Starting phenix.real_space_refine on Tue Feb 13 10:58:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpv_34945/02_2024/8hpv_34945.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpv_34945/02_2024/8hpv_34945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpv_34945/02_2024/8hpv_34945.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpv_34945/02_2024/8hpv_34945.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpv_34945/02_2024/8hpv_34945.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hpv_34945/02_2024/8hpv_34945.pdb" } resolution = 2.65 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= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9426 atoms to isotropic. 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 189 5.16 5 C 28278 2.51 5 N 7455 2.21 5 O 8718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "M TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 89": "OD1" <-> "OD2" Residue "M PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 70": "OD1" <-> "OD2" Residue "N PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 74": "OD1" <-> "OD2" Residue "L TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 166": "OE1" <-> "OE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 105": "OD1" <-> "OD2" Residue "I TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 44640 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8131 Classifications: {'peptide': 1040} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 8 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1665 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "N" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1642 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Chain: "H" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1756 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 214} Chain: "L" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain: "B" Number of atoms: 8131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8131 Classifications: {'peptide': 1040} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 8 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1756 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 214} Chain: "Q" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain: "E" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1665 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "F" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1642 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Chain: "C" Number of atoms: 8131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8131 Classifications: {'peptide': 1040} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 8 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1756 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 214} Chain: "J" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain: "R" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1665 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "S" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1642 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 17.31, per 1000 atoms: 0.39 Number of scatterers: 44640 At special positions: 0 Unit cell: (235.4, 223.416, 249.952, 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 189 16.00 O 8718 8.00 N 7455 7.00 C 28278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=72, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.04 Simple disulfide: pdb=" SG CYS M 149 " - pdb=" SG CYS M 205 " distance=2.03 Simple disulfide: pdb=" SG CYS M 225 " - pdb=" SG CYS N 216 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 136 " - pdb=" SG CYS N 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS H 231 " - pdb=" SG CYS L 215 " 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 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 97 " distance=2.03 Simple disulfide: pdb=" SG CYS P 155 " - pdb=" SG CYS P 211 " distance=2.03 Simple disulfide: pdb=" SG CYS P 231 " - pdb=" SG CYS Q 215 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 89 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 135 " - pdb=" SG CYS Q 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS E 149 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 225 " - pdb=" SG CYS F 216 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 136 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 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 738 " - pdb=" SG CYS C 760 " 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=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 155 " - pdb=" SG CYS I 211 " distance=2.03 Simple disulfide: pdb=" SG CYS I 231 " - pdb=" SG CYS J 215 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.04 Simple disulfide: pdb=" SG CYS J 135 " - pdb=" SG CYS J 195 " distance=2.04 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 95 " distance=2.04 Simple disulfide: pdb=" SG CYS R 149 " - pdb=" SG CYS R 205 " distance=2.03 Simple disulfide: pdb=" SG CYS R 225 " - pdb=" SG CYS S 216 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 136 " - pdb=" SG CYS S 196 " 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 Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG D 1 " - " ASN A 343 " " NAG G 1 " - " ASN B 343 " " NAG K 1 " - " ASN C 343 " Time building additional restraints: 12.73 Conformation dependent library (CDL) restraints added in 6.2 seconds 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10758 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 109 sheets defined 17.0% alpha, 40.