Starting phenix.real_space_refine on Thu Feb 22 02:27:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3k_30982/02_2024/7e3k_30982_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3k_30982/02_2024/7e3k_30982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3k_30982/02_2024/7e3k_30982.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3k_30982/02_2024/7e3k_30982.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3k_30982/02_2024/7e3k_30982_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3k_30982/02_2024/7e3k_30982_neut.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 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 134 5.16 5 C 20629 2.51 5 N 5455 2.21 5 O 6321 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 191": "OE1" <-> "OE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 80": "OE1" <-> "OE2" Residue "E ARG 94": "NH1" <-> "NH2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "E TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 214": "OE1" <-> "OE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 80": "OE1" <-> "OE2" Residue "G ARG 94": "NH1" <-> "NH2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 214": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "L ARG 94": "NH1" <-> "NH2" Residue "L GLU 124": "OE1" <-> "OE2" Residue "L TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 214": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32539 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7591 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 49, 'TRANS': 940} Chain breaks: 8 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 97 Chain: "B" Number of atoms: 7571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7571 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 49, 'TRANS': 940} Chain breaks: 8 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 111 Chain: "C" Number of atoms: 7577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7577 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 49, 'TRANS': 940} Chain breaks: 8 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 111 Chain: "D" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1570 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 209} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1594 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 202} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1570 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 209} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "G" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1594 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 202} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1570 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 209} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "L" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1594 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 202} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 17.21, per 1000 atoms: 0.53 Number of scatterers: 32539 At special positions: 0 Unit cell: (137.76, 136.94, 262.4, 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 134 16.00 O 6321 8.00 N 5455 7.00 C 20629 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 106 " distance=2.04 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 106 " distance=2.04 Simple disulfide: pdb=" SG CYS F 150 " - pdb=" SG CYS F 206 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.04 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 195 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.04 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 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 Atom "HETATM32285 O5 NAG A1304 .*. O " rejected from bonding due to valence issues. Atom "HETATM32355 O5 NAG B1301 .*. O " rejected from bonding due to valence issues. Atom "HETATM32369 O5 NAG B1302 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 709 " Time building additional restraints: 16.58 Conformation dependent library (CDL) restraints added in 5.9 seconds 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7980 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 82 sheets defined 19.5% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.930A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.603A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.400A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 739 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.879A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.076A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.590A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.686A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.305A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.300A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.250A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.897A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.603A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.400A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 739 