Starting phenix.real_space_refine on Tue Feb 20 00:22:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lum_0981/02_2024/6lum_0981_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lum_0981/02_2024/6lum_0981.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lum_0981/02_2024/6lum_0981_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lum_0981/02_2024/6lum_0981_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lum_0981/02_2024/6lum_0981_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lum_0981/02_2024/6lum_0981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lum_0981/02_2024/6lum_0981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lum_0981/02_2024/6lum_0981_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lum_0981/02_2024/6lum_0981_neut_updated.pdb" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 33 7.16 5 P 24 5.49 5 S 192 5.16 5 C 16857 2.51 5 N 4407 2.21 5 O 4678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 22": "NH1" <-> "NH2" Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D ASP 29": "OD1" <-> "OD2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 74": "OD1" <-> "OD2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 64": "OE1" <-> "OE2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A ASP 96": "OD1" <-> "OD2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 166": "OD1" <-> "OD2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 283": "OD1" <-> "OD2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 292": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A ASP 463": "OD1" <-> "OD2" Residue "A PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ASP 504": "OD1" <-> "OD2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A GLU 538": "OE1" <-> "OE2" Residue "A ARG 566": "NH1" <-> "NH2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 47": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ASP 103": "OD1" <-> "OD2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B ASP 219": "OD1" <-> "OD2" Residue "G ARG 22": "NH1" <-> "NH2" Residue "G PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 98": "OD1" <-> "OD2" Residue "G PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 78": "NH1" <-> "NH2" Residue "H GLU 86": "OE1" <-> "OE2" Residue "H ASP 152": "OD1" <-> "OD2" Residue "J ARG 20": "NH1" <-> "NH2" Residue "J GLU 59": "OE1" <-> "OE2" Residue "J ASP 61": "OD1" <-> "OD2" Residue "J ASP 81": "OD1" <-> "OD2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J ASP 92": "OD1" <-> "OD2" Residue "J ASP 96": "OD1" <-> "OD2" Residue "J GLU 98": "OE1" <-> "OE2" Residue "J PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 137": "OD1" <-> "OD2" Residue "J ASP 166": "OD1" <-> "OD2" Residue "J PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 208": "NH1" <-> "NH2" Residue "J TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 236": "OD1" <-> "OD2" Residue "J ASP 283": "OD1" <-> "OD2" Residue "J ARG 287": "NH1" <-> "NH2" Residue "J ARG 292": "NH1" <-> "NH2" Residue "J GLU 297": "OE1" <-> "OE2" Residue "J ASP 371": "OD1" <-> "OD2" Residue "J ASP 403": "OD1" <-> "OD2" Residue "J ARG 410": "NH1" <-> "NH2" Residue "J PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 429": "OE1" <-> "OE2" Residue "J ASP 441": "OD1" <-> "OD2" Residue "J GLU 449": "OE1" <-> "OE2" Residue "J ARG 450": "NH1" <-> "NH2" Residue "J ARG 488": "NH1" <-> "NH2" Residue "J ASP 496": "OD1" <-> "OD2" Residue "J GLU 519": "OE1" <-> "OE2" Residue "J GLU 530": "OE1" <-> "OE2" Residue "J ARG 537": "NH1" <-> "NH2" Residue "J ASP 544": "OD1" <-> "OD2" Residue "J ASP 564": "OD1" <-> "OD2" Residue "J ARG 566": "NH1" <-> "NH2" Residue "J TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 581": "OE1" <-> "OE2" Residue "K PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K ARG 55": "NH1" <-> "NH2" Residue "K TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 126": "OE1" <-> "OE2" Residue "K ASP 128": "OD1" <-> "OD2" Residue "K TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 169": "OD1" <-> "OD2" Residue "M ARG 22": "NH1" <-> "NH2" Residue "M ASP 98": "OD1" <-> "OD2" Residue "M PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 78": "NH1" <-> "NH2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "N ASP 152": "OD1" <-> "OD2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 96": "OD1" <-> "OD2" Residue "P ASP 113": "OD1" <-> "OD2" Residue "P ASP 123": "OD1" <-> "OD2" Residue "P ASP 155": "OD1" <-> "OD2" Residue "P GLU 161": "OE1" <-> "OE2" Residue "P ASP 166": "OD1" <-> "OD2" Residue "P PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 208": "NH1" <-> "NH2" Residue "P GLU 235": "OE1" <-> "OE2" Residue "P GLU 269": "OE1" <-> "OE2" Residue "P ASP 288": "OD1" <-> "OD2" Residue "P ASP 371": "OD1" <-> "OD2" Residue "P GLU 384": "OE1" <-> "OE2" Residue "P PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 417": "OE1" <-> "OE2" Residue "P ASP 426": "OD1" <-> "OD2" Residue "P GLU 445": "OE1" <-> "OE2" Residue "P ARG 450": "NH1" <-> "NH2" Residue "P ASP 463": "OD1" <-> "OD2" Residue "P GLU 472": "OE1" <-> "OE2" Residue "P GLU 473": "OE1" <-> "OE2" Residue "P ASP 481": "OD1" <-> "OD2" Residue "P ARG 488": "NH1" <-> "NH2" Residue "P ASP 504": "OD1" <-> "OD2" Residue "P GLU 507": "OE1" <-> "OE2" Residue "P GLU 516": "OE1" <-> "OE2" Residue "P ARG 537": "NH1" <-> "NH2" Residue "P ASP 539": "OD1" <-> "OD2" Residue "P TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 560": "OD1" <-> "OD2" Residue "P GLU 581": "OE1" <-> "OE2" Residue "Q GLU 36": "OE1" <-> "OE2" Residue "Q ASP 39": "OD1" <-> "OD2" Residue "Q PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q ASP 138": "OD1" <-> "OD2" Residue "Q PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 169": "OD1" <-> "OD2" Residue "Q ASP 219": "OD1" <-> "OD2" Residue "Q GLU 252": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26191 Number of models: 1 Model: "" Number of chains: 28 Chain: "C" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 978 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "D" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1193 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 137} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 256 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "A" Number of atoms: 4129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4129 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 20, 'TRANS': 518} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1873 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 221} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 989 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "H" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 991 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "I" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 256 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "J" Number of atoms: 4109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4109 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 513} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1938 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 227} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 990 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 961 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain: "O" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 256 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "P" Number of atoms: 4025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4025 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 20, 'TRANS': 518} Chain breaks: 1 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 103 Chain: "Q" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1849 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 221} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'PEV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "D" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 262 Unusual residues: {'CDL': 1, 'HEM': 2, 'LPP': 1, 'MQ9': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'MQ9:plan-3': 