 1.68: 239 1.68 - 1.82: 168 Bond restraints: 29528 Sorted by residual: bond pdb=" C PHE V 329 " pdb=" O PHE V 329 " ideal model delta sigma weight residual 1.235 1.136 0.099 1.29e-02 6.01e+03 5.94e+01 bond pdb=" C TYR C 266 " pdb=" O TYR C 266 " ideal model delta sigma weight residual 1.234 1.150 0.084 1.16e-02 7.43e+03 5.23e+01 bond pdb=" C ASN S 717 " pdb=" O ASN S 717 " ideal model delta sigma weight residual 1.236 1.167 0.069 9.90e-03 1.02e+04 4.79e+01 bond pdb=" N LEU S 518 " pdb=" CA LEU S 518 " ideal model delta sigma weight residual 1.457 1.540 -0.083 1.29e-02 6.01e+03 4.14e+01 bond pdb=" C ILE C 332 " pdb=" O ILE C 332 " ideal model delta sigma weight residual 1.236 1.174 0.062 9.90e-03 1.02e+04 3.92e+01 ... (remaining 29523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 38077 3.61 - 7.21: 2052 7.21 - 10.82: 50 10.82 - 14.42: 14 14.42 - 18.03: 8 Bond angle restraints: 40201 Sorted by residual: angle pdb=" C TYR C 495 " pdb=" CA TYR C 495 " pdb=" CB TYR C 495 " ideal model delta sigma weight residual 110.88 94.19 16.69 1.57e+00 4.06e-01 1.13e+02 angle pdb=" C THR C 333 " pdb=" CA THR C 333 " pdb=" CB THR C 333 " ideal model delta sigma weight residual 109.55 93.43 16.12 1.68e+00 3.54e-01 9.20e+01 angle pdb=" C THR S 415 " pdb=" CA THR S 415 " pdb=" CB THR S 415 " ideal model delta sigma weight residual 109.80 124.41 -14.61 1.65e+00 3.67e-01 7.84e+01 angle pdb=" CA LEU V 335 " pdb=" C LEU V 335 " pdb=" N CYS V 336 " ideal model delta sigma weight residual 116.57 128.54 -11.97 1.39e+00 5.18e-01 7.42e+01 angle pdb=" N LEU V 335 " pdb=" CA LEU V 335 " pdb=" C LEU V 335 " ideal model delta sigma weight residual 109.15 97.16 11.99 1.44e+00 4.82e-01 6.93e+01 ... (remaining 40196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.37: 17303 22.37 - 44.73: 766 44.73 - 67.10: 143 67.10 - 89.47: 54 89.47 - 111.83: 5 Dihedral angle restraints: 18271 sinusoidal: 7668 harmonic: 10603 Sorted by residual: dihedral pdb=" C THR S 415 " pdb=" N THR S 415 " pdb=" CA THR S 415 " pdb=" CB THR S 415 " ideal model delta harmonic sigma weight residual -122.00 -149.03 27.03 0 2.50e+00 1.60e-01 1.17e+02 dihedral pdb=" N THR S 415 " pdb=" C THR S 415 " pdb=" CA THR S 415 " pdb=" CB THR S 415 " ideal model delta harmonic sigma weight residual 123.40 145.10 -21.70 0 2.50e+00 1.60e-01 7.53e+01 dihedral pdb=" C TYR C 495 " pdb=" N TYR C 495 " pdb=" CA TYR C 495 " pdb=" CB TYR C 495 " ideal model delta harmonic sigma weight residual -122.60 -103.11 -19.49 0 2.50e+00 1.60e-01 6.08e+01 ... (remaining 18268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.204: 4540 0.204 - 0.408: 215 0.408 - 0.612: 12 0.612 - 0.816: 2 0.816 - 1.020: 3 Chirality restraints: 4772 Sorted by residual: chirality pdb=" C1 BMA A 3 " pdb=" O4 NAG A 2 " pdb=" C2 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.77 0.37 2.00e-02 2.50e+03 3.49e+02 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.39e+02 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.39e+01 ... (remaining 4769 not shown) Planarity restraints: 5145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG V1212 " 0.328 2.00e-02 2.50e+03 2.76e-01 9.51e+02 pdb=" C7 NAG V1212 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG V1212 " 0.193 2.00e-02 2.50e+03 pdb=" N2 NAG V1212 " -0.476 2.00e-02 2.50e+03 pdb=" O7 NAG V1212 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " -0.280 2.00e-02 2.50e+03 2.46e-01 7.60e+02 pdb=" C7 NAG A 2 " 0.053 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " -0.032 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " 0.436 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " -0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S1208 " -0.244 2.00e-02 2.50e+03 2.08e-01 5.42e+02 pdb=" C7 NAG S1208 " 0.051 2.00e-02 2.50e+03 pdb=" C8 NAG S1208 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG S1208 " 0.345 2.00e-02 2.50e+03 pdb=" O7 NAG S1208 " -0.185 2.00e-02 2.50e+03 ... (remaining 5142 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 17 2.01 - 2.73: 977 2.73 - 3.45: 41111 3.45 - 4.18: 69475 4.18 - 4.90: 121918 Nonbonded interactions: 233498 Sorted by model distance: nonbonded pdb=" CG2 VAL V 395 " pdb=" CA PHE V 515 " model vdw 1.285 3.890 nonbonded pdb=" CG2 THR V 393 " pdb=" CA ALA V 522 " model vdw 1.345 3.890 nonbonded pdb=" OH TYR V 380 " pdb=" CG2 VAL V 433 " model vdw 1.489 3.460 nonbonded pdb=" CE1 PHE V 392 " pdb=" O GLU V 516 " model vdw 1.628 3.340 nonbonded pdb=" NZ LYS S 386 " pdb=" O LEU V 981 " model vdw 1.676 3.120 ... (remaining 233493 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 'B' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'W' } ncs_group { reference = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 200 through 211 or resid 215 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 527 or (resid 528 thro \ ugh 529 and (name N or name CA or name C or name O or name CB )) or resid 530 th \ rough 553 or (resid 554 and (name N or name CA or name C or name O or name CB )) \ or resid 555 through 567 or (resid 568 and (name N or name CA or name C or name \ O or name CB )) or resid 569 through 570 or (resid 571 and (name N or name CA o \ r name C or name O or name CB )) or resid 572 through 581 or (resid 582 through \ 583 and (name N or name CA or name C or name O or name CB )) or resid 584 throug \ h 585 or (resid 586 and (name N or name CA or name C or name O or name CB )) or \ resid 587 through 618 or (resid 619 and (name N or name CA or name C or name O o \ r name CB )) or resid 620 through 645 or (resid 646 through 647 and (name N or n \ ame CA or name C or name O or name CB )) or resid 648 through 793 or (resid 794 \ and (name N or name CA or name C or name O or name CB )) or resid 795 or (resid \ 796 and (name N or name CA or name C or name O or name CB )) or resid 797 throug \ h 920 or (resid 921 and (name N or name CA or name C or name O or name CB )) or \ resid 922 through 1072 or (resid 1073 and (name N or name CA or name C or name O \ or name CB )) or resid 1074 through 1117 or (resid 1118 and (name N or name CA \ or name C or name O or name CB )) or resid 1119 through 1141 or (resid 1142 and \ (name N or name CA or name C or name O or name CB )) or resid 1143 or (resid 114 \ 4 through 1146 and (name N or name CA or name C or name O or name CB )) or resid \ 1147 through 1210)) selection = (chain 'S' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 166 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 200 through 210 or (resid 211 and (name \ N or name CA or name C or name O or name CB )) or (resid 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 528 or (resid 529 and (name N or name CA or name C or name O or name CB )) \ or resid 530 through 553 or (resid 554 and (name N or name CA or name C or name \ O or name CB )) or resid 555 through 793 or (resid 794 and (name N or name CA or \ name C or name O or name CB )) or resid 795 or (resid 796 and (name N or name C \ A or name C or name O or name CB )) or resid 797 through 810 or (resid 811 and ( \ name N or name CA or name C or name O or name CB )) or resid 813 through 827 or \ resid 856 through 866 or (resid 867 through 868 and (name N or name CA or name C \ or name O or name CB )) or resid 869 through 939 or (resid 940 and (name N or n \ ame CA or name C or name O or name CB )) or resid 941 through 984 or (resid 985 \ and (name N or name CA or name C or name O or name CB )) or resid 986 through 98 \ 7 or (resid 988 through 989 and (name N or name CA or name C or name O or name C \ B )) or resid 990 through 1141 or (resid 1142 and (name N or name CA or name C o \ r name O or name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 an \ d (name N or name CA or name C or name O or name CB )) or resid 1147 through 121 \ 0)) selection = (chain 'V' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 210 or (resid 211 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 280 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 567 or (resid 568 and (name N or name CA or name C or \ name O or name CB )) or resid 569 through 570 or (resid 571 and (name N or name \ CA or name C or name O or name CB )) or resid 572 through 581 or (resid 582 thr \ ough 583 and (name N or name CA or name C or name O or name CB )) or resid 584 t \ hrough 585 or (resid 586 and (name N or name CA or name C or name O or name CB ) \ ) or resid 587 through 613 or (resid 614 and (name N or name CA or name C or nam \ e O or name CB )) or resid 615 through 618 or (resid 619 and (name N or name CA \ or name C or name O or name CB )) or resid 620 through 676 or resid 690 through \ 744 or (resid 745 and (name N or name CA or name C or name O or name CB )) or re \ sid 746 through 810 or (resid 811 and (name N or name CA or name C or name O or \ name CB )) or resid 813 through 827 or resid 856 through 866 or (resid 867 throu \ gh 868 and (name N or name CA or name C or name O or name CB )) or resid 869 thr \ ough 920 or (resid 921 and (name N or name CA or name C or name O or name CB )) \ or resid 922 through 939 or (resid 940 and (name N or name CA or name C or name \ O or name CB )) or resid 941 through 984 or (resid 985 and (name N or name CA or \ name C or name O or name CB )) or resid 986 through 987 or (resid 988 through 9 \ 89 and (name N or name CA or name C or name O or name CB )) or resid 990 through \ 1072 or (resid 1073 and (name N or name CA or name C or name O or name CB )) or \ resid 1074 through 1117 or (resid 1118 and (name N or name CA or name C or name \ O or name CB )) or resid 1119 through 1143 or (resid 1144 through 1146 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1147 through 1210)) } ncs_group { reference = chain 'H' selection = chain 'a' selection = chain 'd' } ncs_group { reference = chain 'L' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.040 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.430 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 : 0.014 0.355 29620 Z= 0.884 Angle : 1.912 23.288 40439 Z= 1.247 Chirality : 0.110 1.020 4772 Planarity : 0.016 0.276 5099 Dihedral : 13.965 111.831 11370 Min Nonbonded Distance : 1.285 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.68 % Favored : 92.76 % Rotamer: Outliers : 3.00 % Allowed : 5.31 % Favored : 91.69 % Cbeta Deviations : 0.79 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.13), residues: 3579 helix: -1.63 (0.16), residues: 666 sheet: -0.38 (0.19), residues: 687 loop : -1.06 (0.12), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 346 TYR 0.110 0.020 TYR d 32 PHE 0.078 0.012 PHE C 86 TRP 0.132 0.026 TRP a 47 HIS 0.010 0.003 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.01371 (29528) covalent geometry : angle 1.88042 (40201) SS BOND : bond 0.01518 ( 29) SS BOND : angle 2.03512 ( 58) hydrogen bonds : bond 0.15943 ( 1177) hydrogen bonds : angle 8.73078 ( 3165) Misc. bond : bond 0.34473 ( 3) link_BETA1-4 : bond 0.02191 ( 14) link_BETA1-4 : angle 5.80764 ( 42) link_NAG-ASN : bond 0.04129 ( 46) link_NAG-ASN : angle 5.40397 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 321 time to evaluate : 1.019 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: S 414 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8028 (mm-40) REVERT: S 448 ASN cc_start: 0.6992 (t0) cc_final: 0.6677 (t0) REVERT: S 518 LEU cc_start: 0.3190 (OUTLIER) cc_final: 0.2519 (mt) REVERT: S 697 MET cc_start: 0.8551 (ptm) cc_final: 0.8339 (ptp) REVERT: V 868 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7922 (tm-30) REVERT: C 54 LEU cc_start: 0.8897 (mt) cc_final: 0.8675 (mp) REVERT: C 265 TYR cc_start: 0.7763 (OUTLIER) cc_final: 0.5419 (p90) REVERT: C 374 PHE cc_start: 0.7892 (m-10) cc_final: 0.7541 (m-80) REVERT: C 376 THR cc_start: 0.8261 (m) cc_final: 0.7945 (p) REVERT: C 453 TYR cc_start: 0.7702 (p90) cc_final: 0.6929 (p90) REVERT: C 493 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7598 (tm-30) REVERT: C 501 ASN cc_start: 0.6837 (OUTLIER) cc_final: 0.6497 (m-40) REVERT: C 508 TYR cc_start: 0.6388 (m-80) cc_final: 0.6092 (m-10) REVERT: L 46 LEU cc_start: 0.4136 (tt) cc_final: 0.2772 (tt) outliers start: 92 outliers final: 43 residues processed: 406 average time/residue: 0.1838 time to fit residues: 118.8706 Evaluate side-chains 223 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 175 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain S residue 122 ASN Chi-restraints excluded: chain S residue 231 ILE Chi-restraints excluded: chain S residue 233 ILE Chi-restraints excluded: chain S residue 235 ILE Chi-restraints excluded: chain S residue 237 ARG Chi-restraints excluded: chain S residue 367 VAL Chi-restraints excluded: chain S residue 408 ARG Chi-restraints excluded: chain S residue 414 GLN Chi-restraints excluded: chain S residue 415 THR Chi-restraints excluded: chain S residue 518 LEU Chi-restraints excluded: chain S residue 519 HIS Chi-restraints excluded: chain S residue 546 LEU Chi-restraints excluded: chain S residue 565 PHE Chi-restraints excluded: chain S residue 887 THR Chi-restraints excluded: chain S residue 975 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 333 THR Chi-restraints excluded: chain V residue 334 ASN Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 351 TYR Chi-restraints excluded: chain V residue 353 TRP Chi-restraints excluded: chain V residue 358 ILE Chi-restraints excluded: chain V residue 370 ASN Chi-restraints excluded: chain V residue 373 SER Chi-restraints excluded: chain V residue 385 THR Chi-restraints excluded: chain V residue 390 LEU Chi-restraints excluded: chain V residue 393 THR Chi-restraints excluded: chain V residue 394 ASN Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 396 TYR Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain V residue 567 ARG Chi-restraints excluded: chain V residue 791 THR Chi-restraints excluded: chain V residue 931 ILE Chi-restraints excluded: chain V residue 1004 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain d residue 94 ARG Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 388 ASN ** S 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 564 GLN S 919 ASN ** S 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 121 ASN ** V 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 501 ASN V 856 ASN V 957 GLN V1048 HIS V1083 HIS V1088 HIS C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN C 907 ASN C1088 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.175732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.113824 restraints weight = 47830.041| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.70 r_work: 0.3281 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29620 Z= 0.162 Angle : 0.769 14.882 40439 Z= 0.391 Chirality : 0.049 0.455 4772 Planarity : 0.005 0.068 5099 Dihedral : 8.347 77.175 5270 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.66 % Favored : 96.20 % Rotamer: Outliers : 2.54 % Allowed : 8.34 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.13), residues: 3579 helix: 0.20 (0.20), residues: 669 sheet: -0.49 (0.15), residues: 951 loop : -0.87 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 509 TYR 0.034 0.002 TYR V 380 PHE 0.025 0.002 PHE C 329 TRP 0.043 0.003 TRP c 35 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00354 (29528) covalent geometry : angle 0.73514 (40201) SS BOND : bond 0.00755 ( 29) SS BOND : angle 1.97601 ( 58) hydrogen bonds : bond 0.04432 ( 1177) hydrogen bonds : angle 6.56357 ( 3165) Misc. bond : bond 0.00439 ( 3) link_BETA1-4 : bond 0.00375 ( 14) link_BETA1-4 : angle 3.81241 ( 42) link_NAG-ASN : bond 0.00414 ( 46) link_NAG-ASN : angle 3.10726 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 201 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 197 ILE cc_start: 0.7909 (mm) cc_final: 0.7128 (tt) REVERT: S 529 LYS cc_start: 0.8587 (mttt) cc_final: 0.8320 (mmtm) REVERT: S 569 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8901 (mm) REVERT: V 567 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.7793 (mpt90) REVERT: V 975 SER cc_start: 0.8733 (m) cc_final: 0.8477 (p) REVERT: C 238 PHE cc_start: 0.7755 (p90) cc_final: 0.6966 (p90) REVERT: C 239 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7405 (tp40) REVERT: C 334 ASN cc_start: 0.7330 (OUTLIER) cc_final: 0.6908 (p0) REVERT: C 376 THR cc_start: 0.8436 (m) cc_final: 0.7909 (p) REVERT: C 501 ASN cc_start: 0.6812 (OUTLIER) cc_final: 0.6400 (m-40) REVERT: H 53 MET cc_start: 0.7314 (tpp) cc_final: 0.7041 (mmm) REVERT: H 100 ASP cc_start: 0.7178 (t70) cc_final: 0.6657 (m-30) REVERT: L 32 TYR cc_start: 0.6868 (m-10) cc_final: 0.6396 (m-80) REVERT: c 4 MET cc_start: 0.5176 (tpp) cc_final: 0.4933 (tpp) REVERT: c 34 ASN cc_start: 0.5146 (m110) cc_final: 0.4760 (m-40) REVERT: c 35 TRP cc_start: 0.6431 (m100) cc_final: 0.5045 (m100) outliers start: 78 outliers final: 33 