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.881A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.077A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.590A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.686A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.306A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.302A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.249A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.930A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.602A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.399A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.880A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.076A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.589A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.685A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.306A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 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 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.301A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.249A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.848A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 200 removed outlier: 4.092A pdb=" N GLY D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 200' Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 122 through 129 removed outlier: 3.603A pdb=" N LEU E 126 " --> pdb=" O SER E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.848A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 200 removed outlier: 4.093A pdb=" N GLY F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 196 through 200' Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 122 through 129 removed outlier: 3.602A pdb=" N LEU G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.849A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 200 removed outlier: 4.093A pdb=" N GLY H 200 " --> pdb=" O SER H 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 196 through 200' Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 122 through 129 removed outlier: 3.602A pdb=" N LEU L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31 removed outlier: 3.858A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.248A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.236A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.665A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.826A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.197A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.498A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.647A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.651A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 722 removed outlier: 6.764A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 722 removed outlier: 6.764A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.673A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB9, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.858A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.249A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.237A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.664A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.825A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.197A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.505A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.646A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.652A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 722 removed outlier: 6.765A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 722 removed outlier: 6.765A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.671A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD7, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.858A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.248A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 9.453A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 49 removed outlier: 3.665A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 49 removed outlier: 3.825A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.197A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.645A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 611 " --> pdb=" O SER C 596 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 609 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 327 removed outlier: 3.647A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.653A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.764A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.764A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.673A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AF5, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.594A pdb=" N ALA D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.511A pdb=" N GLU D 10 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 92 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.511A pdb=" N GLU D 10 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 92 " --> pdb=" O VAL D 119 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 145 through 155 removed outlier: 5.596A pdb=" N TYR D 186 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 145 through 155 removed outlier: 5.596A pdb=" N TYR D 186 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 160 through 164 removed outlier: 4.034A pdb=" N CYS D 206 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS D 219 " --> pdb=" O CYS D 