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.93 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.068A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.928A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.078A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.879A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.554A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.502A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.533A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.042A 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 1032 removed outlier: 4.268A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'M' and resid 86 through 90 Processing helix chain 'M' and resid 165 through 167 No H-bonds generated for 'chain 'M' and resid 165 through 167' Processing helix chain 'M' and resid 194 through 199 removed outlier: 4.035A pdb=" N GLY M 199 " --> pdb=" O SER M 196 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 128 Processing helix chain 'N' and resid 184 through 191 removed outlier: 3.880A pdb=" N LYS N 190 " --> pdb=" O ALA N 186 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N HIS N 191 " --> pdb=" O ASP N 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 200 through 204 removed outlier: 3.514A pdb=" N LEU H 204 " --> pdb=" O SER H 201 " (cutoff:3.500A) 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 184 through 189 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.636A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.550A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.016A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.513A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.313A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.951A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.778A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.619A 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 removed outlier: 3.572A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.008A 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 removed outlier: 3.510A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.251A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.651A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 67 No H-bonds generated for 'chain 'P' and resid 65 through 67' Processing helix chain 'P' and resid 88 through 92 removed outlier: 3.973A pdb=" N THR P 92 " --> pdb=" O PRO P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 171 through 173 No H-bonds generated for 'chain 'P' and resid 171 through 173' Processing helix chain 'P' and resid 200 through 204 Processing helix chain 'Q' and resid 30 through 34 removed outlier: 3.719A pdb=" N LEU Q 34 " --> pdb=" O SER Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 84 removed outlier: 3.946A pdb=" N PHE Q 84 " --> pdb=" O PRO Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 184 through 188 Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 194 through 199 removed outlier: 4.151A pdb=" N GLY E 199 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 128 Processing helix chain 'F' and resid 185 through 191 removed outlier: 3.612A pdb=" N LYS F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS F 191 " --> pdb=" O ASP F 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.509A pdb=" N ASN C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.862A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.658A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.987A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.805A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.529A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.548A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.056A 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 945 through 965 removed outlier: 3.542A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.420A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 88 through 92 removed outlier: 4.062A pdb=" N THR I 92 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 173 No H-bonds generated for 'chain 'I' and resid 171 through 173' Processing helix chain 'I' and resid 200 through 204 Processing helix chain 'J' and resid 30 through 32 No H-bonds generated for 'chain 'J' and resid 30 through 32' Processing helix chain 'J' and resid 80 through 84 removed outlier: 3.951A pdb=" N PHE J 84 " --> pdb=" O PRO J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 188 Processing helix chain 'R' and resid 28 through 32 removed outlier: 3.567A pdb=" N SER R 31 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN R 32 " --> pdb=" O VAL R 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 28 through 32' Processing helix chain 'R' and resid 86 through 90 removed outlier: 3.775A pdb=" N THR R 90 " --> pdb=" O ALA R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 167 No H-bonds generated for 'chain 'R' and resid 165 through 167' Processing helix chain 'R' and resid 194 through 199 removed outlier: 3.628A pdb=" N GLY R 199 " --> pdb=" O SER R 196 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 83 removed outlier: 4.124A pdb=" N PHE S 83 " --> pdb=" O PRO S 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 128 Processing helix chain 'S' and resid 185 through 190 removed outlier: 3.729A pdb=" N LYS S 190 " --> pdb=" O ALA S 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.997A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.990A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.948A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 11.663A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.505A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.370A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.306A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.013A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.748A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.997A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.725A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.899A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 11.663A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.505A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.370A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.306A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.212A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.552A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.090A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.833A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.833A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.627A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.384A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.097A pdb=" N GLY M 10 " --> pdb=" O THR M 119 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 129 through 133 removed outlier: 5.935A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 129 through 133 removed outlier: 5.935A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER M 186 " --> pdb=" O VAL M 178 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 160 through 163 Processing sheet with id=AC5, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.382A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.820A pdb=" N GLN N 90 " --> pdb=" O SER N 99 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER N 99 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 116 through 120 