residues processed: 266 average time/residue: 0.1801 time to fit residues: 78.3521 Evaluate side-chains 191 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 122 ASN Chi-restraints excluded: chain S residue 235 ILE Chi-restraints excluded: chain S residue 367 VAL Chi-restraints excluded: chain S residue 408 ARG Chi-restraints excluded: chain S residue 519 HIS Chi-restraints excluded: chain S residue 565 PHE Chi-restraints excluded: chain S residue 569 ILE Chi-restraints excluded: chain S residue 856 ASN Chi-restraints excluded: chain S residue 975 SER Chi-restraints excluded: chain S residue 988 GLU Chi-restraints excluded: chain V residue 66 HIS Chi-restraints excluded: chain V residue 121 ASN Chi-restraints excluded: chain V residue 353 TRP Chi-restraints excluded: chain V residue 358 ILE Chi-restraints excluded: chain V residue 370 ASN Chi-restraints excluded: chain V residue 390 LEU Chi-restraints excluded: chain V residue 392 PHE Chi-restraints excluded: chain V residue 534 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain V residue 560 LEU Chi-restraints excluded: chain V residue 567 ARG Chi-restraints excluded: chain V residue 584 ILE Chi-restraints excluded: chain V residue 641 ASN Chi-restraints excluded: chain V residue 747 THR Chi-restraints excluded: chain V residue 820 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain a residue 17 SER Chi-restraints excluded: chain d residue 53 MET Chi-restraints excluded: chain b residue 29 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 52 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 108 optimal weight: 0.0470 chunk 37 optimal weight: 20.0000 chunk 205 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S1002 GLN V 394 ASN ** V 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1005 GLN C 207 HIS C 218 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.172233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.110909 restraints weight = 47962.598| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.99 r_work: 0.3209 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 29620 Z= 0.242 Angle : 0.723 10.924 40439 Z= 0.367 Chirality : 0.050 0.462 4772 Planarity : 0.004 0.077 5099 Dihedral : 7.367 76.616 5210 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.55 % Favored : 95.39 % Rotamer: Outliers : 3.19 % Allowed : 9.74 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.13), residues: 3579 helix: 0.29 (0.20), residues: 669 sheet: -0.64 (0.15), residues: 977 loop : -0.85 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 357 TYR 0.039 0.002 TYR L 92 PHE 0.020 0.002 PHE C 168 TRP 0.017 0.002 TRP a 36 HIS 0.005 0.001 HIS V1064 Details of bonding type rmsd covalent geometry : bond 0.00576 (29528) covalent geometry : angle 0.69754 (40201) SS BOND : bond 0.00415 ( 29) SS BOND : angle 1.58587 ( 58) hydrogen bonds : bond 0.04336 ( 1177) hydrogen bonds : angle 6.26920 ( 3165) Misc. bond : bond 0.00362 ( 3) link_BETA1-4 : bond 0.00368 ( 14) link_BETA1-4 : angle 3.26406 ( 42) link_NAG-ASN : bond 0.00388 ( 46) link_NAG-ASN : angle 2.65589 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 173 time to evaluate : 0.816 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: S 197 ILE cc_start: 0.7889 (mm) cc_final: 0.7536 (tt) REVERT: S 414 GLN cc_start: 0.8363 (tt0) cc_final: 0.7563 (mm-40) REVERT: S 452 LEU cc_start: 0.7590 (mt) cc_final: 0.7271 (mt) REVERT: S 529 LYS cc_start: 0.8774 (mttt) cc_final: 0.8494 (mmtm) REVERT: S 605 SER cc_start: 0.9114 (t) cc_final: 0.8908 (m) REVERT: V 567 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.7845 (mpt90) REVERT: V 868 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8256 (tm-30) REVERT: V 981 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8596 (mm) REVERT: C 238 PHE cc_start: 0.7778 (p90) cc_final: 0.6913 (p90) REVERT: C 239 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7445 (tp40) REVERT: C 269 TYR cc_start: 0.8058 (m-80) cc_final: 0.7588 (m-80) REVERT: C 334 ASN cc_start: 0.7476 (OUTLIER) cc_final: 0.7044 (p0) REVERT: C 376 THR cc_start: 0.8469 (m) cc_final: 0.7908 (p) REVERT: C 453 TYR cc_start: 0.7520 (p90) cc_final: 0.6638 (p90) REVERT: C 501 ASN cc_start: 0.6809 (OUTLIER) cc_final: 0.6214 (m-40) REVERT: H 53 MET cc_start: 0.7284 (tpp) cc_final: 0.6366 (mmm) REVERT: L 32 TYR cc_start: 0.6724 (m-10) cc_final: 0.6233 (m-80) REVERT: L 35 TRP cc_start: 0.5316 (m100) cc_final: 0.4341 (m100) REVERT: c 4 MET cc_start: 0.5639 (tpp) cc_final: 0.5293 (tpp) REVERT: c 73 LEU cc_start: 0.6660 (pt) cc_final: 0.6174 (tt) REVERT: c 89 GLN cc_start: 0.7058 (tm-30) cc_final: 0.6734 (tm-30) REVERT: d 100 MET cc_start: 0.3457 (mmt) cc_final: 0.2379 (mtm) REVERT: b 29 ILE cc_start: 0.2054 (OUTLIER) cc_final: 0.1608 (mm) outliers start: 98 outliers final: 55 residues processed: 258 average time/residue: 0.1701 time to fit residues: 73.2164 Evaluate side-chains 210 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 149 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 122 ASN Chi-restraints excluded: chain S residue 235 ILE Chi-restraints excluded: chain S residue 289 VAL Chi-restraints excluded: chain S residue 367 VAL Chi-restraints excluded: chain S residue 408 ARG Chi-restraints excluded: chain S residue 524 VAL Chi-restraints excluded: chain S residue 546 LEU Chi-restraints excluded: chain S residue 551 VAL Chi-restraints excluded: chain S residue 565 PHE Chi-restraints excluded: chain S residue 584 ILE Chi-restraints excluded: chain S residue 615 VAL Chi-restraints excluded: chain S residue 723 THR Chi-restraints excluded: chain S residue 788 ILE Chi-restraints excluded: chain S residue 856 ASN Chi-restraints excluded: chain S residue 975 SER Chi-restraints excluded: chain S residue 1127 ASP Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 66 HIS Chi-restraints excluded: chain V residue 117 LEU Chi-restraints excluded: chain V residue 236 THR Chi-restraints excluded: chain V residue 353 TRP Chi-restraints excluded: chain V residue 358 ILE Chi-restraints excluded: chain V residue 370 ASN Chi-restraints excluded: chain V residue 379 CYS Chi-restraints excluded: chain V residue 390 LEU Chi-restraints excluded: chain V residue 392 PHE Chi-restraints excluded: chain V residue 394 ASN Chi-restraints excluded: chain V residue 534 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain V residue 560 LEU Chi-restraints excluded: chain V residue 567 ARG Chi-restraints excluded: chain V residue 584 ILE Chi-restraints excluded: chain V residue 708 SER Chi-restraints excluded: chain V residue 791 THR Chi-restraints excluded: chain V residue 820 ASP Chi-restraints excluded: chain V residue 856 ASN Chi-restraints excluded: chain V residue 981 LEU Chi-restraints excluded: chain V residue 1021 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain H residue 54 PHE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain d residue 53 MET Chi-restraints excluded: chain d residue 94 ARG Chi-restraints excluded: chain b residue 29 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 132 optimal weight: 30.0000 chunk 172 optimal weight: 0.6980 chunk 138 optimal weight: 40.0000 chunk 328 optimal weight: 8.9990 chunk 283 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 314 optimal weight: 50.0000 chunk 18 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 121 ASN V 394 ASN ** V 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 955 ASN C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.173665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.110980 restraints weight = 47508.253| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.60 r_work: 0.3268 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 29620 Z= 0.142 Angle : 0.641 13.074 40439 Z= 0.323 Chirality : 0.047 0.408 4772 Planarity : 0.004 0.043 5099 Dihedral : 6.907 77.692 5207 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.69 % Favored : 96.26 % Rotamer: Outliers : 2.57 % Allowed : 11.18 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.13), residues: 3579 helix: 0.68 (0.21), residues: 669 sheet: -0.56 (0.15), residues: 966 loop : -0.79 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 408 TYR 0.027 0.001 TYR C 508 PHE 0.020 0.001 PHE C 201 TRP 0.037 0.001 TRP c 35 HIS 0.003 0.001 HIS S1064 Details of bonding type rmsd covalent geometry : bond 0.00325 (29528) covalent geometry : angle 0.61378 (40201) SS BOND : bond 