206 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.538A pdb=" N THR E 5 " --> pdb=" O ARG E 24 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER E 64 " --> pdb=" O THR E 75 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.823A pdb=" N VAL E 86 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 115 through 119 removed outlier: 3.760A pdb=" N SER E 115 " --> pdb=" O ASN E 138 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN E 138 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL E 134 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER E 132 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU E 182 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL E 134 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU E 180 " --> pdb=" O VAL E 134 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU E 136 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N SER E 178 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ASN E 138 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU E 176 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.518A pdb=" N TYR E 193 " --> pdb=" O PHE E 210 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 150 through 151 Processing sheet with id=AG7, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.593A pdb=" N ALA F 79 " --> pdb=" O CYS F 22 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.510A pdb=" N GLU F 10 " --> pdb=" O MET F 118 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 92 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.510A pdb=" N GLU F 10 " --> pdb=" O MET F 118 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 92 " --> pdb=" O VAL F 119 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 145 through 155 removed outlier: 5.596A pdb=" N TYR F 186 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 145 through 155 removed outlier: 5.596A pdb=" N TYR F 186 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 160 through 164 removed outlier: 4.034A pdb=" N CYS F 206 " --> pdb=" O LYS F 219 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS F 219 " --> pdb=" O CYS F 206 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.539A pdb=" N THR G 5 " --> pdb=" O ARG G 24 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER G 64 " --> pdb=" O THR G 75 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.823A pdb=" N VAL G 86 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 115 through 119 removed outlier: 3.762A pdb=" N SER G 115 " --> pdb=" O ASN G 138 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN G 138 " --> pdb=" O SER G 115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL G 134 " --> pdb=" O PHE G 119 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER G 132 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU G 182 " --> pdb=" O SER G 132 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL G 134 " --> pdb=" O LEU G 180 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU G 180 " --> pdb=" O VAL G 134 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU G 136 " --> pdb=" O SER G 178 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N SER G 178 " --> pdb=" O LEU G 136 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASN G 138 " --> pdb=" O LEU G 176 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU G 176 " --> pdb=" O ASN G 138 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 146 through 148 removed outlier: 3.517A pdb=" N TYR G 193 " --> pdb=" O PHE G 210 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 150 through 151 Processing sheet with id=AH9, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.594A pdb=" N ALA H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.511A pdb=" N GLU H 10 " --> pdb=" O MET H 118 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA H 92 " --> pdb=" O VAL H 119 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.511A pdb=" N GLU H 10 " --> pdb=" O MET H 118 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA H 92 " --> pdb=" O VAL H 119 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'H' and resid 145 through 155 removed outlier: 5.596A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 145 through 155 removed outlier: 5.596A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 160 through 164 removed outlier: 4.035A pdb=" N CYS H 206 " --> pdb=" O LYS H 219 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS H 219 " --> pdb=" O CYS H 206 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.539A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER L 64 " --> pdb=" O THR L 75 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.823A pdb=" N VAL L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.761A pdb=" N SER L 115 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN L 138 " --> pdb=" O SER L 115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER L 132 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU L 182 " --> pdb=" O SER L 132 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL L 134 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU L 180 " --> pdb=" O VAL L 134 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LEU L 136 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N SER L 178 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASN L 138 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU L 176 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'L' and resid 146 through 148 removed outlier: 3.517A pdb=" N TYR L 193 " --> pdb=" O PHE L 210 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 150 through 151 1228 hydrogen bonds defined for protein. 