2, 'MQ9:plan-2': 2, 'MQ9:plan-10': 2, 'MQ9:plan-6': 2, 'MQ9:plan-5': 2, 'MQ9:plan-4': 2, 'MQ9:plan-9': 2} Unresolved non-hydrogen planarities: 68 Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'PIE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "H" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 285 Unusual residues: {'CDL': 1, 'HEM': 2, 'LPP': 1, 'MQ9': 1, 'PIE': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'MQ9:plan-3': 1, 'MQ9:plan-2': 1, 'MQ9:plan-10': 1, 'MQ9:plan-6': 1, 'MQ9:plan-5': 1, 'MQ9:plan-4': 1, 'MQ9:plan-9': 1} Unresolved non-hydrogen planarities: 35 Chain: "J" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {'F3S': 1, 'FES': 1, 'PEV': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "M" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 135 Unusual residues: {'HEM': 1, 'PEV': 1, 'PIE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "N" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 241 Unusual residues: {'CDL': 1, 'HEM': 1, 'LPP': 1, 'MQ9': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'MQ9:plan-3': 3, 'MQ9:plan-2': 3, 'MQ9:plan-10': 3, 'MQ9:plan-6': 3, 'MQ9:plan-5': 3, 'MQ9:plan-4': 3, 'MQ9:plan-9': 3} Unresolved non-hydrogen planarities: 104 Chain: "P" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {'F3S': 1, 'FES': 1, 'PEV': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7005 SG CYS B 77 99.408 67.715 51.220 1.00 5.32 S ATOM 7037 SG CYS B 82 95.374 66.168 51.476 1.00 9.75 S ATOM 7144 SG CYS B 97 101.425 66.489 56.040 1.00 24.51 S ATOM 7798 SG CYS B 180 87.869 68.988 65.143 1.00 6.28 S ATOM 7781 SG CYS B 177 92.574 67.789 60.331 1.00 5.72 S ATOM 8272 SG CYS B 240 93.389 73.414 63.714 1.00 12.32 S ATOM 7759 SG CYS B 174 87.337 72.421 59.239 1.00 6.05 S ATOM 7824 SG CYS B 184 84.918 66.640 72.367 1.00 24.51 S ATOM 8195 SG CYS B 230 83.610 72.361 74.706 1.00 3.96 S ATOM 8245 SG CYS B 236 88.744 71.671 70.970 1.00 5.76 S ATOM 15288 SG CYS K 77 36.575 41.113 50.382 1.00 9.71 S ATOM 15320 SG CYS K 82 37.190 44.673 50.407 1.00 5.96 S ATOM 15427 SG CYS K 97 34.151 39.513 55.057 1.00 8.82 S ATOM 16081 SG CYS K 180 41.776 50.609 64.475 1.00 3.48 S ATOM 16064 SG CYS K 177 38.921 46.880 59.644 1.00 4.26 S ATOM 16555 SG CYS K 240 43.353 43.719 63.322 1.00 6.63 S ATOM 16042 SG CYS K 174 45.492 49.404 58.761 1.00 5.82 S ATOM 16107 SG CYS K 184 40.538 54.607 71.422 1.00 5.33 S ATOM 16478 SG CYS K 230 45.955 53.196 74.269 1.00 4.91 S ATOM 16528 SG CYS K 236 43.429 48.873 70.473 1.00 6.30 S ATOM 23527 SG CYS Q 97 43.352 113.457 52.931 1.00 13.81 S ATOM 23393 SG CYS Q 77 43.717 110.192 48.516 1.00 19.64 S ATOM 23420 SG CYS Q 82 46.221 107.691 48.440 1.00 11.90 S ATOM 24166 SG CYS Q 180 48.029 100.925 62.877 1.00 6.58 S ATOM 24149 SG CYS Q 177 46.582 105.319 57.675 1.00 7.54 S ATOM 24636 SG CYS Q 240 41.447 103.593 61.300 1.00 10.36 S ATOM 24127 SG CYS Q 174 45.288 98.294 57.087 1.00 12.42 S ATOM 24192 SG CYS Q 184 51.758 99.915 70.042 1.00 6.03 S ATOM 24559 SG CYS Q 230 47.504 96.178 72.709 1.00 10.47 S ATOM 24609 SG CYS Q 236 45.363 100.750 68.765 1.00 12.97 S Time building chain proxies: 14.55, per 1000 atoms: 0.56 Number of scatterers: 26191 At special positions: 0 Unit cell: (136.94, 145.14, 132.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 33 26.01 S 192 16.00 P 24 15.00 O 4678 8.00 N 4407 7.00 C 16857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=15, symmetry=0 Number of additional bonds: simple=15, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.17 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 303 " pdb="FE1 F3S B 303 " - pdb=" SG CYS B 184 " pdb="FE4 F3S B 303 " - pdb=" SG CYS B 236 " pdb="FE3 F3S B 303 " - pdb=" SG CYS B 230 " pdb=" F3S K 303 " pdb="FE3 F3S K 303 " - pdb=" SG CYS K 230 " pdb="FE4 F3S K 303 " - pdb=" SG CYS K 236 " pdb="FE1 F3S K 303 " - pdb=" SG CYS K 184 " pdb=" F3S Q 303 " pdb="FE1 F3S Q 303 " - pdb=" SG CYS Q 184 " pdb="FE3 F3S Q 303 " - pdb=" SG CYS Q 230 " pdb="FE4 F3S Q 303 " - pdb=" SG CYS Q 236 " pdb=" FES B 301 