0.00387 ( 29) SS BOND : angle 2.29739 ( 58) hydrogen bonds : bond 0.03739 ( 1177) hydrogen bonds : angle 5.97519 ( 3165) Misc. bond : bond 0.00155 ( 3) link_BETA1-4 : bond 0.00306 ( 14) link_BETA1-4 : angle 2.85257 ( 42) link_NAG-ASN : bond 0.00401 ( 46) link_NAG-ASN : angle 2.47079 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 172 time to evaluate : 1.051 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: S 197 ILE cc_start: 0.7965 (mm) cc_final: 0.7589 (tt) REVERT: S 361 CYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7263 (p) REVERT: S 414 GLN cc_start: 0.8407 (tt0) cc_final: 0.7602 (mm110) REVERT: S 452 LEU cc_start: 0.7634 (mt) cc_final: 0.7285 (mt) REVERT: S 950 ASP cc_start: 0.8682 (t0) cc_final: 0.8311 (m-30) REVERT: V 567 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.7890 (mpt90) REVERT: V 868 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8154 (tm-30) REVERT: V 975 SER cc_start: 0.8825 (m) cc_final: 0.8493 (p) REVERT: C 238 PHE cc_start: 0.7741 (p90) cc_final: 0.6920 (p90) REVERT: C 239 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7519 (tp40) REVERT: C 269 TYR cc_start: 0.8012 (m-80) cc_final: 0.7287 (m-10) REVERT: C 334 ASN cc_start: 0.7408 (OUTLIER) cc_final: 0.7139 (p0) REVERT: C 453 TYR cc_start: 0.7653 (p90) cc_final: 0.6612 (p90) REVERT: C 501 ASN cc_start: 0.6837 (OUTLIER) cc_final: 0.6428 (m-40) REVERT: H 29 PHE cc_start: 0.4442 (p90) cc_final: 0.4226 (p90) REVERT: H 53 MET cc_start: 0.7019 (tpp) cc_final: 0.6498 (mmm) REVERT: L 32 TYR cc_start: 0.6840 (m-10) cc_final: 0.6371 (m-80) REVERT: L 33 LEU cc_start: 0.6224 (tp) cc_final: 0.5881 (tp) REVERT: L 35 TRP cc_start: 0.5358 (m100) cc_final: 0.4541 (m100) REVERT: L 87 TYR cc_start: 0.0976 (m-80) cc_final: 0.0706 (m-80) REVERT: a 52 ILE cc_start: 0.7583 (mp) cc_final: 0.7296 (mm) REVERT: a 90 TYR cc_start: 0.5640 (m-80) cc_final: 0.5427 (m-80) REVERT: c 73 LEU cc_start: 0.6822 (pt) cc_final: 0.6279 (tt) REVERT: c 89 GLN cc_start: 0.6598 (tm-30) cc_final: 0.5959 (tm-30) REVERT: d 100 MET cc_start: 0.3493 (mmt) cc_final: 0.2157 (mtm) outliers start: 79 outliers final: 45 residues processed: 237 average time/residue: 0.1619 time to fit residues: 64.4797 Evaluate side-chains 202 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 152 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 122 ASN Chi-restraints excluded: chain S residue 235 ILE Chi-restraints excluded: chain S residue 361 CYS Chi-restraints excluded: chain S residue 408 ARG Chi-restraints excluded: chain S residue 524 VAL Chi-restraints excluded: chain S residue 551 VAL Chi-restraints excluded: chain S residue 565 PHE Chi-restraints excluded: chain S residue 584 ILE Chi-restraints excluded: chain S residue 856 ASN Chi-restraints excluded: chain S residue 916 LEU Chi-restraints excluded: chain S residue 975 SER Chi-restraints excluded: chain S residue 977 LEU Chi-restraints excluded: chain S residue 988 GLU Chi-restraints excluded: chain V residue 66 HIS Chi-restraints excluded: chain V residue 110 LEU Chi-restraints excluded: chain V residue 353 TRP Chi-restraints excluded: chain V residue 358 ILE Chi-restraints excluded: chain V residue 370 ASN Chi-restraints excluded: chain V residue 379 CYS Chi-restraints excluded: chain V residue 390 LEU Chi-restraints excluded: chain V residue 392 PHE Chi-restraints excluded: chain V residue 394 ASN Chi-restraints excluded: chain V residue 534 VAL Chi-restraints excluded: chain V residue 567 ARG Chi-restraints excluded: chain V residue 584 ILE Chi-restraints excluded: chain V residue 747 THR Chi-restraints excluded: chain V residue 856 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain a residue 17 SER Chi-restraints excluded: chain a residue 96 MET Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain d residue 53 MET Chi-restraints excluded: chain d residue 94 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 111 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 340 optimal weight: 50.0000 chunk 73 optimal weight: 0.8980 chunk 345 optimal weight: 0.4980 chunk 223 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 307 optimal weight: 40.0000 chunk 66 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 935 GLN S1113 GLN ** V 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 414 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.173543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.113301 restraints weight = 47736.412| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.12 r_work: 0.3283 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 29620 Z= 0.158 Angle : 0.621 11.655 40439 Z= 0.313 Chirality : 0.046 0.401 4772 Planarity : 0.004 0.042 5099 Dihedral : 6.512 78.397 5201 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.60 % Favored : 96.34 % Rotamer: Outliers : 3.16 % Allowed : 11.47 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.13), residues: 3579 helix: 0.80 (0.21), residues: 670 sheet: -0.49 (0.16), residues: 969 loop : -0.82 (0.13), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 408 TYR 0.019 0.001 TYR S1067 PHE 0.016 0.001 PHE C 374 TRP 0.023 0.001 TRP c 35 HIS 0.004 0.001 HIS S1064 Details of bonding type rmsd covalent geometry : bond 0.00369 (29528) covalent geometry : angle 0.59520 (40201) SS BOND : bond 0.00484 ( 29) SS BOND : angle 2.25229 ( 58) hydrogen bonds : bond 0.03670 ( 1177) hydrogen bonds : angle 5.80743 ( 3165) Misc. bond : bond 0.00103 ( 3) link_BETA1-4 : bond 0.00346 ( 14) link_BETA1-4 : angle 2.76951 ( 42) link_NAG-ASN : bond 0.00330 ( 46) link_NAG-ASN : angle 2.27287 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 162 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 95 THR cc_start: 0.7790 (p) cc_final: 0.7485 (t) REVERT: S 197 ILE cc_start: 0.7987 (mm) cc_final: 0.7609 (tt) REVERT: S 361 CYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7305 (p) REVERT: S 408 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8120 (ppt170) REVERT: S 414 GLN cc_start: 0.8409 (tt0) cc_final: 0.7600 (mm-40) REVERT: S 452 LEU cc_start: 0.7727 (mt) cc_final: 0.7394 (mt) REVERT: V 118 LEU cc_start: 0.8767 (tt) cc_final: 0.8507 (tt) REVERT: V 523 THR cc_start: 0.4879 (OUTLIER) cc_final: 0.4569 (t) REVERT: V 567 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.7936 (mpt90) REVERT: V 868 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8168 (tm-30) REVERT: V 975 SER cc_start: 0.8806 (m) cc_final: 0.8487 (p) REVERT: V 981 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8519 (mm) REVERT: C 47 VAL cc_start: 0.9216 (p) cc_final: 0.8938 (m) REVERT: C 238 PHE cc_start: 0.7665 (p90) cc_final: 0.6847 (p90) REVERT: C 239 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7422 (tp40) REVERT: C 269 TYR cc_start: 0.7948 (m-80) cc_final: 0.7326 (m-10) REVERT: C 334 ASN cc_start: 0.7433 (OUTLIER) cc_final: 0.7138 (p0) REVERT: C 453 TYR cc_start: 0.7601 (p90) cc_final: 0.6523 (p90) REVERT: C 501 ASN cc_start: 0.6685 (OUTLIER) cc_final: 0.6421 (m-40) REVERT: H 53 MET cc_start: 0.6925 (tpp) cc_final: 0.6386 (mmm) REVERT: L 32 TYR cc_start: 0.6945 (m-10) cc_final: 0.6512 (m-80) REVERT: L 35 TRP cc_start: 0.5276 (m100) cc_final: 0.5016 (m100) REVERT: c 4 MET cc_start: 0.5510 (tpp) cc_final: 0.5279 (tpp) REVERT: d 100 MET cc_start: 0.3491 (mmt) cc_final: 0.2143 (mtt) REVERT: b 4 MET cc_start: 0.3067 (mtt) cc_final: 0.2537 (mpp) outliers start: 97 outliers final: 61 residues processed: 247 average time/residue: 0.1679 time to fit residues: 69.6615 Evaluate side-chains 221 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 152 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 122 ASN Chi-restraints excluded: chain S residue 235 ILE Chi-restraints excluded: chain S residue 361 CYS Chi-restraints excluded: chain S residue 408 ARG Chi-restraints excluded: chain S residue 524 VAL Chi-restraints excluded: chain S residue 551 VAL Chi-restraints excluded: chain S residue 565 PHE Chi-restraints excluded: chain S residue 584 ILE Chi-restraints excluded: chain S residue 788 ILE Chi-restraints excluded: chain S residue 856 ASN Chi-restraints excluded: chain S residue 873 TYR Chi-restraints excluded: chain S residue 916 LEU Chi-restraints excluded: chain S residue 975 SER Chi-restraints excluded: chain S residue 977 LEU Chi-restraints excluded: chain S residue 988 GLU Chi-restraints excluded: chain S residue 1127 ASP Chi-restraints excluded: chain V residue 66 HIS