3300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.10 Time building geometry restraints manager: 17.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8938 1.33 - 1.45: 6751 1.45 - 1.58: 17398 1.58 - 1.70: 0 1.70 - 1.82: 169 Bond restraints: 33256 Sorted by residual: bond pdb=" N LYS G 108 " pdb=" CA LYS G 108 " ideal model delta sigma weight residual 1.457 1.488 -0.032 6.40e-03 2.44e+04 2.45e+01 bond pdb=" N LYS E 108 " pdb=" CA LYS E 108 " ideal model delta sigma weight residual 1.457 1.488 -0.032 6.40e-03 2.44e+04 2.42e+01 bond pdb=" N LYS L 108 " pdb=" CA LYS L 108 " ideal model delta sigma weight residual 1.457 1.488 -0.031 6.40e-03 2.44e+04 2.39e+01 bond pdb=" C ASP C 808 " pdb=" N PRO C 809 " ideal model delta sigma weight residual 1.334 1.368 -0.035 8.40e-03 1.42e+04 1.71e+01 bond pdb=" N CYS A 617 " pdb=" CA CYS A 617 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.29e-02 6.01e+03 1.25e+01 ... (remaining 33251 not shown) Histogram of bond angle deviations from ideal: 99.86 - 106.71: 997 106.71 - 113.56: 18515 113.56 - 120.41: 12205 120.41 - 127.27: 13332 127.27 - 134.12: 288 Bond angle restraints: 45337 Sorted by residual: angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 113.23 104.03 9.20 1.24e+00 6.50e-01 5.50e+01 angle pdb=" N THR A 618 " pdb=" CA THR A 618 " pdb=" C THR A 618 " ideal model delta sigma weight residual 113.97 105.15 8.82 1.28e+00 6.10e-01 4.75e+01 angle pdb=" N THR C 618 " pdb=" CA THR C 618 " pdb=" C THR C 618 " ideal model delta sigma weight residual 113.72 104.95 8.77 1.30e+00 5.92e-01 4.55e+01 angle pdb=" N THR C 602 " pdb=" CA THR C 602 " pdb=" C THR C 602 " ideal model delta sigma weight residual 111.28 103.95 7.33 1.09e+00 8.42e-01 4.52e+01 angle pdb=" CA ASP A 138 " pdb=" C ASP A 138 " pdb=" N PRO A 139 " ideal model delta sigma weight residual 117.43 122.94 -5.51 8.50e-01 1.38e+00 4.20e+01 ... (remaining 45332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.87: 18813 20.87 - 41.73: 1064 41.73 - 62.60: 112 62.60 - 83.46: 38 83.46 - 104.33: 20 Dihedral angle restraints: 20047 sinusoidal: 7642 harmonic: 12405 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.30 -86.30 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.26 -86.26 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.26 -86.26 1 1.00e+01 1.00e-02 8.97e+01 ... (remaining 20044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.264: 5246 0.264 - 0.527: 11 0.527 - 0.791: 1 0.791 - 1.054: 6 1.054 - 1.318: 1 Chirality restraints: 5265 Sorted by residual: chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.08 -1.32 2.00e-01 2.50e+01 4.34e+01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.36 -1.04 2.00e-01 2.50e+01 2.71e+01 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.27e+01 ... (remaining 5262 not shown) Planarity restraints: 5879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " 0.297 2.00e-02 2.50e+03 2.55e-01 8.12e+02 pdb=" C7 NAG A1301 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " 0.170 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " -0.447 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1305 " -0.284 2.00e-02 2.50e+03 2.45e-01 7.49e+02 pdb=" C7 NAG A1305 " 0.066 2.00e-02 2.50e+03 pdb=" C8 NAG A1305 " -0.162 2.00e-02 2.50e+03 pdb=" N2 NAG A1305 " 0.431 2.00e-02 2.50e+03 pdb=" O7 NAG A1305 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " 0.203 2.00e-02 2.50e+03 2.15e-01 5.75e+02 pdb=" CG ASN A 234 " -0.089 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " -0.149 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " -0.264 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.299 2.00e-02 2.50e+03 ... (remaining 5876 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 320 2.59 - 3.17: 28431 3.17 - 3.74: 46057 3.74 - 4.32: 63647 4.32 - 4.90: 107094 Nonbonded interactions: 245549 Sorted by model distance: nonbonded pdb=" OD1 ASN A 234 " pdb=" C1 NAG A1304 " model vdw 2.011 2.776 nonbonded pdb=" O ASN B 616 " pdb=" OD1 ASN B 616 " model vdw 2.065 3.040 nonbonded pdb=" O PRO A1053 " pdb=" NE2 GLN A1054 " model vdw 2.241 2.520 nonbonded pdb=" OD1 ASN A 196 " pdb=" N ILE A 197 " model vdw 2.241 2.520 nonbonded pdb=" O PRO C1053 " pdb=" NE2 GLN C1054 " model vdw 2.242 2.520 ... (remaining 245544 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 132 or (resid 133 through 134 and (name N or na \ me CA or name C or name O or name CB )) or resid 135 through 137 or (resid 138 a \ nd (name N or name CA or name C or name O or name CB )) or resid 139 through 197 \ or (resid 198 and (name N or name CA or name C or name O or name CB )) or resid \ 199 through 200 or (resid 201 and (name N or name CA or name C or name O or nam \ e CB )) or resid 202 through 739 or (resid 740 and (name N or name CA or name C \ or name O or name CB )) or resid 741 through 810 or (resid 811 and (name N or na \ me CA or name C or name O or name CB )) or resid 812 