Starting phenix.real_space_refine on Tue Feb 20 21:44:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tht_25904/02_2024/7tht_25904.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tht_25904/02_2024/7tht_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tht_25904/02_2024/7tht_25904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tht_25904/02_2024/7tht_25904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tht_25904/02_2024/7tht_25904.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tht_25904/02_2024/7tht_25904.pdb" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Residue "S PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 100": "OD1" <-> "OD2" Residue "d TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 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: {'PHE:plan': 2, 'GLU:plan': 7, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 8} 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: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 5} 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: {'GLN:plan1': 2, 'GLU:plan': 10, 'ASN:plan1': 4, 'ASP:plan': 9} 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: 15.18, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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 " Time building additional restraints: 11.40 Conformation dependent library (CDL) restraints added in 5.3 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: 4.10 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: 15.20 Time building geometry restraints manager: 12.31 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: 93.43 - 101.82: 67 101.82 - 110.21: 6889 110.21 - 118.60: 15455 118.60 - 126.98: 17465 126.98 - 135.37: 325 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: 20 2.01 - 2.73: 979 2.73 - 3.45: 41119 3.45 - 4.18: 69475 4.18 - 4.90: 121918 Nonbonded interactions: 233511 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 2.520 ... (remaining 233506 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '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 or resid 1201 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 or resid 12 \ 01 through 1210)) 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 or resid 1201 thr \ ough 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.580 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 82.060 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.030 ------------------------------------------------------------------------------- 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 0.116 29528 Z= 0.892 Angle : 1.880 18.026 40201 Z= 1.244 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 : 8.40 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (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 TRP 0.132 0.026 TRP a 47 HIS 0.010 0.003 HIS C 655 PHE 0.078 0.012 PHE C 86 TYR 0.110 0.020 TYR d 32 ARG 0.016 0.001 ARG C 346 *********************** 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 fitting. rotamer outliers: 92 poor density : 321 time to evaluate : 3.019 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: 0.8031 (mm-40) REVERT: S 448 ASN cc_start: 0.6992 (t0) cc_final: 0.6672 (t0) REVERT: S 518 LEU cc_start: 0.3190 (OUTLIER) cc_final: 0.2530 (mt) REVERT: S 697 MET cc_start: 0.8551 (ptm) cc_final: 0.8338 (ptp) REVERT: V 868 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7921 (tm-30) REVERT: C 54 LEU cc_start: 0.8897 (mt) cc_final: 0.8676 (mp) REVERT: C 265 TYR cc_start: 0.7763 (OUTLIER) cc_final: 0.5418 (p90) REVERT: C 376 THR cc_start: 0.8261 (m) cc_final: 0.7946 (p) REVERT: C 453 TYR cc_start: 0.7702 (p90) cc_final: 0.6927 (p90) REVERT: C 493 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7600 (tm-30) REVERT: C 501 ASN cc_start: 0.6837 (OUTLIER) cc_final: 0.6498 (m-40) REVERT: C 508 TYR cc_start: 0.6388 (m-80) cc_final: 0.6090 (m-10) REVERT: L 46 LEU cc_start: 0.4136 (tt) cc_final: 0.2770 (tt) REVERT: c 4 MET cc_start: 0.3683 (mtp) cc_final: 0.3059 (ppp) outliers start: 92 outliers final: 44 residues processed: 406 average time/residue: 0.4144 time to fit residues: 264.7805 Evaluate side-chains 222 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 173 time to evaluate : 2.991 ------------------------------------------------------------------------------- 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 461 LEU 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 305 optimal weight: 20.0000 chunk 274 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 185 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 283 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 chunk 328 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 207 HIS S 388 ASN ** S 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 564 GLN S 919 ASN V 121 ASN ** V 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 501 ASN V 957 GLN V1048 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 C1005 GLN C1088 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29528 Z= 0.214 Angle : 0.716 13.264 40201 Z= 0.374 Chirality : 0.049 0.383 4772 Planarity : 0.004 0.061 5099 Dihedral : 8.407 72.817 5272 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.80 % Favored : 96.06 % Rotamer: Outliers : 2.67 % Allowed : 8.37 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.13), residues: 3579 helix: 0.12 (0.20), residues: 689 sheet: -0.50 (0.15), residues: 956 loop : -0.88 (0.13), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP c 35 HIS 0.004 0.001 HIS S1083 PHE 0.024 0.002 PHE C 329 TYR 0.034 0.002 TYR V 380 ARG 0.009 0.001 ARG S 357 *********************** 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 284 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 202 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 197 ILE cc_start: 0.8122 (mm) cc_final: 0.7638 (tt) REVERT: S 569 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8879 (mm) REVERT: S 950 ASP cc_start: 0.7898 (t70) cc_final: 0.7637 (t0) REVERT: V 392 PHE cc_start: 0.5433 (OUTLIER) cc_final: 0.4672 (m-80) REVERT: V 567 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.6603 (mpt90) REVERT: C 238 PHE cc_start: 0.7937 (p90) cc_final: 0.7402 (p90) REVERT: C 239 GLN cc_start: 0.7821 (tt0) cc_final: 0.7411 (tp40) REVERT: H 100 ASP cc_start: 0.6249 (t70) cc_final: 0.5844 (m-30) REVERT: c 34 ASN cc_start: 0.4405 (m110) cc_final: 0.4076 (m-40) REVERT: c 35 TRP cc_start: 0.5303 (m100) cc_final: 0.4761 (m100) REVERT: c 48 ILE cc_start: 0.6758 (OUTLIER) cc_final: 0.6527 (mt) outliers start: 82 outliers final: 40 residues processed: 271 average time/residue: 0.3835 time to fit residues: 170.8445 Evaluate side-chains 197 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 153 time to evaluate : 3.207 ------------------------------------------------------------------------------- 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 461 LEU 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 887 THR 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 335 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 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 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 334 ASN Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 54 PHE Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain a residue 17 SER Chi-restraints excluded: chain c residue 48 ILE 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 182 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 273 optimal weight: 1.9990 chunk 223 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 329 optimal weight: 40.0000 chunk 355 optimal weight: 20.0000 chunk 293 optimal weight: 0.9980 chunk 326 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 264 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 218 GLN ** 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 856 ASN C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 29528 Z= 0.318 Angle : 0.661 9.998 40201 Z= 0.342 Chirality : 0.048 0.406 4772 Planarity : 0.004 0.042 5099 Dihedral : 7.281 66.294 5210 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.73 % Rotamer: Outliers : 2.83 % Allowed : 10.36 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.13), residues: 3579 helix: 0.43 (0.21), residues: 675 sheet: -0.48 (0.15), residues: 953 loop : -0.89 (0.13), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 35 HIS 0.005 0.001 HIS V1064 PHE 0.016 0.002 PHE C 86 TYR 0.032 0.002 TYR L 92 ARG 0.009 0.001 ARG C 403 *********************** 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 248 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 161 time to evaluate : 3.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 197 ILE cc_start: 0.8206 (mm) cc_final: 0.7954 (tt) REVERT: S 361 CYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7300 (p) REVERT: S 414 GLN cc_start: 0.8081 (tt0) cc_final: 0.7748 (mm-40) REVERT: S 452 LEU cc_start: 0.7664 (mt) cc_final: 0.7452 (mt) REVERT: V 392 PHE cc_start: 0.5690 (OUTLIER) cc_final: 0.4679 (m-80) REVERT: V 567 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.7869 (mpt90) REVERT: V 868 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7732 (tm-30) REVERT: C 238 PHE cc_start: 0.7921 (p90) cc_final: 0.7367 (p90) REVERT: C 239 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7429 (tp40) REVERT: C 487 ASN cc_start: 0.5469 (m-40) cc_final: 0.5257 (m-40) REVERT: L 34 ASN cc_start: 0.5866 (m110) cc_final: 0.5397 (t0) REVERT: L 46 LEU cc_start: 0.3569 (tt) cc_final: 0.2939 (tt) REVERT: c 4 MET cc_start: 0.4607 (tpp) cc_final: 0.4204 (tmm) REVERT: c 73 LEU cc_start: 0.6065 (pt) cc_final: 0.5526 (tt) REVERT: c 89 GLN cc_start: 0.7427 (tm-30) cc_final: 0.7182 (tm-30) REVERT: b 29 ILE cc_start: 0.1031 (OUTLIER) cc_final: 0.0477 (mm) outliers start: 87 outliers final: 49 residues processed: 236 average time/residue: 0.3829 time to fit residues: 148.6805 Evaluate side-chains 202 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 148 time to evaluate : 2.998 ------------------------------------------------------------------------------- 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 461 LEU 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 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 335 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 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 567 ARG Chi-restraints excluded: chain V residue 584 ILE 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 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 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 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain d residue 53 MET 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 325 optimal weight: 0.2980 chunk 247 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 330 optimal weight: 3.9990 chunk 349 optimal weight: 30.0000 chunk 172 optimal weight: 0.9990 chunk 313 optimal weight: 30.0000 chunk 94 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 218 GLN S 540 ASN V 370 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 690 GLN C 901 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29528 Z= 0.186 Angle : 0.603 9.380 40201 Z= 0.308 Chirality : 0.046 0.386 4772 Planarity : 0.004 0.041 5099 Dihedral : 6.713 62.439 5205 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.63 % Favored : 96.31 % Rotamer: Outliers : 2.90 % Allowed : 10.95 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 3579 helix: 0.78 (0.21), residues: 677 sheet: -0.43 (0.15), residues: 966 loop : -0.80 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP c 35 HIS 0.003 0.001 HIS S1064 PHE 0.021 0.001 PHE C 201 TYR 0.033 0.001 TYR C 508 ARG 0.004 0.000 ARG S 466 *********************** 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 261 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 172 time to evaluate : 3.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 197 ILE cc_start: 0.8164 (mm) cc_final: 0.7865 (tt) REVERT: S 361 CYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7345 (p) REVERT: S 414 GLN cc_start: 0.8030 (tt0) cc_final: 0.7719 (mm-40) REVERT: S 452 LEU cc_start: 0.7634 (mt) cc_final: 0.7402 (mt) REVERT: V 370 ASN cc_start: 0.7542 (OUTLIER) cc_final: 0.7088 (p0) REVERT: V 567 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.7886 (mpt90) REVERT: V 981 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7920 (mm) REVERT: C 239 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7509 (tp40) REVERT: C 361 CYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7376 (p) REVERT: C 453 TYR cc_start: 0.7518 (p90) cc_final: 0.6853 (p90) REVERT: C 487 ASN cc_start: 0.5257 (m-40) cc_final: 0.5051 (m-40) REVERT: C 567 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7873 (mtt180) REVERT: L 35 TRP cc_start: 0.5125 (m100) cc_final: 0.4877 (m100) REVERT: c 4 MET cc_start: 0.4709 (tpp) cc_final: 0.4356 (tmm) REVERT: c 73 LEU cc_start: 0.6202 (pt) cc_final: 0.5715 (tt) REVERT: d 100 MET cc_start: 0.3725 (mtp) cc_final: 0.3106 (ptm) outliers start: 89 outliers final: 45 residues processed: 244 average time/residue: 0.3879 time to fit residues: 155.6978 Evaluate side-chains 197 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 145 time to evaluate : 3.357 ------------------------------------------------------------------------------- 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 367 VAL Chi-restraints excluded: chain S residue 408 ARG Chi-restraints excluded: chain S residue 461 LEU 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 V residue 66 HIS Chi-restraints excluded: chain V residue 117 LEU Chi-restraints excluded: chain V residue 335 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 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 560 LEU 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 V residue 981 LEU 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 239 GLN 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 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 943 SER 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 a residue 34 ILE Chi-restraints excluded: chain a residue 96 MET Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain d residue 53 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 291 optimal weight: 0.7980 chunk 198 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 260 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 298 optimal weight: 9.9990 chunk 241 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 314 optimal weight: 50.0000 chunk 88 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1113 GLN V 394 ASN ** V 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1083 HIS C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29528 Z= 0.191 Angle : 0.569 9.271 40201 Z= 0.292 Chirality : 0.045 0.383 4772 Planarity : 0.004 0.040 5099 Dihedral : 6.303 58.545 5200 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.66 % Favored : 96.28 % Rotamer: Outliers : 2.90 % Allowed : 12.25 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.13), residues: 3579 helix: 0.95 (0.21), residues: 678 sheet: -0.35 (0.16), residues: 958 loop : -0.83 (0.13), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP c 35 HIS 0.003 0.001 HIS S1064 PHE 0.018 0.001 PHE S 400 TYR 0.025 0.001 TYR C 170 ARG 0.005 0.000 ARG C 408 *********************** 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 260 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 171 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 197 ILE cc_start: 0.8257 (mm) cc_final: 0.7961 (tt) REVERT: S 361 CYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7391 (p) REVERT: S 408 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8086 (ppt170) REVERT: S 414 GLN cc_start: 0.7974 (tt0) cc_final: 0.7749 (mm-40) REVERT: S 452 LEU cc_start: 0.7664 (mt) cc_final: 0.7447 (mt) REVERT: V 370 ASN cc_start: 0.7500 (OUTLIER) cc_final: 0.7080 (p0) REVERT: V 387 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6220 (tp) REVERT: V 567 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.7910 (mpt90) REVERT: V 975 SER cc_start: 0.8566 (m) cc_final: 0.8181 (p) REVERT: C 239 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7530 (tp40) REVERT: C 361 CYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7368 (p) REVERT: C 421 TYR cc_start: 0.8047 (m-10) cc_final: 0.7563 (m-10) REVERT: C 453 TYR cc_start: 0.7496 (p90) cc_final: 0.6858 (p90) REVERT: C 567 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7824 (mtt180) REVERT: d 100 MET cc_start: 0.3513 (mtp) cc_final: 0.2972 (ptm) REVERT: b 4 MET cc_start: 0.2149 (mtt) cc_final: 0.1260 (mpp) outliers start: 89 outliers final: 58 residues processed: 246 average time/residue: 0.3708 time to fit residues: 151.4998 Evaluate side-chains 214 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 148 time to evaluate : 2.998 ------------------------------------------------------------------------------- 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 361 CYS Chi-restraints excluded: chain S residue 408 ARG Chi-restraints excluded: chain S residue 461 LEU 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 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 V residue 66 HIS Chi-restraints excluded: chain V residue 117 LEU Chi-restraints excluded: chain V residue 121 ASN Chi-restraints excluded: chain V residue 335 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 379 CYS Chi-restraints excluded: chain V residue 387 LEU 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 567 ARG Chi-restraints excluded: chain V residue 584 ILE Chi-restraints excluded: chain V residue 645 THR 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 1027 THR 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 239 GLN 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 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 943 SER 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 a residue 96 MET 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 117 optimal weight: 4.9990 chunk 315 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 350 optimal weight: 30.0000 chunk 290 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1002 GLN ** V 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29528 Z= 0.289 Angle : 0.589 9.340 40201 Z= 0.302 Chirality : 0.046 0.378 4772 Planarity : 0.004 0.041 5099 Dihedral : 6.305 59.678 5200 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 3.16 % Allowed : 12.94 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 3579 helix: 0.88 (0.21), residues: 678 sheet: -0.38 (0.15), residues: 998 loop : -0.82 (0.13), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP c 35 HIS 0.005 0.001 HIS V1064 PHE 0.021 0.002 PHE C 486 TYR 0.020 0.001 TYR S1067 ARG 0.007 0.000 ARG C 408 *********************** 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 253 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 156 time to evaluate : 3.