Chi-restraints excluded: chain V residue 117 LEU Chi-restraints excluded: chain V residue 353 TRP Chi-restraints excluded: chain V residue 354 ASN Chi-restraints excluded: chain V residue 358 ILE Chi-restraints excluded: chain V residue 370 ASN Chi-restraints excluded: chain V residue 390 LEU Chi-restraints excluded: chain V residue 392 PHE Chi-restraints excluded: chain V residue 394 ASN Chi-restraints excluded: chain V residue 523 THR Chi-restraints excluded: chain V residue 534 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain V residue 567 ARG Chi-restraints excluded: chain V residue 584 ILE Chi-restraints excluded: chain V residue 645 THR Chi-restraints excluded: chain V residue 708 SER Chi-restraints excluded: chain V residue 747 THR Chi-restraints excluded: chain V residue 791 THR Chi-restraints excluded: chain V residue 820 ASP Chi-restraints excluded: chain V residue 856 ASN Chi-restraints excluded: chain V residue 981 LEU Chi-restraints excluded: chain V residue 1104 VAL Chi-restraints excluded: chain V residue 1105 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain a residue 96 MET Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain a residue 100 TYR Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain d residue 53 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 268 optimal weight: 0.6980 chunk 314 optimal weight: 50.0000 chunk 76 optimal weight: 0.5980 chunk 171 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 318 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 307 optimal weight: 30.0000 chunk 99 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 501 ASN S 935 GLN V 370 ASN V 394 ASN ** V 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.168059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.123777 restraints weight = 46699.891| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.48 r_work: 0.3219 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29620 Z= 0.169 Angle : 0.621 11.253 40439 Z= 0.310 Chirality : 0.047 0.408 4772 Planarity : 0.004 0.095 5099 Dihedral : 6.474 78.144 5201 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.80 % Favored : 96.14 % Rotamer: Outliers : 3.10 % Allowed : 12.32 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.13), residues: 3579 helix: 0.81 (0.21), residues: 670 sheet: -0.47 (0.16), residues: 971 loop : -0.80 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG d 94 TYR 0.019 0.001 TYR S1138 PHE 0.026 0.001 PHE a 54 TRP 0.028 0.002 TRP c 35 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00398 (29528) covalent geometry : angle 0.59106 (40201) SS BOND : bond 0.00406 ( 29) SS BOND : angle 2.06822 ( 58) hydrogen bonds : bond 0.03608 ( 1177) hydrogen bonds : angle 5.73939 ( 3165) Misc. bond : bond 0.00125 ( 3) link_BETA1-4 : bond 0.00307 ( 14) link_BETA1-4 : angle 2.68592 ( 42) link_NAG-ASN : bond 0.00328 ( 46) link_NAG-ASN : angle 2.69759 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 159 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 197 ILE cc_start: 0.8138 (mm) cc_final: 0.7934 (tt) REVERT: S 361 CYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7365 (p) REVERT: S 408 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8135 (ppt170) REVERT: S 414 GLN cc_start: 0.8320 (tt0) cc_final: 0.7744 (mm-40) REVERT: S 452 LEU cc_start: 0.7955 (mt) cc_final: 0.7657 (mt) REVERT: S 569 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8985 (mm) REVERT: S 950 ASP cc_start: 0.8663 (t0) cc_final: 0.8272 (m-30) REVERT: S 1138 TYR cc_start: 0.8072 (t80) cc_final: 0.7784 (t80) REVERT: V 523 THR cc_start: 0.5503 (OUTLIER) cc_final: 0.5183 (t) REVERT: V 567 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8095 (mpt90) REVERT: V 975 SER cc_start: 0.8776 (m) cc_final: 0.8461 (p) REVERT: V 981 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8436 (mm) REVERT: C 47 VAL cc_start: 0.9252 (p) cc_final: 0.9028 (m) REVERT: C 239 GLN cc_start: 0.8174 (tt0) cc_final: 0.7695 (tp40) REVERT: C 269 TYR cc_start: 0.7960 (m-80) cc_final: 0.7519 (m-10) REVERT: C 453 TYR cc_start: 0.7813 (p90) cc_final: 0.7205 (p90) REVERT: L 32 TYR cc_start: 0.6672 (m-10) cc_final: 0.6259 (m-80) REVERT: L 35 TRP cc_start: 0.5564 (m100) cc_final: 0.5122 (m100) REVERT: a 90 TYR cc_start: 0.5423 (m-80) cc_final: 0.5055 (m-80) REVERT: c 34 ASN cc_start: 0.4710 (m-40) cc_final: 0.4321 (m110) REVERT: c 89 GLN cc_start: 0.7203 (tm-30) cc_final: 0.6539 (tm-30) REVERT: d 100 MET cc_start: 0.3380 (mmt) cc_final: 0.2175 (mtt) outliers start: 95 outliers final: 69 residues processed: 243 average time/residue: 0.1678 time to fit residues: 69.1483 Evaluate side-chains 223 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 148 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 122 ASN Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain S residue 235 ILE Chi-restraints excluded: chain S residue 361 CYS Chi-restraints excluded: chain S residue 408 ARG Chi-restraints excluded: chain S residue 501 ASN Chi-restraints excluded: chain S residue 524 VAL Chi-restraints excluded: chain S residue 546 LEU Chi-restraints excluded: chain S residue 551 VAL Chi-restraints excluded: chain S residue 565 PHE Chi-restraints excluded: chain S residue 569 ILE Chi-restraints excluded: chain S residue 584 ILE Chi-restraints excluded: chain S residue 720 ILE Chi-restraints excluded: chain S residue 788 ILE Chi-restraints excluded: chain S residue 856 ASN Chi-restraints excluded: chain S residue 878 LEU Chi-restraints excluded: chain S residue 916 LEU Chi-restraints excluded: chain S residue 975 SER Chi-restraints excluded: chain S residue 977 LEU Chi-restraints excluded: chain S residue 988 GLU Chi-restraints excluded: chain S residue 1127 ASP Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 66 HIS Chi-restraints excluded: chain V residue 117 LEU Chi-restraints excluded: chain V residue 316 SER Chi-restraints excluded: chain V residue 353 TRP Chi-restraints excluded: chain V residue 354 ASN Chi-restraints excluded: chain V residue 358 ILE Chi-restraints excluded: chain V residue 370 ASN Chi-restraints excluded: chain V residue 390 LEU Chi-restraints excluded: chain V residue 392 PHE Chi-restraints excluded: chain V residue 394 ASN Chi-restraints excluded: chain V residue 483 VAL Chi-restraints excluded: chain V residue 523 THR Chi-restraints excluded: chain V residue 534 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain V residue 567 ARG Chi-restraints excluded: chain V residue 584 ILE Chi-restraints excluded: chain V residue 645 THR Chi-restraints excluded: chain V residue 708 SER Chi-restraints excluded: chain V residue 747 THR Chi-restraints excluded: chain V residue 791 THR Chi-restraints excluded: chain V residue 820 ASP Chi-restraints excluded: chain V residue 856 ASN Chi-restraints excluded: chain V residue 981 LEU Chi-restraints excluded: chain V residue 1021 SER Chi-restraints excluded: chain V residue 1104 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain a residue 96 MET Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain d residue 53 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 326 optimal weight: 20.0000 chunk 361 optimal weight: 5.9990 chunk 347 optimal weight: 0.0970 chunk 116 optimal weight: 6.9990 chunk 250 optimal weight: 0.9990 chunk 239 optimal weight: 8.9990 chunk 185 optimal weight: 0.8980 chunk 333 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 414 GLN S 501 ASN V 394 ASN ** V 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.168650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.125738 restraints weight = 46877.288| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.51 r_work: 0.3248 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 29620 Z= 0.141 Angle : 0.600 12.980 40439 Z= 0.301 Chirality : 0.046 0.421 4772 Planarity : 0.004 0.068 5099 Dihedral : 6.258 78.372 5199 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.88 % Favored : 96.06 % Rotamer: Outliers : 3.06 % Allowed : 12.68 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.14), residues: 3579 helix: 0.91 (0.21), residues: 671 sheet: -0.45 (0.16), residues: 978 loop : -0.77 (0.13), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 408 TYR 0.018 0.001 TYR S1067 PHE 0.017 0.001 PHE V 106 TRP 0.025 0.001 TRP c 35 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00328 (29528) covalent geometry : angle 0.57142 (40201) SS BOND : bond 0.00492 ( 