through 982 or (resid 983 a \ nd (name N or name CA or name C or name O or name CB )) or resid 984 through 114 \ 7 or resid 1301 through 1306)) selection = (chain 'B' and (resid 27 through 132 or (resid 133 through 134 and (name N or na \ me CA or name C or name O or name CB )) or resid 135 through 197 or (resid 198 a \ nd (name N or name CA or name C or name O or name CB )) or resid 199 through 226 \ or (resid 227 and (name N or name CA or name C or name O or name CB )) or resid \ 228 through 1147 or resid 1301 through 1306)) selection = (chain 'C' and (resid 27 through 739 or (resid 740 and (name N or name CA or nam \ e C or name O or name CB )) or resid 741 through 778 or (resid 779 and (name N o \ r name CA or name C or name O or name CB )) or resid 780 through 810 or (resid 8 \ 11 and (name N or name CA or name C or name O or name CB )) or resid 812 through \ 982 or (resid 983 and (name N or name CA or name C or name O or name CB )) or r \ esid 984 through 1147 or resid 1301 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.060 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: 0.050 Extract box with map and model: 28.120 Check model and map are aligned: 0.530 Set scattering table: 0.310 Process input model: 92.580 Find NCS groups from input model: 2.550 Set up NCS constraints: 0.290 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:3.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5987 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 33256 Z= 0.517 Angle : 0.944 12.429 45337 Z= 0.580 Chirality : 0.069 1.318 5265 Planarity : 0.008 0.255 5857 Dihedral : 12.980 104.329 11926 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.93 % Favored : 91.98 % Rotamer: Outliers : 0.12 % Allowed : 1.43 % Favored : 98.45 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.56 % 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: -1.92 (0.13), residues: 4212 helix: 0.79 (0.20), residues: 720 sheet: -1.38 (0.14), residues: 1240 loop : -1.92 (0.13), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 50 HIS 0.005 0.001 HIS B1088 PHE 0.043 0.002 PHE C 92 TYR 0.026 0.002 TYR L 187 ARG 0.010 0.001 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 230 time to evaluate : 4.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 80 TYR cc_start: 0.5185 (m-10) cc_final: 0.4619 (m-80) REVERT: G 184 LYS cc_start: 0.4932 (tptt) cc_final: 0.4186 (tptt) REVERT: G 188 GLU cc_start: 0.5590 (mp0) cc_final: 0.4434 (tp30) outliers start: 4 outliers final: 1 residues processed: 233 average time/residue: 0.6028 time to fit residues: 206.3858 Evaluate side-chains 121 residues out of total 3723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 3.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 815 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 5.9990 chunk 322 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 172 optimal weight: 0.3980 chunk 333 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 248 optimal weight: 0.0870 chunk 386 optimal weight: 20.0000 overall best weight: 2.0964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 784 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN L 38 GLN ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 33256 Z= 0.218 Angle : 0.623 7.621 45337 Z= 0.329 Chirality : 0.045 0.175 5265 Planarity : 0.005 0.082 5857 Dihedral : 5.982 58.882 5031 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.84 % Favored : 95.13 % Rotamer: Outliers : 0.58 % Allowed : 6.80 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.13), residues: 4212 helix: 1.68 (0.21), residues: 701 sheet: -1.03 (0.14), residues: 1265 loop : -1.42 (0.13), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 36 HIS 0.003 0.001 HIS A1048 PHE 0.028 0.001 PHE L 72 TYR 0.026 0.001 TYR H 80 ARG 0.010 0.001 ARG F 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 3.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 184 LYS cc_start: 0.4026 (tptt) cc_final: 0.3380 (tptt) REVERT: G 188 GLU cc_start: 0.5508 (mp0) cc_final: 0.4255 (tp30) REVERT: G 189 LYS cc_start: 0.7340 (mtpt) cc_final: 0.7136 (mtpt) REVERT: H 161 THR cc_start: 0.5098 (p) cc_final: 0.4676 (t) outliers start: 20 outliers final: 11 residues processed: 151 average time/residue: 0.6381 time to fit residues: 141.8326 Evaluate side-chains 124 residues out of total 3723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 3.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain L residue 204 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 214 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 321 optimal weight: 30.0000 chunk 263 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 387 optimal weight: 20.0000 chunk 418 optimal weight: 50.0000 chunk 345 optimal weight: 40.0000 chunk 384 optimal weight: 0.6980 chunk 132 optimal weight: 8.9990 chunk 310 optimal weight: 2.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN L 43 GLN L 167 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 33256 Z= 0.385 Angle : 0.687 7.824 45337 Z= 0.358 Chirality : 0.045 0.191 5265 Planarity : 0.005 0.075 5857 Dihedral : 5.792 59.425 5027 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.20 % Allowed : 9.45 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.20 (0.13), residues: 4212 helix: 1.50 (0.20), residues: 700 sheet: -1.03 (0.14), residues: 1275 loop : -1.39 (0.13), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 36 HIS 0.007 0.002 HIS A1048 PHE 0.031 0.002 PHE C 855 TYR 0.023 0.002 TYR H 100 ARG 0.012 0.001 ARG E 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 120 time to evaluate : 3.