removed outlier: 6.080A pdb=" N TYR N 175 " --> pdb=" O ASN N 140 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER N 176 " --> pdb=" O THR N 166 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 146 through 152 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.764A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.263A pdb=" N PHE H 101 " --> pdb=" O PHE H 115 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N PHE H 115 " --> pdb=" O PHE H 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 135 through 139 Processing sheet with id=AD5, first strand: chain 'H' and resid 135 through 139 Processing sheet with id=AD6, first strand: chain 'H' and resid 166 through 169 removed outlier: 3.809A pdb=" N TYR H 209 " --> pdb=" O VAL H 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.354A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.861A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 146 through 151 Processing sheet with id=AE2, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AE3, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.184A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.177A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.634A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.977A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.742A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.512A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.856A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.708A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.633A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.749A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.637A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.512A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.633A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 325 through 328 removed outlier: 4.099A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AF3, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AF4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AF6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.233A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.682A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.682A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.466A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.434A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AG3, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AG4, first strand: chain 'P' and resid 59 through 61 removed outlier: 6.606A pdb=" N TRP P 38 " --> pdb=" O LEU P 50 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU P 52 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL P 36 " --> pdb=" O LEU P 52 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE P 101 " --> pdb=" O TRP P 114 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP P 114 " --> pdb=" O PHE P 101 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P' and resid 59 through 61 removed outlier: 6.606A pdb=" N TRP P 38 " --> pdb=" O LEU P 50 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU P 52 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL P 36 " --> pdb=" O LEU P 52 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 135 through 139 removed outlier: 6.494A pdb=" N TYR P 191 " --> pdb=" O ASP P 159 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 135 through 139 removed outlier: 6.494A pdb=" N TYR P 191 " --> pdb=" O ASP P 159 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER P 192 " --> pdb=" O VAL P 184 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 166 through 169 removed outlier: 3.899A pdb=" N TYR P 209 " --> pdb=" O VAL P 226 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AH1, first strand: chain 'Q' and resid 10 through 13 removed outlier: 6.675A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 115 through 119 Processing sheet with id=AH3, first strand: chain 'Q' and resid 154 through 155 Processing sheet with id=AH4, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AH5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.254A pdb=" N GLY E 10 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR E 33 " --> pdb=" O GLU E 98 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 129 through 133 removed outlier: 6.104A pdb=" N TYR E 185 " --> pdb=" O ASP E 153 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 129 through 133 removed outlier: 6.104A pdb=" N TYR E 185 " --> pdb=" O ASP E 153 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 160 through 163 Processing sheet with id=AH9, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AI1, first strand: chain 'F' and resid 10 through 13 removed outlier: 7.153A pdb=" N LEU F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N SER F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.711A pdb=" N GLN F 90 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER F 99 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'F' and resid 116 through 120 removed outlier: 6.302A pdb=" N TYR F 175 " --> pdb=" O ASN F 140 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'F' and resid 156 through 157 removed outlier: 4.378A pdb=" N TRP F 150 " --> pdb=" O GLN F 157 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.206A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.644A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.389A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.945A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.653A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.865A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 11.139A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.451A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.621A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.938A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.615A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AJ2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AJ3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AJ4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.179A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.661A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.661A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.593A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AJ9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AK1, first strand: chain 'I' and resid 59 through 61 removed outlier: 5.151A pdb=" N TRP I 49 " --> pdb=" O ARG I 40 