29) SS BOND : angle 2.35078 ( 58) hydrogen bonds : bond 0.03482 ( 1177) hydrogen bonds : angle 5.67564 ( 3165) Misc. bond : bond 0.00159 ( 3) link_BETA1-4 : bond 0.00326 ( 14) link_BETA1-4 : angle 2.59217 ( 42) link_NAG-ASN : bond 0.00417 ( 46) link_NAG-ASN : angle 2.45276 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 163 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 197 ILE cc_start: 0.8306 (mm) cc_final: 0.8102 (tt) REVERT: S 408 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8237 (ppt170) REVERT: S 414 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7662 (mm-40) REVERT: S 452 LEU cc_start: 0.7986 (mt) cc_final: 0.7712 (mt) REVERT: S 569 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8987 (mm) REVERT: S 1138 TYR cc_start: 0.8113 (t80) cc_final: 0.7836 (t80) REVERT: V 567 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8133 (mpt90) REVERT: V 975 SER cc_start: 0.8757 (m) cc_final: 0.8431 (p) REVERT: V 981 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8393 (mm) REVERT: C 47 VAL cc_start: 0.9248 (p) cc_final: 0.9040 (m) REVERT: C 197 ILE cc_start: 0.8137 (mm) cc_final: 0.7881 (tp) REVERT: C 238 PHE cc_start: 0.8004 (p90) cc_final: 0.7346 (p90) REVERT: C 239 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7798 (tp40) REVERT: C 269 TYR cc_start: 0.7881 (m-80) cc_final: 0.7589 (m-10) REVERT: C 421 TYR cc_start: 0.8362 (m-10) cc_final: 0.7801 (m-10) REVERT: C 453 TYR cc_start: 0.7687 (p90) cc_final: 0.7142 (p90) REVERT: H 100 MET cc_start: 0.4020 (tpp) cc_final: 0.3510 (tpp) REVERT: L 32 TYR cc_start: 0.6490 (m-10) cc_final: 0.6157 (m-80) REVERT: L 34 ASN cc_start: 0.5694 (m110) cc_final: 0.4638 (t0) REVERT: a 90 TYR cc_start: 0.5311 (m-80) cc_final: 0.5012 (m-80) REVERT: c 4 MET cc_start: 0.5041 (tpp) cc_final: 0.4581 (tmm) REVERT: c 34 ASN cc_start: 0.4695 (m-40) cc_final: 0.4330 (m110) REVERT: c 89 GLN cc_start: 0.7125 (tm-30) cc_final: 0.5930 (tm-30) REVERT: d 48 MET cc_start: 0.1452 (ptt) cc_final: 0.1178 (ttp) REVERT: d 100 MET cc_start: 0.3066 (mmt) cc_final: 0.2233 (mtt) REVERT: b 4 MET cc_start: 0.2333 (mtt) cc_final: 0.1221 (mpp) outliers start: 94 outliers final: 70 residues processed: 243 average time/residue: 0.1684 time to fit residues: 69.5800 Evaluate side-chains 229 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 153 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 122 ASN Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain S residue 235 ILE Chi-restraints excluded: chain S residue 402 ILE Chi-restraints excluded: chain S residue 408 ARG Chi-restraints excluded: chain S residue 414 GLN Chi-restraints excluded: chain S residue 524 VAL Chi-restraints excluded: chain S residue 551 VAL Chi-restraints excluded: chain S residue 565 PHE Chi-restraints excluded: chain S residue 569 ILE Chi-restraints excluded: chain S residue 584 ILE Chi-restraints excluded: chain S residue 615 VAL Chi-restraints excluded: chain S residue 720 ILE Chi-restraints excluded: chain S residue 788 ILE Chi-restraints excluded: chain S residue 856 ASN Chi-restraints excluded: chain S residue 873 TYR Chi-restraints excluded: chain S residue 887 THR Chi-restraints excluded: chain S residue 975 SER Chi-restraints excluded: chain S residue 977 LEU Chi-restraints excluded: chain S residue 988 GLU Chi-restraints excluded: chain S residue 1127 ASP Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 66 HIS Chi-restraints excluded: chain V residue 117 LEU Chi-restraints excluded: chain V residue 236 THR Chi-restraints excluded: chain V residue 316 SER Chi-restraints excluded: chain V residue 353 TRP Chi-restraints excluded: chain V residue 354 ASN Chi-restraints excluded: chain V residue 358 ILE Chi-restraints excluded: chain V residue 370 ASN Chi-restraints excluded: chain V residue 379 CYS Chi-restraints excluded: chain V residue 390 LEU Chi-restraints excluded: chain V residue 392 PHE Chi-restraints excluded: chain V residue 394 ASN Chi-restraints excluded: chain V residue 483 VAL Chi-restraints excluded: chain V residue 534 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain V residue 567 ARG Chi-restraints excluded: chain V residue 584 ILE Chi-restraints excluded: chain V residue 645 THR Chi-restraints excluded: chain V residue 708 SER Chi-restraints excluded: chain V residue 747 THR Chi-restraints excluded: chain V residue 791 THR Chi-restraints excluded: chain V residue 856 ASN Chi-restraints excluded: chain V residue 981 LEU Chi-restraints excluded: chain V residue 1104 VAL Chi-restraints excluded: chain V residue 1105 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain a residue 17 SER Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain a residue 100 TYR Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain d residue 53 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 331 optimal weight: 40.0000 chunk 213 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 312 optimal weight: 6.9990 chunk 353 optimal weight: 30.0000 chunk 91 optimal weight: 0.8980 chunk 309 optimal weight: 20.0000 chunk 143 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 198 optimal weight: 0.7980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 901 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.162897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.123257 restraints weight = 47443.805| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.36 r_work: 0.3100 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 29620 Z= 0.249 Angle : 0.659 12.070 40439 Z= 0.330 Chirality : 0.048 0.410 4772 Planarity : 0.004 0.058 5099 Dihedral : 6.349 76.463 5199 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.73 % Rotamer: Outliers : 3.10 % Allowed : 12.87 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.13), residues: 3579 helix: 0.72 (0.21), residues: 660 sheet: -0.48 (0.16), residues: 975 loop : -0.87 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 408 TYR 0.020 0.002 TYR S1067 PHE 0.027 0.002 PHE a 54 TRP 0.032 0.002 TRP L 35 HIS 0.006 0.001 HIS V1064 Details of bonding type rmsd covalent geometry : bond 0.00598 (29528) covalent geometry : angle 0.63002 (40201) SS BOND : bond 0.00536 ( 29) SS BOND : angle 2.78550 ( 58) hydrogen bonds : bond 0.03810 ( 1177) hydrogen bonds : angle 5.83381 ( 3165) Misc. bond : bond 0.00141 ( 3) link_BETA1-4 : bond 0.00350 ( 14) link_BETA1-4 : angle 2.72343 ( 42) link_NAG-ASN : bond 0.00423 ( 46) link_NAG-ASN : angle 2.50171 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 160 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 340 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8499 (mp0) REVERT: S 408 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8265 (ppt170) REVERT: S 414 GLN cc_start: 0.8290 (tt0) cc_final: 0.7805 (mm-40) REVERT: S 452 LEU cc_start: 0.8052 (mt) cc_final: 0.7778 (mt) REVERT: S 950 ASP cc_start: 0.8611 (t0) cc_final: 0.8277 (m-30) REVERT: S 1138 TYR cc_start: 0.8156 (t80) cc_final: 0.7858 (t80) REVERT: V 168 PHE cc_start: 0.7663 (t80) cc_final: 0.7410 (t80) REVERT: V 461 LEU cc_start: 0.2293 (OUTLIER) cc_final: 0.1501 (mp) REVERT: V 523 THR cc_start: 0.5398 (OUTLIER) cc_final: 0.5078 (t) REVERT: V 975 SER cc_start: 0.8782 (m) cc_final: 0.8456 (p) REVERT: V 981 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8494 (mm) REVERT: C 197 ILE cc_start: 0.8151 (mm) cc_final: 0.7904 (tp) REVERT: C 239 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7941 (tp40) REVERT: C 269 TYR cc_start: 0.7953 (m-80) cc_final: 0.7613 (m-10) REVERT: C 358 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8814 (mt) REVERT: C 421 TYR cc_start: 0.8386 (m-10) cc_final: 0.7867 (m-10) REVERT: C 453 TYR cc_start: 0.7705 (p90) cc_final: 0.7167 (p90) REVERT: H 100 MET cc_start: 0.3854 (tpp) cc_final: 0.3290 (tpp) REVERT: L 32 TYR cc_start: 0.6554 (m-10) cc_final: 0.6196 (m-80) REVERT: L 34 ASN cc_start: 0.5924 (m110) cc_final: 0.4569 (t0) REVERT: a 90 TYR cc_start: 0.5362 (m-80) cc_final: 0.5039 (m-80) REVERT: c 4 MET cc_start: 0.5190 (tpp) cc_final: 0.4722 (tmm) REVERT: c 34 ASN cc_start: 0.5037 (m-40) cc_final: 0.4620 (m110) REVERT: c 89 GLN cc_start: 0.7381 (tm-30) cc_final: 0.6150 (tm-30) REVERT: d 68 THR cc_start: 0.6097 (OUTLIER) cc_final: 0.5715 (m) REVERT: d 100 MET cc_start: 0.2952 (mmt) cc_final: 0.2064 (mtt) REVERT: b 4 MET cc_start: 0.2447 (mtt) cc_final: 0.1319 (mpp) outliers start: 95 outliers final: 76 residues processed: 