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 212 ARG cc_start: 0.0673 (mtp85) cc_final: -0.1555 (mmp-170) outliers start: 41 outliers final: 24 residues processed: 153 average time/residue: 0.5877 time to fit residues: 135.6081 Evaluate side-chains 128 residues out of total 3723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 106 CYS Chi-restraints excluded: chain H residue 111 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 382 optimal weight: 0.0040 chunk 291 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 260 optimal weight: 0.6980 chunk 388 optimal weight: 3.9990 chunk 411 optimal weight: 30.0000 chunk 203 optimal weight: 5.9990 chunk 368 optimal weight: 40.0000 chunk 110 optimal weight: 6.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A 957 GLN A 965 GLN B 955 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN H 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6145 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 33256 Z= 0.147 Angle : 0.541 7.589 45337 Z= 0.284 Chirality : 0.043 0.202 5265 Planarity : 0.004 0.075 5857 Dihedral : 5.165 59.910 5027 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.08 % Allowed : 11.14 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.13), residues: 4212 helix: 2.16 (0.20), residues: 702 sheet: -0.79 (0.14), residues: 1238 loop : -1.15 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 104 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE E 72 TYR 0.017 0.001 TYR H 100 ARG 0.010 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 113 time to evaluate : 3.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 111 ASP cc_start: 0.4269 (t0) cc_final: 0.4042 (t0) REVERT: G 188 GLU cc_start: 0.5302 (mp0) cc_final: 0.3661 (mm-30) outliers start: 37 outliers final: 20 residues processed: 143 average time/residue: 0.5812 time to fit residues: 125.8206 Evaluate side-chains 125 residues out of total 3723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 184 LYS Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 106 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 342 optimal weight: 20.0000 chunk 233 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 306 optimal weight: 0.9980 chunk 169 optimal weight: 10.0000 chunk 351 optimal weight: 5.9990 chunk 284 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 369 optimal weight: 40.0000 chunk 103 optimal weight: 7.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN H 39 GLN H 43 GLN L 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 33256 Z= 0.432 Angle : 0.707 9.099 45337 Z= 0.365 Chirality : 0.045 0.208 5265 Planarity : 0.005 0.077 5857 Dihedral : 5.697 59.828 5027 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.46 % Favored : 93.52 % Rotamer: Outliers : 1.98 % Allowed : 11.90 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.03 (0.13), residues: 4212 helix: 1.64 (0.20), residues: 698 sheet: -0.87 (0.14), residues: 1271 loop : -1.33 (0.13), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 886 HIS 0.007 0.002 HIS A1048 PHE 0.034 0.002 PHE C 855 TYR 0.019 0.002 TYR A 200 ARG 0.006 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 113 time to evaluate : 3.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1101 HIS cc_start: 0.6774 (OUTLIER) cc_final: 0.6406 (m90) REVERT: C 869 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.7049 (mtm) REVERT: F 216 LYS cc_start: 0.5487 (mptt) cc_final: 0.3740 (tptt) REVERT: G 62 ARG cc_start: 0.4377 (OUTLIER) cc_final: 0.3886 (ptp-110) REVERT: G 78 ARG cc_start: 0.5929 (ptp-170) cc_final: 0.5724 (ptp-170) REVERT: G 188 GLU cc_start: 0.5464 (mp0) cc_final: 0.3677 (mm-30) REVERT: L 212 ARG cc_start: 0.0353 (mtp85) cc_final: -0.1502 (mmp-170) outliers start: 68 outliers final: 41 residues processed: 172 average time/residue: 0.5341 time to fit residues: 142.1371 Evaluate side-chains 151 residues out of total 3723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 107 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 106 CYS Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 204 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 138 optimal weight: 6.9990 chunk 370 optimal weight: 0.0970 chunk 81 optimal weight: 1.9990 chunk 241 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 412 optimal weight: 20.0000 chunk 342 optimal weight: 0.7980 chunk 190 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 136 optimal weight: 8.9990 chunk 216 optimal weight: 5.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 ASN B 49 HIS C 334 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN H 43 GLN ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33256 Z= 0.192 Angle : 0.551 9.161 45337 Z= 0.288 Chirality : 0.043 0.196 5265 Planarity : 0.004 0.076 5857 Dihedral : 5.181 59.704 5027 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.25 % Favored : 95.73 % Rotamer: Outliers : 1.63 % Allowed : 12.86 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.70 (0.13), residues: 4212 helix: 2.04 (0.20), residues: 722 sheet: -0.74 (0.14), residues: 1238 loop : -1.13 (0.13), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 104 HIS 0.005 0.001 HIS G 199 PHE 0.009 0.001 PHE C 855 TYR 0.024 0.001 TYR H 100 ARG 0.013 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 109 time to evaluate : 3.