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 97 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 82 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 77 " pdb=" FES K 301 " pdb="FE2 FES K 301 " - pdb=" SG CYS K 97 " pdb="FE1 FES K 301 " - pdb=" SG CYS K 82 " pdb="FE1 FES K 301 " - pdb=" SG CYS K 77 " pdb=" FES Q 301 " pdb="FE2 FES Q 301 " - pdb=" SG CYS Q 82 " pdb="FE1 FES Q 301 " - pdb=" SG CYS Q 97 " pdb="FE2 FES Q 301 " - pdb=" SG CYS Q 77 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 177 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 240 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 180 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 174 " pdb=" SF4 K 302 " pdb="FE1 SF4 K 302 " - pdb=" SG CYS K 180 " pdb="FE2 SF4 K 302 " - pdb=" SG CYS K 177 " pdb="FE3 SF4 K 302 " - pdb=" SG CYS K 240 " pdb="FE4 SF4 K 302 " - pdb=" SG CYS K 174 " pdb=" SF4 Q 302 " pdb="FE2 SF4 Q 302 " - pdb=" SG CYS Q 177 " pdb="FE3 SF4 Q 302 " - pdb=" SG CYS Q 240 " pdb="FE1 SF4 Q 302 " - pdb=" SG CYS Q 180 " pdb="FE4 SF4 Q 302 " - pdb=" SG CYS Q 174 " Number of angles added : 75 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 18 sheets defined 45.3% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.87 Creating SS restraints... Processing helix chain 'C' and resid 25 through 55 removed outlier: 4.664A pdb=" N VAL C 54 " --> pdb=" O ASP C 50 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARG C 55 " --> pdb=" O THR C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 67 Processing helix chain 'C' and resid 71 through 99 Processing helix chain 'C' and resid 103 through 106 No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 110 through 134 Processing helix chain 'D' and resid 26 through 29 Processing helix chain 'D' and resid 43 through 70 removed outlier: 4.224A pdb=" N PHE D 60 " --> pdb=" O ILE D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 78 Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.540A pdb=" N ALA D 89 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 119 Processing helix chain 'D' and resid 123 through 149 Processing helix chain 'E' and resid 2 through 28 Processing helix chain 'A' and resid 16 through 28 Proline residue: A 27 - end of helix Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 43 through 46 Processing helix chain 'A' and resid 63 through 73 Processing helix chain 'A' and resid 80 through 100 removed outlier: 5.127A pdb=" N ASP A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 153 Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 257 through 260 No H-bonds generated for 'chain 'A' and resid 257 through 260' Processing helix chain 'A' and resid 274 through 277 No H-bonds generated for 'chain 'A' and resid 274 through 277' Processing helix chain 'A' and resid 287 through 300 Processing helix chain 'A' and resid 399 through 421 Processing helix chain 'A' and resid 431 through 443 removed outlier: 4.164A pdb=" N MET A 434 " --> pdb=" O PRO A 431 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 439 " --> pdb=" O VAL A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 465 Processing helix chain 'A' and resid 472 through 488 Processing helix chain 'A' and resid 503 through 527 removed outlier: 3.553A pdb=" N PHE A 513 " --> pdb=" O ILE A 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 65 Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.796A pdb=" N ALA B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 No H-bonds generated for 'chain 'B' and resid 165 through 168' Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 185 through 188 No H-bonds generated for 'chain 'B' and resid 185 through 188' Processing helix chain 'B' and resid 196 through 206 removed outlier: 4.176A pdb=" N PHE B 205 " --> pdb=" O ASN B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 220 Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 246 through 258 Processing helix chain 'G' and resid 25 through 55 removed outlier: 4.704A pdb=" N VAL G 54 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ARG