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ARG I 40 " --> pdb=" O TRP I 49 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'I' and resid 59 through 61 removed outlier: 5.151A pdb=" N TRP I 49 " --> pdb=" O ARG I 40 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ARG I 40 " --> pdb=" O TRP I 49 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'I' and resid 135 through 139 removed outlier: 6.414A pdb=" N TYR I 191 " --> pdb=" O ASP I 159 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'I' and resid 135 through 139 removed outlier: 6.414A pdb=" N TYR I 191 " --> pdb=" O ASP I 159 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'I' and resid 166 through 169 removed outlier: 3.759A pdb=" N TYR I 209 " --> pdb=" O VAL I 226 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AK7, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.494A pdb=" N LEU J 11 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N TYR J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'J' and resid 115 through 119 removed outlier: 5.823A pdb=" N TYR J 174 " --> pdb=" O ASN J 139 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'J' and resid 154 through 155 Processing sheet with id=AL1, first strand: chain 'R' and resid 3 through 7 Processing sheet with id=AL2, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.164A pdb=" N GLY R 10 " --> pdb=" O THR R 119 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR R 33 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ARG R 38 " --> pdb=" O TRP R 47 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N TRP R 47 " --> pdb=" O ARG R 38 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.164A pdb=" N GLY R 10 " --> pdb=" O THR R 119 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE R 111 " --> pdb=" O ARG R 97 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'R' and resid 129 through 133 removed outlier: 6.071A pdb=" N TYR R 185 " --> pdb=" O ASP R 153 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'R' and resid 129 through 133 removed outlier: 6.071A pdb=" N TYR R 185 " --> pdb=" O ASP R 153 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER R 186 " --> pdb=" O VAL R 178 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'R' and resid 160 through 163 Processing sheet with id=AL7, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.610A pdb=" N ASP S 70 " --> pdb=" O SER S 67 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'S' and resid 10 through 12 removed outlier: 7.023A pdb=" N LEU S 33 " --> pdb=" O SER S 49 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N SER S 49 " --> pdb=" O LEU S 33 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP S 35 " --> pdb=" O LEU S 47 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'S' and resid 116 through 120 removed outlier: 6.262A pdb=" N TYR S 175 " --> pdb=" O ASN S 140 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER S 176 " --> pdb=" O THR S 166 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'S' and resid 146 through 152 2025 hydrogen bonds defined for protein. 5328 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: 21.38 Time building geometry restraints manager: 14.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.19: 1 1.19 - 1.35: 14381 1.35 - 1.51: 13792 1.51 - 1.67: 17267 1.67 - 1.83: 234 Bond restraints: 45675 Sorted by residual: bond pdb=" CG PRO S 44 " pdb=" CD PRO S 44 " ideal model delta sigma weight residual 1.503 1.027 0.476 3.40e-02 8.65e+02 1.96e+02 bond pdb=" N PRO S 44 " pdb=" CD PRO S 44 " ideal model delta sigma weight residual 1.473 1.565 -0.092 1.40e-02 5.10e+03 4.33e+01 bond pdb=" CB PRO R 158 " pdb=" CG PRO R 158 " ideal model delta sigma weight residual 1.506 1.646 -0.140 3.90e-02 6.57e+02 1.29e+01 bond pdb=" CB PRO S 44 " pdb=" CG PRO S 44 " ideal model delta sigma weight residual 1.492 1.631 -0.139 5.00e-02 4.00e+02 7.75e+00 bond pdb=" CB PRO I 164 " pdb=" CG PRO I 164 " ideal model delta sigma weight residual 1.506 1.607 -0.101 3.90e-02 6.57e+02 6.65e+00 ... (remaining 45670 not shown) Histogram of bond angle deviations from ideal: 80.56 - 92.89: 2 92.89 - 105.22: 954 105.22 - 117.55: 32909 117.55 - 129.88: 28094 129.88 - 142.21: 210 Bond angle restraints: 62169 Sorted by residual: angle pdb=" N PRO S 44 " pdb=" CD PRO S 44 " pdb=" CG PRO S 44 " ideal model delta sigma weight residual 103.20 80.56 22.64 1.50e+00 4.44e-01 2.28e+02 angle pdb=" CA PRO S 44 " pdb=" N PRO S 44 " pdb=" CD PRO S 44 " ideal model delta sigma weight residual 112.00 96.43 15.57 1.40e+00 5.10e-01 1.24e+02 angle pdb=" CA PRO I 164 " pdb=" N PRO I 164 " pdb=" CD PRO I 164 " ideal model delta sigma weight residual 111.50 99.34 12.16 1.40e+00 5.10e-01 7.54e+01 angle pdb=" CA PRO S 44 " pdb=" CB PRO S 44 " pdb=" CG PRO S 44 " ideal model delta sigma weight residual 104.50 88.03 16.47 1.90e+00 2.77e-01 7.51e+01 angle pdb=" CA PRO R 158 " pdb=" N PRO R 158 " pdb=" CD PRO R 158 " ideal model delta sigma weight residual 111.50 100.39 11.11 1.40e+00 5.10e-01 6.29e+01 ... (remaining 62164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 25258 17.83 - 35.66: 1735 35.66 - 53.50: 284 53.50 - 71.33: 84 71.33 - 89.16: 62 Dihedral angle restraints: 27423 sinusoidal: 10677 harmonic: 16746 Sorted by residual: dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual -86.00 -3.08 -82.92 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual -86.00 -7.19 -78.81 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CA ASP I 116 " pdb=" C ASP I 116 " pdb=" N PRO I 117 " pdb=" CA PRO I 117 " ideal model delta harmonic sigma weight residual 180.00 -136.51 -43.49 0 5.00e+00 4.00e-02 7.57e+01 ... (remaining 27420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 5009 0.043 - 0.086: 1445 0.086 - 0.130: 573 0.130 - 0.173: 38 0.173 - 0.216: 9 Chirality restraints: 7074 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 1.84e+00 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.30e+00 chirality pdb=" CA ILE C 105 " pdb=" N ILE C 105 " pdb=" C ILE C 105 " pdb=" CB ILE C 105 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 7071 not shown) Planarity restraints: 8022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 81 " -0.084 5.00e-02 4.00e+02 1.28e-01 2.61e+01 pdb=" N PRO A 82 " 0.221 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU I 163 " 0.088 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO I 164 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO I 164 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO I 164 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA S 43 " -0.084 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO S 44 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO S 44 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO S 44 " -0.059 5.00e-02 4.00e+02 ... (remaining 8019 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 707 2.68 - 3.23: 40007 3.23 - 3.79: 65994 3.79 - 4.34: 92152 4.34 - 4.90: 152954 Nonbonded interactions: 351814 Sorted by model distance: nonbonded pdb=" OG SER Q 163 " pdb=" OG SER Q 177 " model vdw 2.124 2.440 nonbonded pdb=" OG SER L 163 " pdb=" OG SER L 177 " model vdw 2.137 2.440 nonbonded pdb=" OG SER J 163 " pdb=" OG SER J 177 " model vdw 2.143 2.440 nonbonded pdb=" OD2 ASP F 172 " pdb=" OG1 THR F 174 " model vdw 2.166 2.440 nonbonded pdb=" OD2 ASP N 172 " pdb=" OG1 THR N 174 " model vdw 2.168 2.440 ... (remaining 351809 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'M' selection = chain 'R' } ncs_group { reference = chain 'F' selection = chain 'N' selection = chain 'S' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'P' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.040 Extract box with map and model: 27.480 Check model and map are aligned: 0.710 Set scattering table: 0.340 Process input model: 96.700 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 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 : 0.004 0.476 45675 Z= 0.294 Angle : 0.675 22.637 62169 Z= 0.381 Chirality : 0.046 0.216 7074 Planarity : 0.006 0.128 8019 Dihedral : 13.097 89.158 16449 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.04 % Allowed : 0.16 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.31 % 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: 0.25 (0.11), residues: 5703 helix: 1.31 (0.20), residues: 727 sheet: 1.23 (0.12), residues: 1890 loop : -0.82 (0.11), residues: 3086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 886 HIS 0.007 0.001 HIS H 99 PHE 0.032 0.002 PHE B 906 TYR 0.023 0.001 TYR I 110 ARG 0.006 0.000 ARG N 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 5037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 277 time to evaluate : 3.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 108 LYS cc_start: 0.2989 (ttpp) cc_final: 0.2785 (ptmm) REVERT: S 209 LYS cc_start: 0.0093 (tptm) cc_final: -0.0915 (tptp) outliers start: 2 outliers final: 0 residues processed: 278 average time/residue: 1.1631 time to fit residues: 408.5504 Evaluate side-chains 202 residues out of total 5037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 3.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 483 optimal weight: 3.9990 chunk 434 optimal weight: 7.9990 chunk 240 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 292 optimal weight: 0.0980 chunk 232 optimal weight: 0.9990 chunk 449 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 273 optimal weight: 3.9990 chunk 334 optimal weight: 9.9990 chunk 520 optimal weight: 0.9980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 450 ASN N 139 ASN ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 108 ASN F 34 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 901 GLN I 103 HIS ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 45675 Z= 0.213 Angle : 0.572 10.305 62169 Z= 0.302 Chirality : 0.045 0.189 7074 Planarity : 0.005 0.086 8019 Dihedral : 4.578 37.531 6312 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.91 % Allowed : 5.15 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.31 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.11), residues: 5703 helix: 1.55 (0.20), residues: 725 sheet: 1.24 (0.12), residues: 1916 loop : -0.78 (0.11), residues: 3062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 886 HIS 0.008 0.001 HIS C 207 PHE 0.023 0.002 PHE C 157 TYR 0.020 0.001 TYR C1067 ARG 0.004 0.000 ARG N 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 5037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 222 time to evaluate : 3.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 569 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8294 (mm) REVERT: A 725 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7940 (tt0) REVERT: M 35 ASN cc_start: 0.5333 (OUTLIER) cc_final: 0.4826 (m-40) REVERT: N 100 PHE cc_start: 0.3588 (OUTLIER) cc_final: 0.1977 (t80) REVERT: L 108 LYS cc_start: 0.3067 (ttpp) cc_final: 0.2849 (ptmm) REVERT: C 314 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: I 103 HIS cc_start: 0.2717 (t-90) cc_final: 0.1935 (t-170) REVERT: S 209 LYS cc_start: 0.0204 (tptm) cc_final: -0.0831 (tptp) outliers start: 46 outliers final: 16 residues processed: 247 average time/residue: 1.1358 time to fit residues: 358.6470 Evaluate side-chains 222 residues out of total 5037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 201 time to evaluate : 3.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 289 optimal weight: 0.9990 chunk 161 optimal weight: 8.9990 chunk 433 optimal weight: 0.6980 chunk 354 optimal weight: 20.0000 chunk 143 optimal weight: 40.0000 chunk 521 optimal weight: 0.0030 chunk 563 optimal weight: 10.0000 chunk 464 optimal weight: 1.9990 chunk 516 optimal weight: 20.0000 chunk 177 optimal weight: 10.0000 chunk 418 optimal weight: 20.0000 overall best weight: 2.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 450 ASN ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C1011 GLN J 125 GLN ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 45675 Z= 0.321 Angle : 0.613 10.143 62169 Z= 0.326 Chirality : 0.047 0.192 7074 Planarity : 0.005 0.068 8019 Dihedral : 4.717 33.579 6312 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.31 % Allowed : 7.55 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.31 % 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: 0.24 (0.11), residues: 5703 helix: 1.45 (0.20), residues: 717 sheet: 1.13 (0.12), residues: 1948 loop : -0.85 (0.11), residues: 3038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 114 HIS 0.009 0.001 HIS C 207 PHE 0.025 0.002 PHE C 157 TYR 0.022 0.002 TYR B 380 ARG 0.013 0.001 ARG M 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 5037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 213 time to evaluate : 3.980 Fit side-chains REVERT: A 569 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8301 (mm) REVERT: A 725 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: N 100 PHE cc_start: 0.3670 (OUTLIER) cc_final: 0.2162 (t80) REVERT: H 24 PHE cc_start: 0.4715 (p90) cc_final: 0.4505 (p90) REVERT: L 43 GLN cc_start: -0.0098 (OUTLIER) cc_final: -0.0422 (pm20) REVERT: L 108 LYS cc_start: 0.3132 (ttpp) cc_final: 0.2829 (ptmm) REVERT: B 239 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.6861 (tm-30) REVERT: E 117 MET cc_start: 0.0999 (OUTLIER) cc_final: 0.0126 (ppp) REVERT: F 79 GLN cc_start: 0.3631 (mm110) cc_final: 0.3350 (pp30) REVERT: C 1010 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7565 (pp30) REVERT: I 103 HIS cc_start: 0.2393 (t-90) cc_final: 0.1979 (t-170) REVERT: J 188 GLU cc_start: 0.2314 (mm-30) cc_final: 0.1973 (tp30) outliers start: 66 outliers final: 27 residues processed: 253 average time/residue: 1.0545 time to fit residues: 345.8971 Evaluate side-chains 218 residues out of total 5037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 184 time to evaluate : 3.