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 14 PRO cc_start: 0.5730 (Cg_exo) cc_final: 0.5198 (Cg_endo) REVERT: F 74 MET cc_start: 0.3158 (mmt) cc_final: 0.2582 (mmt) REVERT: F 216 LYS cc_start: 0.5510 (mptt) cc_final: 0.3872 (tptt) REVERT: G 188 GLU cc_start: 0.5211 (mp0) cc_final: 0.3675 (mm-30) REVERT: H 220 LYS cc_start: 0.3308 (pptt) cc_final: 0.2515 (mmmt) REVERT: L 184 LYS cc_start: 0.1725 (mmmt) cc_final: 0.1525 (mmmt) outliers start: 56 outliers final: 39 residues processed: 157 average time/residue: 0.5635 time to fit residues: 135.7313 Evaluate side-chains 142 residues out of total 3723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 103 time to evaluate : 3.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 184 LYS Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 204 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 397 optimal weight: 50.0000 chunk 46 optimal weight: 5.9990 chunk 234 optimal weight: 0.0000 chunk 300 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 chunk 346 optimal weight: 20.0000 chunk 230 optimal weight: 5.9990 chunk 410 optimal weight: 10.0000 chunk 256 optimal weight: 7.9990 chunk 250 optimal weight: 0.3980 chunk 189 optimal weight: 5.9990 overall best weight: 3.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 926 GLN C 321 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN H 43 GLN ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33256 Z= 0.281 Angle : 0.592 9.320 45337 Z= 0.308 Chirality : 0.043 0.181 5265 Planarity : 0.004 0.076 5857 Dihedral : 5.261 59.820 5027 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.89 % Favored : 94.09 % Rotamer: Outliers : 1.87 % Allowed : 12.86 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.69 (0.13), residues: 4212 helix: 1.99 (0.20), residues: 723 sheet: -0.77 (0.14), residues: 1272 loop : -1.08 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 36 HIS 0.004 0.001 HIS A1048 PHE 0.021 0.001 PHE C 855 TYR 0.016 0.001 TYR B1067 ARG 0.007 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 109 time to evaluate : 3.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1050 MET cc_start: 0.7991 (ptt) cc_final: 0.7735 (ptt) REVERT: C 1101 HIS cc_start: 0.7063 (OUTLIER) cc_final: 0.6560 (m90) REVERT: F 74 MET cc_start: 0.2870 (mmt) cc_final: 0.2606 (mmt) REVERT: F 216 LYS cc_start: 0.5867 (mptt) cc_final: 0.4450 (tptp) REVERT: G 62 ARG cc_start: 0.4510 (OUTLIER) cc_final: 0.3906 (ptp-110) REVERT: G 78 ARG cc_start: 0.5779 (ptp-170) cc_final: 0.5423 (ptp-170) REVERT: H 157 PRO cc_start: 0.7630 (Cg_endo) cc_final: 0.7406 (Cg_exo) REVERT: H 220 LYS cc_start: 0.3096 (pptt) cc_final: 0.2554 (mmmt) outliers start: 64 outliers final: 45 residues processed: 165 average time/residue: 0.5322 time to fit residues: 135.4857 Evaluate side-chains 152 residues out of total 3723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 105 time to evaluate : 4.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 204 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 254 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 245 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 279 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 322 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN G 190 HIS H 43 GLN ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33256 Z= 0.235 Angle : 0.566 9.529 45337 Z= 0.296 Chirality : 0.043 0.182 5265 Planarity : 0.004 0.072 5857 Dihedral : 5.122 59.350 5027 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.68 % Favored : 95.30 % Rotamer: Outliers : 1.81 % Allowed : 13.13 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.58 (0.13), residues: 4212 helix: 2.03 (0.20), residues: 740 sheet: -0.68 (0.14), residues: 1272 loop : -1.02 (0.13), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.003 0.001 HIS G 199 PHE 0.027 0.001 PHE C 392 TYR 0.016 0.001 TYR B1067 ARG 0.006 0.000 ARG F 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 112 time to evaluate : 3.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1050 MET cc_start: 0.8027 (ptt) cc_final: 0.7784 (ptt) REVERT: F 216 LYS cc_start: 0.6134 (mptt) cc_final: 0.4818 (tptp) REVERT: H 2 MET cc_start: 0.4992 (tmm) cc_final: 0.4537 (tpt) REVERT: H 220 LYS cc_start: 0.3048 (pptt) cc_final: 0.2630 (mmmt) outliers start: 62 outliers final: 49 residues processed: 168 average time/residue: 0.5407 time to fit residues: 139.9713 Evaluate side-chains 152 residues out of total 3723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 103 time to evaluate : 3.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 204 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 373 optimal weight: 7.9990 chunk 393 optimal weight: 7.9990 chunk 358 optimal weight: 30.0000 chunk 382 optimal weight: 4.9990 chunk 230 optimal weight: 0.9980 chunk 166 optimal weight: 0.0070 chunk 300 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 345 optimal weight: 5.9990 chunk 361 optimal weight: 10.0000 chunk 381 optimal weight: 10.0000 overall best weight: 3.