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 197 ILE cc_start: 0.8277 (mm) cc_final: 0.7994 (tt) REVERT: S 408 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8160 (ppt170) REVERT: S 414 GLN cc_start: 0.7973 (tt0) cc_final: 0.7682 (mm-40) REVERT: V 129 LYS cc_start: 0.7220 (mmmt) cc_final: 0.6467 (mmmt) REVERT: V 370 ASN cc_start: 0.7362 (OUTLIER) cc_final: 0.6929 (p0) REVERT: V 387 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6264 (tp) REVERT: V 567 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.7901 (mpt90) REVERT: V 975 SER cc_start: 0.8614 (m) cc_final: 0.8230 (p) REVERT: C 239 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7556 (tp40) REVERT: C 361 CYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7534 (p) REVERT: C 421 TYR cc_start: 0.8169 (m-10) cc_final: 0.7674 (m-10) REVERT: C 453 TYR cc_start: 0.7495 (p90) cc_final: 0.6826 (p90) REVERT: C 567 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7844 (mtt180) REVERT: a 96 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.6381 (mtp) REVERT: d 100 MET cc_start: 0.3417 (OUTLIER) cc_final: 0.2820 (ptm) outliers start: 97 outliers final: 70 residues processed: 237 average time/residue: 0.3737 time to fit residues: 147.8411 Evaluate side-chains 227 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 148 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 95 THR 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 408 ARG Chi-restraints excluded: chain S residue 461 LEU 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 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 878 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 1050 MET 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 121 ASN Chi-restraints excluded: chain V residue 308 VAL Chi-restraints excluded: chain V residue 316 SER Chi-restraints excluded: chain V residue 335 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 379 CYS Chi-restraints excluded: chain V residue 387 LEU 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 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 1004 LEU Chi-restraints excluded: chain V residue 1027 THR 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 239 GLN 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 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 943 SER 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 H residue 54 PHE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain a residue 51 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 Chi-restraints excluded: chain d residue 100 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 337 optimal weight: 30.0000 chunk 39 optimal weight: 20.0000 chunk 199 optimal weight: 1.9990 chunk 255 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 294 optimal weight: 3.9990 chunk 195 optimal weight: 0.6980 chunk 348 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 317 ASN S 414 GLN ** S 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 493 GLN S 501 ASN V 394 ASN ** V 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 29528 Z= 0.212 Angle : 0.559 9.260 40201 Z= 0.286 Chirality : 0.045 0.365 4772 Planarity : 0.004 0.043 5099 Dihedral : 6.140 59.558 5200 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.34 % Rotamer: Outliers : 3.00 % Allowed : 13.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3579 helix: 0.95 (0.21), residues: 669 sheet: -0.32 (0.16), residues: 993 loop : -0.84 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP a 36 HIS 0.003 0.001 HIS V1064 PHE 0.017 0.001 PHE V 106 TYR 0.018 0.001 TYR S1067 ARG 0.007 0.000 ARG C 408 *********************** 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 251 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 159 time to evaluate : 3.233 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: S 197 ILE cc_start: 0.8394 (mm) cc_final: 0.8122 (tt) REVERT: S 408 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8215 (ppt170) REVERT: S 414 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7581 (mm-40) REVERT: V 387 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6190 (tp) REVERT: V 567 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.6576 (mpt90) REVERT: V 975 SER cc_start: 0.8553 (m) cc_final: 0.8207 (p) REVERT: C 197 ILE cc_start: 0.8011 (mm) cc_final: 0.7765 (tp) REVERT: C 239 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7554 (tp40) REVERT: C 361 CYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7435 (p) REVERT: C 421 TYR cc_start: 0.8159 (m-10) cc_final: 0.7709 (m-10) REVERT: C 453 TYR cc_start: 0.7410 (p90) cc_final: 0.6756 (p90) REVERT: C 567 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7845 (mtt180) REVERT: a 90 TYR cc_start: 0.5048 (m-80) cc_final: 0.4752 (m-80) REVERT: a 96 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6475 (mtp) REVERT: d 100 MET cc_start: 0.3354 (OUTLIER) cc_final: 0.2799 (ptm) outliers start: 92 outliers final: 67 residues processed: 236 average time/residue: 0.3755 time to fit residues: 149.8378 Evaluate side-chains 226 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 150 time to evaluate : 3.