244 average time/residue: 0.1666 time to fit residues: 69.0486 Evaluate side-chains 237 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 154 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain S residue 235 ILE Chi-restraints excluded: chain S residue 402 ILE Chi-restraints excluded: chain S residue 408 ARG Chi-restraints excluded: chain S residue 524 VAL Chi-restraints excluded: chain S residue 546 LEU Chi-restraints excluded: chain S residue 551 VAL Chi-restraints excluded: chain S residue 565 PHE Chi-restraints excluded: chain S residue 584 ILE Chi-restraints excluded: chain S residue 615 VAL Chi-restraints excluded: chain S residue 720 ILE Chi-restraints excluded: chain S residue 788 ILE Chi-restraints excluded: chain S residue 791 THR Chi-restraints excluded: chain S residue 856 ASN Chi-restraints excluded: chain S residue 873 TYR Chi-restraints excluded: chain S residue 878 LEU Chi-restraints excluded: chain S residue 916 LEU Chi-restraints excluded: chain S residue 977 LEU Chi-restraints excluded: chain S residue 988 GLU Chi-restraints excluded: chain S residue 1127 ASP Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 66 HIS Chi-restraints excluded: chain V residue 117 LEU Chi-restraints excluded: chain V residue 236 THR Chi-restraints excluded: chain V residue 241 LEU Chi-restraints excluded: chain V residue 316 SER Chi-restraints excluded: chain V residue 353 TRP Chi-restraints excluded: chain V residue 354 ASN Chi-restraints excluded: chain V residue 358 ILE Chi-restraints excluded: chain V residue 370 ASN Chi-restraints excluded: chain V residue 379 CYS Chi-restraints excluded: chain V residue 390 LEU Chi-restraints excluded: chain V residue 392 PHE Chi-restraints excluded: chain V residue 461 LEU Chi-restraints excluded: chain V residue 483 VAL Chi-restraints excluded: chain V residue 523 THR Chi-restraints excluded: chain V residue 534 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain V residue 567 ARG Chi-restraints excluded: chain V residue 584 ILE Chi-restraints excluded: chain V residue 645 THR Chi-restraints excluded: chain V residue 708 SER Chi-restraints excluded: chain V residue 747 THR Chi-restraints excluded: chain V residue 791 THR Chi-restraints excluded: chain V residue 820 ASP Chi-restraints excluded: chain V residue 856 ASN Chi-restraints excluded: chain V residue 981 LEU Chi-restraints excluded: chain V residue 1021 SER Chi-restraints excluded: chain V residue 1104 VAL Chi-restraints excluded: chain V residue 1105 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain a residue 17 SER Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain a residue 100 TYR Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain d residue 68 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 235 optimal weight: 9.9990 chunk 233 optimal weight: 0.8980 chunk 359 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 337 optimal weight: 40.0000 chunk 55 optimal weight: 0.6980 chunk 190 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 329 optimal weight: 30.0000 chunk 207 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 334 ASN V 394 ASN ** V 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN d 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.162828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.122406 restraints weight = 47374.933| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.44 r_work: 0.3095 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 29620 Z= 0.230 Angle : 0.645 11.632 40439 Z= 0.323 Chirality : 0.047 0.398 4772 Planarity : 0.004 0.070 5099 Dihedral : 6.365 74.356 5196 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.23 % Allowed : 13.10 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.13), residues: 3579 helix: 0.61 (0.21), residues: 673 sheet: -0.49 (0.16), residues: 969 loop : -0.88 (0.13), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG S 509 TYR 0.021 0.001 TYR S1067 PHE 0.019 0.002 PHE C 347 TRP 0.035 0.002 TRP L 35 HIS 0.005 0.001 HIS V1064 Details of bonding type rmsd covalent geometry : bond 0.00551 (29528) covalent geometry : angle 0.61827 (40201) SS BOND : bond 0.00517 ( 29) SS BOND : angle 2.47476 ( 58) hydrogen bonds : bond 0.03765 ( 1177) hydrogen bonds : angle 5.85397 ( 3165) Misc. bond : bond 0.00121 ( 3) link_BETA1-4 : bond 0.00325 ( 14) link_BETA1-4 : angle 2.64932 ( 42) link_NAG-ASN : bond 0.00387 ( 46) link_NAG-ASN : angle 2.44615 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 157 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 414 GLN cc_start: 0.8132 (tt0) cc_final: 0.7685 (mm-40) REVERT: S 950 ASP cc_start: 0.8607 (t0) cc_final: 0.8261 (m-30) REVERT: S 1138 TYR cc_start: 0.8185 (t80) cc_final: 0.7918 (t80) REVERT: V 461 LEU cc_start: 0.2128 (OUTLIER) cc_final: 0.1598 (mp) REVERT: V 523 THR cc_start: 0.5388 (OUTLIER) cc_final: 0.5062 (t) REVERT: V 975 SER cc_start: 0.8782 (m) cc_final: 0.8452 (p) REVERT: V 981 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8505 (mm) REVERT: C 197 ILE cc_start: 0.8144 (mm) cc_final: 0.7916 (tp) REVERT: C 239 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7967 (tp40) REVERT: C 269 TYR cc_start: 0.8011 (m-80) cc_final: 0.7660 (m-10) REVERT: C 358 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8881 (mm) REVERT: C 421 TYR cc_start: 0.8414 (m-10) cc_final: 0.7917 (m-10) REVERT: C 453 TYR cc_start: 0.7668 (p90) cc_final: 0.7112 (p90) REVERT: H 100 MET cc_start: 0.4003 (tpp) cc_final: 0.3343 (tpp) REVERT: L 32 TYR cc_start: 0.6459 (m-10) cc_final: 0.6053 (m-80) REVERT: L 34 ASN cc_start: 0.5924 (m110) cc_final: 0.4592 (t0) REVERT: a 90 TYR cc_start: 0.5472 (m-80) cc_final: 0.5152 (m-80) REVERT: c 4 MET cc_start: 0.5284 (tpp) cc_final: 0.4795 (tmm) REVERT: c 34 ASN cc_start: 0.5107 (m-40) cc_final: 0.4724 (m110) REVERT: c 89 GLN cc_start: 0.7398 (tm-30) cc_final: 0.6246 (tm-30) REVERT: d 48 MET cc_start: 0.1491 (ptt) cc_final: 0.1253 (ttp) REVERT: d 68 THR cc_start: 0.6103 (OUTLIER) cc_final: 0.5720 (m) REVERT: d 100 MET cc_start: 0.3015 (mmt) cc_final: 0.2140 (mtt) REVERT: b 4 MET cc_start: 0.2449 (mtt) cc_final: 0.1310 (mpp) outliers start: 99 outliers final: 78 residues processed: 245 average time/residue: 0.1537 time to fit residues: 64.2793 Evaluate side-chains 233 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 149 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain S residue 235 ILE Chi-restraints excluded: chain S residue 368 LEU Chi-restraints excluded: chain S residue 402 ILE Chi-restraints excluded: chain S residue 524 VAL Chi-restraints excluded: chain S residue 546 LEU Chi-restraints excluded: chain S residue 551 VAL Chi-restraints excluded: chain S residue 565 PHE Chi-restraints excluded: chain S residue 584 ILE Chi-restraints excluded: chain S residue 615 VAL Chi-restraints excluded: chain S residue 788 ILE Chi-restraints excluded: chain S residue 791 THR Chi-restraints excluded: chain S residue 856 ASN Chi-restraints excluded: chain S residue 873 TYR Chi-restraints excluded: chain S residue 878 LEU Chi-restraints excluded: chain S residue 916 LEU Chi-restraints excluded: chain S residue 977 LEU Chi-restraints excluded: chain S residue 988 GLU Chi-restraints excluded: chain S residue 1127 ASP Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 66 HIS Chi-restraints excluded: chain V residue 117 LEU Chi-restraints excluded: chain V residue 236 THR Chi-restraints excluded: chain V residue 241 LEU Chi-restraints excluded: chain V residue 316 SER Chi-restraints excluded: chain V residue 353 TRP Chi-restraints excluded: chain V residue 354 ASN Chi-restraints excluded: chain V residue 358 ILE Chi-restraints excluded: chain V residue 370 ASN Chi-restraints excluded: chain V residue 379 CYS Chi-restraints excluded: chain V residue 390 LEU Chi-restraints excluded: chain V residue 392 PHE Chi-restraints excluded: chain V residue 394 ASN Chi-restraints excluded: chain V residue 461 LEU Chi-restraints excluded: chain V residue 483 VAL Chi-restraints excluded: chain V residue 523 THR Chi-restraints excluded: chain V residue 534 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain V residue 560 LEU Chi-restraints excluded: chain V residue 567 ARG Chi-restraints excluded: chain V residue 584 ILE Chi-restraints excluded: chain V residue 645 THR Chi-restraints excluded: chain V residue 708 SER Chi-restraints excluded: chain V residue 747 THR Chi-restraints