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain L residue 43 GLN Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain J residue 162 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 515 optimal weight: 9.9990 chunk 391 optimal weight: 6.9990 chunk 270 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 350 optimal weight: 9.9990 chunk 523 optimal weight: 20.0000 chunk 553 optimal weight: 4.9990 chunk 273 optimal weight: 1.9990 chunk 495 optimal weight: 20.0000 chunk 149 optimal weight: 30.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN E 81 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 370 ASN C 501 ASN ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 45675 Z= 0.313 Angle : 0.607 9.967 62169 Z= 0.323 Chirality : 0.047 0.195 7074 Planarity : 0.005 0.065 8019 Dihedral : 4.748 30.227 6312 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.81 % Allowed : 9.32 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.31 % 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: 0.18 (0.11), residues: 5703 helix: 1.42 (0.20), residues: 721 sheet: 1.10 (0.12), residues: 1946 loop : -0.89 (0.11), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 35 HIS 0.010 0.001 HIS C 207 PHE 0.026 0.002 PHE C 157 TYR 0.023 0.002 TYR C 265 ARG 0.006 0.001 ARG N 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 5037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 190 time to evaluate : 3.807 Fit side-chains REVERT: A 203 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7406 (mp) REVERT: A 569 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8316 (mm) REVERT: A 725 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: N 100 PHE cc_start: 0.3737 (OUTLIER) cc_final: 0.2241 (t80) REVERT: B 239 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.6900 (tm-30) REVERT: P 165 VAL cc_start: 0.1809 (OUTLIER) cc_final: 0.1542 (t) REVERT: E 117 MET cc_start: 0.1175 (OUTLIER) cc_final: 0.0275 (ppp) REVERT: F 79 GLN cc_start: 0.3620 (mm110) cc_final: 0.3359 (pp30) REVERT: C 646 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7068 (ttp-170) REVERT: C 1010 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7560 (pp30) REVERT: I 103 HIS cc_start: 0.2309 (t-90) cc_final: 0.1918 (t-170) outliers start: 91 outliers final: 43 residues processed: 255 average time/residue: 0.9103 time to fit residues: 311.3470 Evaluate side-chains 229 residues out of total 5037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 177 time to evaluate : 3.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain S residue 14 SER Chi-restraints excluded: chain S residue 15 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 461 optimal weight: 0.6980 chunk 314 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 412 optimal weight: 0.9990 chunk 228 optimal weight: 20.0000 chunk 472 optimal weight: 0.8980 chunk 382 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 282 optimal weight: 0.8980 chunk 497 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 450 ASN ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN C 81 ASN C 207 HIS ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 45675 Z= 0.165 Angle : 0.531 9.474 62169 Z= 0.280 Chirality : 0.044 0.188 7074 Planarity : 0.004 0.061 8019 Dihedral : 4.415 27.361 6312 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.41 % Allowed : 10.71 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.11), residues: 5703 helix: 1.85 (0.20), residues: 720 sheet: 1.19 (0.12), residues: 1949 loop : -0.75 (0.11), residues: 3034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP N 35 HIS 0.010 0.001 HIS C 207 PHE 0.028 0.001 PHE Q 92 TYR 0.021 0.001 TYR I 110 ARG 0.007 0.000 ARG N 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 5037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 206 time to evaluate : 3.769 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7378 (tt0) REVERT: A 500 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.7285 (t) REVERT: A 740 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7727 (ttt) REVERT: N 100 PHE cc_start: 0.3571 (OUTLIER) cc_final: 0.2011 (t80) REVERT: B 239 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.6807 (tm-30) REVERT: P 165 VAL cc_start: 0.1835 (OUTLIER) cc_final: 0.1558 (t) REVERT: I 87 MET cc_start: 0.0240 (ppp) cc_final: -0.0261 (pmm) REVERT: R 117 MET cc_start: 0.4432 (tmt) cc_final: 0.4056 (tmt) REVERT: S 128 LYS cc_start: 0.2614 (pmtt) cc_final: 0.2098 (mppt) outliers start: 71 outliers final: 25 residues processed: 259 average time/residue: 0.9809 time to fit residues: 334.5842 Evaluate side-chains 211 residues out of total 5037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 180 time to evaluate : 3.