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33256 Z= 0.288 Angle : 0.603 8.944 45337 Z= 0.313 Chirality : 0.043 0.181 5265 Planarity : 0.004 0.071 5857 Dihedral : 5.209 59.773 5027 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.98 % Favored : 93.99 % Rotamer: Outliers : 1.78 % Allowed : 13.36 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.57 (0.13), residues: 4212 helix: 2.01 (0.20), residues: 739 sheet: -0.67 (0.14), residues: 1280 loop : -1.00 (0.13), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 36 HIS 0.012 0.001 HIS G 190 PHE 0.023 0.001 PHE C 392 TYR 0.016 0.001 TYR B 91 ARG 0.010 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 111 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1050 MET cc_start: 0.8010 (ptt) cc_final: 0.7774 (ptt) REVERT: C 1101 HIS cc_start: 0.7058 (OUTLIER) cc_final: 0.6529 (m90) REVERT: F 216 LYS cc_start: 0.6189 (mptt) cc_final: 0.4547 (tptt) REVERT: G 188 GLU cc_start: 0.5204 (mm-30) cc_final: 0.3609 (tp30) REVERT: G 189 LYS cc_start: 0.5671 (pttm) cc_final: 0.5095 (mtmt) REVERT: H 220 LYS cc_start: 0.3171 (pptt) cc_final: 0.2755 (mmmt) outliers start: 61 outliers final: 53 residues processed: 163 average time/residue: 0.5613 time to fit residues: 137.7849 Evaluate side-chains 163 residues out of total 3723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 109 time to evaluate : 3.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 101 CYS Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 188 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 251 optimal weight: 8.9990 chunk 404 optimal weight: 8.9990 chunk 246 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 281 optimal weight: 0.9990 chunk 424 optimal weight: 40.0000 chunk 390 optimal weight: 9.9990 chunk 337 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN B 762 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN G 190 HIS G 211 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33256 Z= 0.250 Angle : 0.588 11.009 45337 Z= 0.305 Chirality : 0.043 0.180 5265 Planarity : 0.004 0.072 5857 Dihedral : 5.178 59.856 5027 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.01 % Favored : 94.97 % Rotamer: Outliers : 1.66 % Allowed : 13.54 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.51 (0.13), residues: 4212 helix: 2.11 (0.20), residues: 740 sheet: -0.69 (0.14), residues: 1268 loop : -0.94 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 113 HIS 0.004 0.001 HIS A1048 PHE 0.022 0.001 PHE C 392 TYR 0.018 0.001 TYR H 100 ARG 0.006 0.001 ARG E 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 109 time to evaluate : 3.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1050 MET cc_start: 0.8033 (ptt) cc_final: 0.7820 (ptt) REVERT: C 1101 HIS cc_start: 0.7017 (OUTLIER) cc_final: 0.6495 (m90) REVERT: F 2 MET cc_start: 0.3690 (tmm) cc_final: 0.3371 (tpp) REVERT: F 216 LYS cc_start: 0.6203 (mptt) cc_final: 0.4568 (tptt) REVERT: G 188 GLU cc_start: 0.5340 (mm-30) cc_final: 0.3685 (tp30) REVERT: H 2 MET cc_start: 0.4626 (tpt) cc_final: 0.4125 (tpt) REVERT: H 220 LYS cc_start: 0.3141 (pptt) cc_final: 0.2722 (mmmt) outliers start: 57 outliers final: 49 residues processed: 157 average time/residue: 0.5617 time to fit residues: 135.7130 Evaluate side-chains 156 residues out of total 3723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 106 time to evaluate : 3.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 101 CYS Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 188 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 268 optimal weight: 5.9990 chunk 360 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 311 optimal weight: 50.0000 chunk 49 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 338 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 347 optimal weight: 7.9990 chunk 42 optimal weight: 0.0040 chunk 62 optimal weight: 9.9990 overall best weight: 4.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 334 ASN C 448 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN F 165 ASN G 190 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.063120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.038236 restraints weight = 292071.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.037841 restraints weight = 159871.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.038040 restraints weight = 111399.803| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 33256 Z= 0.313 Angle : 0.621 9.260 45337 Z= 0.322 Chirality : 0.043 0.175 5265 Planarity : 0.004 0.071 5857 Dihedral : 5.286 59.984 5027 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.36 % Favored : 93.61 % Rotamer: Outliers : 1.75 % Allowed : 13.59 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.61 (0.13), residues: 4212 helix: 2.02 (0.20), residues: 739 sheet: -0.75 (0.14), residues: 1297 loop : -1.02 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 36 HIS 0.027 0.002 HIS G 190 PHE 0.020 0.001 PHE C 392 TYR 0.017 0.001 TYR B 91 ARG 0.007 0.001 ARG E 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5813.16 seconds wall clock time: 110 minutes 56.18 seconds (6656.18 seconds total)