G 55 " --> pdb=" O THR G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 67 Processing helix chain 'G' and resid 71 through 99 Processing helix chain 'G' and resid 104 through 136 removed outlier: 3.851A pdb=" N GLN G 107 " --> pdb=" O PRO G 104 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ARG G 108 " --> pdb=" O ARG G 105 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE G 121 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE G 129 " --> pdb=" O VAL G 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 70 removed outlier: 4.238A pdb=" N PHE H 60 " --> pdb=" O ILE H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 78 Processing helix chain 'H' and resid 81 through 87 Processing helix chain 'H' and resid 91 through 119 Processing helix chain 'H' and resid 123 through 150 Processing helix chain 'I' and resid 2 through 28 Processing helix chain 'J' and resid 16 through 24 Processing helix chain 'J' and resid 43 through 46 Processing helix chain 'J' and resid 63 through 73 Processing helix chain 'J' and resid 80 through 100 removed outlier: 4.353A pdb=" N ASP J 92 " --> pdb=" O LYS J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 153 Processing helix chain 'J' and resid 223 through 229 Processing helix chain 'J' and resid 274 through 277 No H-bonds generated for 'chain 'J' and resid 274 through 277' Processing helix chain 'J' and resid 287 through 298 Processing helix chain 'J' and resid 399 through 421 Processing helix chain 'J' and resid 433 through 443 Processing helix chain 'J' and resid 451 through 464 Processing helix chain 'J' and resid 472 through 488 Processing helix chain 'J' and resid 504 through 527 Processing helix chain 'K' and resid 56 through 65 Processing helix chain 'K' and resid 96 through 98 No H-bonds generated for 'chain 'K' and resid 96 through 98' Processing helix chain 'K' and resid 134 through 142 Processing helix chain 'K' and resid 162 through 165 No H-bonds generated for 'chain 'K' and resid 162 through 165' Processing helix chain 'K' and resid 181 through 183 No H-bonds generated for 'chain 'K' and resid 181 through 183' Processing helix chain 'K' and resid 185 through 188 No H-bonds generated for 'chain 'K' and resid 185 through 188' Processing helix chain 'K' and resid 196 through 206 removed outlier: 4.111A pdb=" N PHE K 205 " --> pdb=" O ASN K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 220 Processing helix chain 'K' and resid 227 through 229 No H-bonds generated for 'chain 'K' and resid 227 through 229' Processing helix chain 'K' and resid 235 through 239 Processing helix chain 'K' and resid 246 through 258 Processing helix chain 'M' and resid 25 through 54 removed outlier: 4.622A pdb=" N VAL M 54 " --> pdb=" O ASP M 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 69 Processing helix chain 'M' and resid 71 through 99 Processing helix chain 'M' and resid 103 through 106 No H-bonds generated for 'chain 'M' and resid 103 through 106' Processing helix chain 'M' and resid 110 through 136 removed outlier: 3.857A pdb=" N ALA M 124 " --> pdb=" O VAL M 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 70 removed outlier: 4.237A pdb=" N PHE N 60 " --> pdb=" O ILE N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 78 Processing helix chain 'N' and resid 81 through 87 Processing helix chain 'N' and resid 91 through 119 Processing helix chain 'N' and resid 123 through 150 Processing helix chain 'O' and resid 2 through 28 Processing helix chain 'P' and resid 16 through 25 Processing helix chain 'P' and resid 43 through 46 Processing helix chain 'P' and resid 63 through 73 Processing helix chain 'P' and resid 80 through 100 removed outlier: 4.121A pdb=" N ASP P 92 " --> pdb=" O LYS P 88 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS P 99 " --> pdb=" O LEU P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 139 through 153 Processing helix chain 'P' and resid 223 through 230 removed outlier: 4.345A pdb=" N LYS P 230 " --> pdb=" O ILE P 226 " (cutoff:3.500A) Processing