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain I residue 15 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 186 optimal weight: 0.8980 chunk 498 optimal weight: 20.0000 chunk 109 optimal weight: 0.9990 chunk 325 optimal weight: 40.0000 chunk 136 optimal weight: 1.9990 chunk 554 optimal weight: 0.0970 chunk 460 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 183 optimal weight: 0.9990 chunk 291 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 450 ASN M 81 GLN M 83 ASN ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** J 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 45675 Z= 0.152 Angle : 0.516 11.133 62169 Z= 0.271 Chirality : 0.043 0.189 7074 Planarity : 0.004 0.063 8019 Dihedral : 4.220 25.899 6312 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.37 % Allowed : 11.33 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.11), residues: 5703 helix: 2.12 (0.20), residues: 720 sheet: 1.17 (0.12), residues: 2001 loop : -0.67 (0.11), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP H 38 HIS 0.010 0.001 HIS C 207 PHE 0.024 0.001 PHE C 157 TYR 0.018 0.001 TYR C1067 ARG 0.007 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 5037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 202 time to evaluate : 3.781 Fit side-chains revert: symmetry clash REVERT: A 500 THR cc_start: 0.7730 (OUTLIER) cc_final: 0.7270 (t) REVERT: A 740 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7754 (ttt) REVERT: M 82 MET cc_start: 0.2762 (pmm) cc_final: 0.2449 (pmm) REVERT: N 100 PHE cc_start: 0.3332 (OUTLIER) cc_final: 0.1804 (t80) REVERT: H 49 TRP cc_start: 0.2314 (t60) cc_final: 0.1924 (p-90) REVERT: B 239 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.6790 (tm-30) REVERT: P 116 ASP cc_start: 0.1116 (OUTLIER) cc_final: 0.0416 (p0) REVERT: P 165 VAL cc_start: 0.1789 (OUTLIER) cc_final: 0.1553 (t) REVERT: I 87 MET cc_start: 0.0165 (OUTLIER) cc_final: -0.1464 (tpp) REVERT: I 103 HIS cc_start: 0.2849 (t-170) cc_final: 0.2384 (t-170) REVERT: S 128 LYS cc_start: 0.2224 (pmtt) cc_final: 0.1709 (mptt) REVERT: S 171 LYS cc_start: 0.1861 (pptt) cc_final: 0.1294 (pttm) outliers start: 69 outliers final: 33 residues processed: 254 average time/residue: 0.9584 time to fit residues: 323.7534 Evaluate side-chains 227 residues out of total 5037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 187 time to evaluate : 3.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain P residue 116 ASP Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain S residue 15 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 534 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 315 optimal weight: 0.9980 chunk 404 optimal weight: 3.9990 chunk 313 optimal weight: 10.0000 chunk 466 optimal weight: 1.9990 chunk 309 optimal weight: 7.9990 chunk 552 optimal weight: 20.0000 chunk 345 optimal weight: 0.0270 chunk 336 optimal weight: 4.9990 chunk 254 optimal weight: 0.0970 overall best weight: 1.4240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 450 ASN ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C1135 ASN I 103 HIS ** J 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 45675 Z= 0.208 Angle : 0.540 9.157 62169 Z= 0.284 Chirality : 0.045 0.188 7074 Planarity : 0.004 0.067 8019 Dihedral : 4.300 26.281 6312 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.61 % Allowed : 11.65 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.11), residues: 5703 helix: 2.02 (0.20), residues: 720 sheet: 1.20 (0.12), residues: 1943 loop : -0.71 (0.11), residues: 3040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP N 35 HIS 0.011 0.001 HIS I 103 PHE 0.025 0.001 PHE C 157 TYR 0.020 0.001 TYR C1067 ARG 0.007 0.000 ARG N 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 5037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 188 time to evaluate : 3.839 Fit side-chains revert: symmetry clash REVERT: M 82 MET cc_start: 0.2547 (pmm) cc_final: 0.2314 (pmm) REVERT: N 100 PHE cc_start: 0.3487 (OUTLIER) cc_final: 0.1959 (t80) REVERT: H 49 TRP cc_start: 0.2396 (t60) cc_final: 0.1955 (p-90) REVERT: H 87 MET cc_start: 0.3042 (mmm) cc_final: 0.2765 (mmp) REVERT: B 239 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.6797 (tm-30) REVERT: P 116 ASP cc_start: 0.1078 (OUTLIER) cc_final: 0.0466 (p0) REVERT: P 165 VAL cc_start: 0.1752 (OUTLIER) cc_final: 0.1519 (t) REVERT: I 87 MET cc_start: 0.0103 (OUTLIER) cc_final: -0.1498 (tpp) REVERT: S 128 LYS cc_start: 0.2242 (pmtt) cc_final: 0.1717 (mptt) outliers start: 81 outliers final: 48 residues processed: 248 average time/residue: 0.9348 time to fit residues: 313.9245 Evaluate side-chains 237 residues out of total 5037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 184 time to evaluate : 3.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain P residue 116 ASP Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain Q residue 33 TYR Chi-restraints excluded: chain Q residue 92 PHE Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain S residue 15 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 341 optimal weight: 30.0000 chunk 220 optimal weight: 10.0000 chunk 329 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 351 optimal weight: 20.0000 chunk 376 optimal weight: 10.0000 chunk 273 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 434 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 450 ASN A 493 GLN A 955 ASN A1135 ASN ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN C 207 HIS C 422 ASN C 779 GLN I 103 HIS J 156 GLN ** J 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 55 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.135 45675 Z= 0.588 Angle : 0.750 9.024 62169 Z= 0.401 Chirality : 0.055 0.306 7074 Planarity : 0.006 0.076 8019 Dihedral : 5.240 38.349 6312 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.15 % Allowed : 11.77 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.11), residues: 5703 helix: 0.98 (0.19), residues: 731 sheet: 0.85 (0.12), residues: 1997 loop : -1.06 (0.11), residues: 2975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 353 HIS 0.011 0.002 HIS C 207 PHE 0.036 0.003 PHE C 157 TYR 0.029 0.003 TYR C 265 ARG 0.009 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 5037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 195 time to evaluate : 3.765 Fit side-chains revert: symmetry clash REVERT: B 740 MET cc_start: 0.7986 (ttt) cc_final: 0.7765 (ttt) REVERT: P 116 ASP cc_start: 0.1235 (OUTLIER) cc_final: 0.0729 (p0) REVERT: C 513 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7711 (mp) REVERT: C 646 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7078 (ttp-170) REVERT: I 87 MET cc_start: 0.0200 (OUTLIER) cc_final: -0.1471 (tpp) REVERT: S 128 LYS cc_start: 0.2411 (pmtt) cc_final: 0.1757 (mptt) REVERT: S 171 LYS cc_start: 0.2114 (pptt) cc_final: 0.1429 (pttm) outliers start: 108 outliers final: 61 residues processed: 275 average time/residue: 0.9165 time to fit residues: 336.8156 Evaluate side-chains 249 residues out of total 5037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 184 time to evaluate : 3.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain P residue 116 ASP Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 85 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 502 optimal weight: 7.9990 chunk 529 optimal weight: 8.9990 chunk 482 optimal weight: 0.7980 chunk 514 optimal weight: 30.0000 chunk 528 optimal weight: 8.9990 chunk 309 optimal weight: 0.0070 chunk 224 optimal weight: 10.0000 chunk 404 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 465 optimal weight: 3.9990 chunk 486 optimal weight: 7.9990 overall best weight: 2.