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 122 ASN Chi-restraints excluded: chain S residue 235 ILE Chi-restraints excluded: chain S residue 408 ARG Chi-restraints excluded: chain S residue 414 GLN Chi-restraints excluded: chain S residue 461 LEU 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 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 1050 MET 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 121 ASN 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 387 LEU 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 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 1027 THR 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 239 GLN 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 414 GLN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 943 SER 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 L residue 48 ILE Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 96 MET Chi-restraints excluded: chain a residue 100 TYR Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain d residue 53 MET Chi-restraints excluded: chain d residue 100 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 215 optimal weight: 6.9990 chunk 139 optimal weight: 0.6980 chunk 208 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 chunk 237 optimal weight: 20.0000 chunk 172 optimal weight: 0.0980 chunk 32 optimal weight: 7.9990 chunk 274 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 493 GLN V 394 ASN ** V 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 29528 Z= 0.246 Angle : 0.569 10.529 40201 Z= 0.290 Chirality : 0.045 0.368 4772 Planarity : 0.004 0.044 5099 Dihedral : 6.111 58.193 5200 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.86 % Favored : 96.12 % Rotamer: Outliers : 3.03 % Allowed : 13.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3579 helix: 0.94 (0.21), residues: 668 sheet: -0.31 (0.16), residues: 987 loop : -0.83 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP c 35 HIS 0.004 0.001 HIS V1064 PHE 0.021 0.001 PHE C 201 TYR 0.019 0.001 TYR S1067 ARG 0.009 0.000 ARG C 408 *********************** 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 249 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 156 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 408 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8185 (ppt170) REVERT: S 414 GLN cc_start: 0.7880 (tt0) cc_final: 0.7628 (mm110) REVERT: V 387 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6245 (tp) REVERT: V 567 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.6592 (mpt90) REVERT: V 975 SER cc_start: 0.8546 (m) cc_final: 0.8215 (p) REVERT: C 197 ILE cc_start: 0.7994 (mm) cc_final: 0.7764 (tp) REVERT: C 239 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7561 (tp40) REVERT: C 351 TYR cc_start: 0.8374 (p90) cc_final: 0.7906 (p90) REVERT: C 361 CYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7489 (p) REVERT: C 421 TYR cc_start: 0.8176 (m-10) cc_final: 0.7741 (m-10) REVERT: C 453 TYR cc_start: 0.7420 (p90) cc_final: 0.6767 (p90) REVERT: C 487 ASN cc_start: 0.4848 (m-40) cc_final: 0.3925 (t0) REVERT: C 567 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7839 (mtt180) REVERT: c 45 LYS cc_start: 0.6890 (tmtt) cc_final: 0.5921 (ttmm) REVERT: d 100 MET cc_start: 0.3364 (OUTLIER) cc_final: 0.2815 (ptm) outliers start: 93 outliers final: 72 residues processed: 235 average time/residue: 0.3817 time to fit residues: 149.8404 Evaluate side-chains 229 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 150 time to evaluate : 3.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 122 ASN Chi-restraints excluded: chain S residue 235 ILE Chi-restraints excluded: chain S residue 408 ARG Chi-restraints excluded: chain S residue 461 LEU 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 585 LEU 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 887 THR 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 1050 MET 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 121 ASN Chi-restraints excluded: chain V residue 308 VAL Chi-restraints excluded: chain V residue 316 SER 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 387 LEU 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 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 747 THR