excluded: chain V residue 791 THR Chi-restraints excluded: chain V residue 856 ASN Chi-restraints excluded: chain V residue 981 LEU Chi-restraints excluded: chain V residue 1021 SER Chi-restraints excluded: chain V residue 1104 VAL Chi-restraints excluded: chain V residue 1105 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain a residue 17 SER Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain a residue 100 TYR Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain d residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 159 optimal weight: 0.0370 chunk 174 optimal weight: 0.5980 chunk 162 optimal weight: 0.9980 chunk 294 optimal weight: 0.0980 chunk 217 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 290 optimal weight: 0.5980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 414 GLN V 394 ASN ** V 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.163190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.122879 restraints weight = 47331.173| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.41 r_work: 0.3116 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.181 29620 Z= 0.192 Angle : 0.745 59.199 40439 Z= 0.397 Chirality : 0.047 0.433 4772 Planarity : 0.004 0.084 5099 Dihedral : 6.350 74.415 5192 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.83 % Allowed : 13.52 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3579 helix: 0.68 (0.21), residues: 673 sheet: -0.48 (0.16), residues: 968 loop : -0.88 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG S 509 TYR 0.035 0.001 TYR S 451 PHE 0.043 0.002 PHE S 347 TRP 0.032 0.002 TRP L 35 HIS 0.004 0.001 HIS V1064 Details of bonding type rmsd covalent geometry : bond 0.00450 (29528) covalent geometry : angle 0.72279 (40201) SS BOND : bond 0.00461 ( 29) SS BOND : angle 2.31753 ( 58) hydrogen bonds : bond 0.03717 ( 1177) hydrogen bonds : angle 5.84859 ( 3165) Misc. bond : bond 0.00111 ( 3) link_BETA1-4 : bond 0.00247 ( 14) link_BETA1-4 : angle 2.64319 ( 42) link_NAG-ASN : bond 0.00385 ( 46) link_NAG-ASN : angle 2.44765 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7158 Ramachandran restraints generated. 3579 Oldfield, 0 Emsley, 3579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 148 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 414 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7656 (mm-40) REVERT: S 950 ASP cc_start: 0.8591 (t0) cc_final: 0.8245 (m-30) REVERT: S 1138 TYR cc_start: 0.8197 (t80) cc_final: 0.7918 (t80) REVERT: V 461 LEU cc_start: 0.2127 (OUTLIER) cc_final: 0.1600 (mp) REVERT: V 523 THR cc_start: 0.5349 (OUTLIER) cc_final: 0.5035 (t) REVERT: V 975 SER cc_start: 0.8777 (m) cc_final: 0.8449 (p) REVERT: V 981 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8517 (mm) REVERT: C 197 ILE cc_start: 0.8147 (mm) cc_final: 0.7927 (tp) REVERT: C 239 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7942 (tp40) REVERT: C 269 TYR cc_start: 0.8027 (m-80) cc_final: 0.7672 (m-10) REVERT: C 358 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8888 (mm) REVERT: C 421 TYR cc_start: 0.8411 (m-10) cc_final: 0.7910 (m-10) REVERT: C 453 TYR cc_start: 0.7692 (p90) cc_final: 0.7147 (p90) REVERT: H 100 MET cc_start: 0.3999 (tpp) cc_final: 0.3613 (tpp) REVERT: L 32 TYR cc_start: 0.6433 (m-10) cc_final: 0.6030 (m-80) REVERT: L 34 ASN cc_start: 0.5922 (m110) cc_final: 0.4616 (t0) REVERT: a 90 TYR cc_start: 0.5437 (m-80) cc_final: 0.5126 (m-80) REVERT: c 4 MET cc_start: 0.5270 (tpp) cc_final: 0.4781 (tmm) REVERT: c 34 ASN cc_start: 0.5076 (m-40) cc_final: 0.4709 (m110) REVERT: c 89 GLN cc_start: 0.7373 (tm-30) cc_final: 0.6234 (tm-30) REVERT: d 68 THR cc_start: 0.6084 (OUTLIER) cc_final: 0.5692 (m) REVERT: d 100 MET cc_start: 0.3005 (mmt) cc_final: 0.2141 (mtt) REVERT: b 4 MET cc_start: 0.2434 (mtt) cc_final: 0.1275 (mpp) outliers start: 87 outliers final: 77 residues processed: 223 average time/residue: 0.1515 time to fit residues: 57.8295 Evaluate side-chains 231 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 147 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain S residue 235 ILE Chi-restraints excluded: chain S residue 368 LEU Chi-restraints excluded: chain S residue 402 ILE Chi-restraints excluded: chain S residue 414 GLN Chi-restraints excluded: chain S residue 524 VAL Chi-restraints excluded: chain S residue 546 LEU Chi-restraints excluded: chain S residue 551 VAL Chi-restraints excluded: chain S residue 565 PHE Chi-restraints excluded: chain S residue 584 ILE Chi-restraints excluded: chain S residue 615 VAL Chi-restraints excluded: chain S residue 788 ILE Chi-restraints excluded: chain S residue 791 THR Chi-restraints excluded: chain S residue 856 ASN Chi-restraints excluded: chain S residue 873 TYR Chi-restraints excluded: chain S residue 878 LEU Chi-restraints excluded: chain S residue 916 LEU Chi-restraints excluded: chain S residue 977 LEU Chi-restraints excluded: chain S residue 988 GLU Chi-restraints excluded: chain S residue 1127 ASP Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 66 HIS Chi-restraints excluded: chain V residue 117 LEU Chi-restraints excluded: chain V residue 236 THR Chi-restraints excluded: chain V residue 241 LEU Chi-restraints excluded: chain V residue 316 SER Chi-restraints excluded: chain V residue 353 TRP Chi-restraints excluded: chain V residue 354 ASN Chi-restraints excluded: chain V residue 358 ILE Chi-restraints excluded: chain V residue 370 ASN Chi-restraints excluded: chain V residue 379 CYS Chi-restraints excluded: chain V residue 390 LEU Chi-restraints excluded: chain V residue 392 PHE Chi-restraints excluded: chain V residue 461 LEU Chi-restraints excluded: chain V residue 483 VAL Chi-restraints excluded: chain V residue 523 THR Chi-restraints excluded: chain V residue 534 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain V residue 560 LEU Chi-restraints excluded: chain V residue 567 ARG Chi-restraints excluded: chain V residue 584 ILE Chi-restraints excluded: chain V residue 645 THR Chi-restraints excluded: chain V residue 708 SER Chi-restraints excluded: chain V residue 747 THR Chi-restraints excluded: chain V residue 791 THR Chi-restraints excluded: chain V residue 820 ASP Chi-restraints excluded: chain V residue 856 ASN Chi-restraints excluded: chain V residue 981 LEU Chi-restraints excluded: chain V residue 1021 SER Chi-restraints excluded: chain V residue 1104 VAL Chi-restraints excluded: chain V residue 1105 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain a residue 17 SER Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 100 ASP Chi-restraints excluded: chain a residue 100 TYR Chi-restraints excluded: chain a residue 112 SER Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain d residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 269 optimal weight: 0.6980 chunk 348 optimal weight: 40.0000 chunk 87 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 332 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 124 optimal weight: 20.0000 chunk 233 optimal weight: 0.0870 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 901 GLN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.165337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.125155 restraints weight = 47783.057| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.41 r_work: 0.3162 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 29620 Z= 0.119 Angle : 0.590 10.901 40439 Z= 0.296 Chirality : 0.045 0.387 4772 Planarity : 0.004 0.061 5099 Dihedral : 6.149 75.166 5192 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.28 % Allowed : 14.17 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.14), residues: 3579 helix: 0.97 (0.21), residues: 674 sheet: -0.35 (0.16), residues: 959 loop : -0.79 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 408 TYR 0.025 0.001 TYR a 100D PHE 0.042 0.001 PHE V 168 TRP 0.034 0.002 TRP c 35 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00266 (29528) covalent geometry : angle 0.56726 (40201) SS BOND : bond 0.00326 ( 29) SS BOND : angle 1.94100 ( 58) hydrogen bonds : bond 0.03401 ( 1177) hydrogen bonds : angle 5.59893 ( 3165) Misc. bond : bond 0.00129 ( 3) link_BETA1-4 : bond 0.00306 ( 14) link_BETA1-4 : angle 2.44857 ( 42) link_NAG-ASN : bond 0.00343 ( 46) link_NAG-ASN : angle 2.20287 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8670.53 seconds wall clock time: 148 minutes 46.80 seconds (8926.80 seconds total)