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 99 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 HIS C 207 HIS I 103 HIS ** J 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 45675 Z= 0.367 Angle : 0.639 9.486 62169 Z= 0.340 Chirality : 0.048 0.192 7074 Planarity : 0.005 0.076 8019 Dihedral : 4.966 36.158 6312 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.67 % Allowed : 12.50 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.11), residues: 5703 helix: 1.18 (0.19), residues: 732 sheet: 0.79 (0.12), residues: 2016 loop : -1.00 (0.11), residues: 2955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 353 HIS 0.012 0.001 HIS C 207 PHE 0.031 0.002 PHE C 157 TYR 0.032 0.002 TYR P 110 ARG 0.006 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 5037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 190 time to evaluate : 4.043 Fit side-chains REVERT: N 108 ILE cc_start: 0.4186 (OUTLIER) cc_final: 0.3376 (mt) REVERT: H 87 MET cc_start: 0.2981 (mmm) cc_final: 0.2722 (tpp) REVERT: B 239 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.6912 (tm-30) REVERT: B 740 MET cc_start: 0.7967 (ttt) cc_final: 0.7763 (ttt) REVERT: P 116 ASP cc_start: 0.1265 (OUTLIER) cc_final: 0.0630 (p0) REVERT: I 87 MET cc_start: 0.0255 (OUTLIER) cc_final: -0.1410 (tpp) REVERT: I 103 HIS cc_start: 0.3478 (OUTLIER) cc_final: 0.2545 (t70) REVERT: S 128 LYS cc_start: 0.2271 (pmtt) cc_final: 0.1608 (mppt) REVERT: S 171 LYS cc_start: 0.2057 (pptt) cc_final: 0.1500 (pttt) REVERT: S 209 LYS cc_start: 0.0452 (tptm) cc_final: -0.0620 (tptp) outliers start: 84 outliers final: 60 residues processed: 256 average time/residue: 0.9475 time to fit residues: 325.1483 Evaluate side-chains 247 residues out of total 5037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 182 time to evaluate : 3.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain N residue 108 ILE Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain P residue 116 ASP Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 103 HIS Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 512 optimal weight: 20.0000 chunk 337 optimal weight: 8.9990 chunk 544 optimal weight: 7.9990 chunk 332 optimal weight: 8.9990 chunk 258 optimal weight: 4.9990 chunk 378 optimal weight: 40.0000 chunk 570 optimal weight: 0.0040 chunk 525 optimal weight: 50.0000 chunk 454 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 351 optimal weight: 8.9990 overall best weight: 5.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B1010 GLN B1135 ASN P 108 ASN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 HIS C 207 HIS I 103 HIS ** J 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.154 45675 Z= 0.621 Angle : 0.789 10.256 62169 Z= 0.422 Chirality : 0.056 0.285 7074 Planarity : 0.007 0.083 8019 Dihedral : 5.540 41.584 6312 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.57 % Allowed : 12.90 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.11), residues: 5703 helix: 0.58 (0.19), residues: 735 sheet: 0.54 (0.12), residues: 1947 loop : -1.24 (0.11), residues: 3021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP B 353 HIS 0.014 0.002 HIS C 207 PHE 0.035 0.003 PHE C 157 TYR 0.031 0.003 TYR C 265 ARG 0.009 0.001 ARG C1000 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11406 Ramachandran restraints generated. 5703 Oldfield, 0 Emsley, 5703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 5037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 194 time to evaluate : 3.974 Fit side-chains revert: symmetry clash REVERT: M 82 MET cc_start: 0.3017 (pmm) cc_final: 0.2728 (pmm) REVERT: N 108 ILE cc_start: 0.4194 (OUTLIER) cc_final: 0.3422 (mt) REVERT: H 87 MET cc_start: 0.3201 (mmm) cc_final: 0.2874 (tpp) REVERT: P 116 ASP cc_start: 0.1282 (OUTLIER) cc_final: 0.0728 (p0) REVERT: C 646 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7067 (ttp-170) REVERT: I 87 MET cc_start: 0.0255 (OUTLIER) cc_final: -0.1471 (tpp) outliers start: 79 outliers final: 65 residues processed: 259 average time/residue: 0.9748 time to fit residues: 335.2456 Evaluate side-chains 251 residues out of total 5037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 182 time to evaluate : 3.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 111 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 100 PHE Chi-restraints excluded: chain N residue 108 ILE Chi-restraints excluded: chain N residue 165 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain P residue 116 ASP Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 573 random chunks: chunk 278 optimal weight: 3.9990 chunk 361 optimal weight: 9.9990 chunk 484 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 419 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 126 optimal weight: 8.9990 chunk 455 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 chunk 467 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** N 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B1010 GLN P 108 ASN F 34 HIS C 207 HIS I 103 HIS ** J 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.225924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.210195 restraints weight = 75698.235| |-----------------------------------------------------------------------------| r_work (start): 0.4643 rms_B_bonded: 1.10 r_work: 0.4275 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.4225 rms_B_bonded: 1.67 restraints_weight: 0.2500 r_work: 0.4125 rms_B_bonded: 3.33 restraints_weight: 0.1250 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 45675 Z= 0.184 Angle : 0.568 10.993 62169 Z= 0.300 Chirality : 0.045 0.194 7074 Planarity : 0.005 0.075 8019 Dihedral : 4.713 32.293 6312 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.05 % Allowed : 13.58 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.11), residues: 5703 helix: 1.59 (0.20), residues: 726 sheet: 0.76 (0.12), residues: 2029 loop : -0.93 (0.11), residues: 2948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP N 35 HIS 0.031 0.001 HIS C 207 PHE 0.029 0.001 PHE C 157 TYR 0.033 0.001 TYR P 110 ARG 0.010 0.000 ARG A 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9800.99 seconds wall clock time: 173 minutes 45.15 seconds (10425.15 seconds total)