Chi-restraints excluded: chain V residue 791 THR Chi-restraints excluded: chain V residue 856 ASN Chi-restraints excluded: chain V residue 1021 SER Chi-restraints excluded: chain V residue 1027 THR 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 239 GLN 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 567 ARG Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 943 SER 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 48 ILE 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 Chi-restraints excluded: chain d residue 100 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 317 optimal weight: 8.9990 chunk 334 optimal weight: 6.9990 chunk 304 optimal weight: 20.0000 chunk 325 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 255 optimal weight: 0.5980 chunk 99 optimal weight: 8.9990 chunk 293 optimal weight: 3.9990 chunk 307 optimal weight: 10.0000 chunk 324 optimal weight: 7.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 334 ASN S 388 ASN ** S 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 493 GLN S 690 GLN S 914 ASN S1135 ASN V 394 ASN ** V 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 89 GLN d 3 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.098 29528 Z= 0.590 Angle : 0.732 11.331 40201 Z= 0.375 Chirality : 0.051 0.423 4772 Planarity : 0.005 0.067 5099 Dihedral : 6.660 64.865 5200 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.09 % Favored : 94.89 % Rotamer: Outliers : 3.36 % Allowed : 13.46 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.13), residues: 3579 helix: 0.24 (0.20), residues: 685 sheet: -0.50 (0.16), residues: 994 loop : -1.05 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP c 35 HIS 0.009 0.002 HIS V1064 PHE 0.029 0.002 PHE S1121 TYR 0.025 0.002 TYR S1067 ARG 0.010 0.001 ARG C 408 *********************** 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 257 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 154 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 408 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8251 (ppt170) REVERT: S 414 GLN cc_start: 0.7888 (tt0) cc_final: 0.7636 (mm-40) REVERT: V 387 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6549 (tp) REVERT: V 392 PHE cc_start: 0.5767 (OUTLIER) cc_final: 0.4707 (m-80) REVERT: C 197 ILE cc_start: 0.8065 (mm) cc_final: 0.7860 (tp) REVERT: C 239 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7625 (tp40) REVERT: C 351 TYR cc_start: 0.8401 (p90) cc_final: 0.7977 (p90) REVERT: C 421 TYR cc_start: 0.8218 (m-10) cc_final: 0.7719 (m-10) REVERT: C 453 TYR cc_start: 0.7574 (p90) cc_final: 0.7156 (p90) REVERT: C 567 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7855 (mtt180) REVERT: H 48 MET cc_start: 0.2870 (ptp) cc_final: 0.2667 (ptt) REVERT: c 34 ASN cc_start: 0.4281 (m110) cc_final: 0.3997 (m-40) REVERT: d 48 MET cc_start: 0.1799 (ptt) cc_final: 0.1589 (ttp) REVERT: d 68 THR cc_start: 0.5599 (OUTLIER) cc_final: 0.4949 (m) REVERT: d 100 MET cc_start: 0.3460 (OUTLIER) cc_final: 0.2889 (ptm) outliers start: 103 outliers final: 74 residues processed: 240 average time/residue: 0.3955 time to fit residues: 159.3921 Evaluate side-chains 229 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 148 time to evaluate : 3.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 95 THR 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 402 ILE Chi-restraints excluded: chain S residue 408 ARG Chi-restraints excluded: chain S residue 422 ASN Chi-restraints excluded: chain S residue 457 ARG Chi-restraints excluded: chain S residue 461 LEU 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 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 1105 THR 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 121 ASN Chi-restraints excluded: chain V residue 308 VAL 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 387 LEU Chi-restraints excluded: chain V residue 390 LEU Chi-restraints excluded: chain V residue 392 PHE 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 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 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 1021 SER Chi-restraints excluded: chain V residue 1027 THR Chi-restraints excluded: chain V residue 1104 VAL Chi-restraints excluded: chain C residue 47 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 239 GLN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 977 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 51 ILE Chi-restraints excluded: chain a residue 112 SER Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain d residue 52 ILE Chi-restraints excluded: chain d residue 68 THR Chi-restraints excluded: chain d residue 100 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 213 optimal weight: 9.9990 chunk 343 optimal weight: 6.9990 chunk 209 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 239 optimal weight: 0.9990 chunk 360 optimal weight: 7.9990 chunk 331 optimal weight: 30.0000 chunk 287 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 394 ASN ** V 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 29528 Z= 0.210 Angle : 0.571 10.412 40201 Z= 0.292 Chirality : 0.045 0.366 4772 Planarity : 0.004 0.043 5099 Dihedral : 6.283 63.667 5200 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.88 % Favored : 96.09 % Rotamer: Outliers : 2.22 % Allowed : 14.83 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3579 helix: 0.68 (0.21), residues: 682 sheet: -0.38 (0.16), residues: 982 loop : -0.93 (0.13), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP c 35 HIS 0.004 0.001 HIS C 207 PHE 0.022 0.001 PHE C 201 TYR 0.019 0.001 TYR V1067 ARG 0.009 0.000 ARG C 408 ********************** 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 229 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 161 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 387 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6329 (tp) REVERT: V 975 SER cc_start: 0.8619 (m) cc_final: 0.8224 (p) REVERT: C 239 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7590 (tp40) REVERT: C 361 CYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7615 (p) REVERT: C 421 TYR cc_start: 0.8228 (m-10) cc_final: 0.7815 (m-10) REVERT: C 453 TYR cc_start: 0.7475 (p90) cc_final: 0.6761 (p90) REVERT: C 567 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7874 (mtt180) REVERT: a 100 MET cc_start: 0.5283 (mtt) cc_final: 0.4946 (mtt) REVERT: c 34 ASN cc_start: 0.4522 (m110) cc_final: 0.3407 (m-40) REVERT: c 45 LYS cc_start: 0.6803 (tmtt) cc_final: 0.6054 (tttp) REVERT: d 68 THR cc_start: 0.5724 (OUTLIER) cc_final: 0.5124 (m) REVERT: d 100 MET cc_start: 0.3354 (OUTLIER) cc_final: 0.2796 (ptm) outliers start: 68 outliers final: 58 residues processed: 220 average time/residue: 0.4032 time to fit residues: 147.1949 Evaluate side-chains 209 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 145 time to evaluate : 3.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 95 THR 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 402 ILE Chi-restraints excluded: chain S residue 461 LEU 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 916 LEU Chi-restraints excluded: chain S residue 977 LEU Chi-restraints excluded: chain S residue 988 GLU 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 121 ASN Chi-restraints excluded: chain V residue 308 VAL 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 387 LEU 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 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 747 THR Chi-restraints excluded: chain V residue 791 THR Chi-restraints excluded: chain V residue 856 ASN 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 239 GLN 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 567 ARG Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 738 CYS 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 943 SER 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 L residue 48 ILE Chi-restraints excluded: chain a residue 17 SER Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain d residue 68 THR Chi-restraints excluded: chain d residue 100 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 228 optimal weight: 0.3980 chunk 305 optimal weight: 40.0000 chunk 87 optimal weight: 1.9990 chunk 264 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 79 optimal weight: 0.4980 chunk 287 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 295 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 89 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 = 0.4141 r_free = 0.4141 target = 0.164488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.122992 restraints weight = 47011.085| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.58 r_work: 0.3171 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.205 29528 Z= 0.253 Angle : 0.699 59.091 40201 Z= 0.387 Chirality : 0.046 0.734 4772 Planarity : 0.004 0.057 5099 Dihedral : 6.262 63.651 5196 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.00 % Favored : 95.98 % Rotamer: Outliers : 2.31 % Allowed : 14.60 % Favored : 83.09 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3579 helix: 0.70 (0.21), residues: 682 sheet: -0.39 (0.16), residues: 984 loop : -0.92 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP c 35 HIS 0.003 0.001 HIS C 207 PHE 0.066 0.002 PHE d 63 TYR 0.019 0.001 TYR S1067 ARG 0.045 0.000 ARG S 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5147.71 seconds wall clock time: 96 minutes 1.59 seconds (5761.59 seconds total)