helix chain 'P' and resid 274 through 277 No H-bonds generated for 'chain 'P' and resid 274 through 277' Processing helix chain 'P' and resid 287 through 300 Processing helix chain 'P' and resid 400 through 421 Processing helix chain 'P' and resid 433 through 443 Processing helix chain 'P' and resid 451 through 465 Processing helix chain 'P' and resid 472 through 490 removed outlier: 4.202A pdb=" N SER P 490 " --> pdb=" O LYS P 486 " (cutoff:3.500A) Processing helix chain 'P' and resid 504 through 527 removed outlier: 3.582A pdb=" N PHE P 513 " --> pdb=" O ILE P 509 " (cutoff:3.500A) Processing helix chain 'P' and resid 545 through 548 No H-bonds generated for 'chain 'P' and resid 545 through 548' Processing helix chain 'Q' and resid 56 through 65 Processing helix chain 'Q' and resid 96 through 98 No H-bonds generated for 'chain 'Q' and resid 96 through 98' Processing helix chain 'Q' and resid 105 through 107 No H-bonds generated for 'chain 'Q' and resid 105 through 107' Processing helix chain 'Q' and resid 134 through 142 Processing helix chain 'Q' and resid 162 through 165 No H-bonds generated for 'chain 'Q' and resid 162 through 165' Processing helix chain 'Q' and resid 181 through 183 No H-bonds generated for 'chain 'Q' and resid 181 through 183' Processing helix chain 'Q' and resid 185 through 188 No H-bonds generated for 'chain 'Q' and resid 185 through 188' Processing helix chain 'Q' and resid 196 through 206 removed outlier: 4.154A pdb=" N PHE Q 205 " --> pdb=" O ASN Q 201 " (cutoff:3.500A) Processing helix chain 'Q' and resid 214 through 221 Processing helix chain 'Q' and resid 227 through 229 No H-bonds generated for 'chain 'Q' and resid 227 through 229' Processing helix chain 'Q' and resid 235 through 239 Processing helix chain 'Q' and resid 246 through 258 Processing sheet with id= A, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.725A pdb=" N GLY A 180 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR A 184 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ALA A 164 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 198 through 201 removed outlier: 6.822A pdb=" N GLU A 157 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N THR A 35 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE A 159 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 169 through 172 Processing sheet with id= D, first strand: chain 'A' and resid 550 through 556 Processing sheet with id= E, first strand: chain 'A' and resid 240 through 243 removed outlier: 5.854A pdb=" N HIS A 243 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N CYS A 353 " --> pdb=" O HIS A 243 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 43 through 48 Processing sheet with id= G, first strand: chain 'J' and resid 4 through 6 removed outlier: 8.289A pdb=" N HIS J 5 " --> pdb=" O ILE J 191 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL J 193 " --> pdb=" O HIS J 5 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY J 180 " --> pdb=" O ALA J 168 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR J 184 " --> pdb=" O ALA J 164 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ALA J 164 " --> pdb=" O TYR J 184 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 199 through 201 removed outlier: 6.355A pdb=" N VAL J 10 " --> pdb=" O VAL J 200 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA J 32 " --> pdb=" O ILE J 11 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLU J 157 " --> pdb=" O VAL J 33 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'J' and resid 169 through 172 Processing sheet with id= J, first strand: chain 'J' and resid 550 through 556 Processing sheet with id= K, first strand: chain 'J' and resid 240 through 243 removed outlier: 5.996A pdb=" N HIS J 243 " --> pdb=" O CYS J 353 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N CYS J 353 " --> pdb=" O HIS J 243 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'K' and resid 42 through 47 Processing sheet with id= M, first strand: chain 'P' and resid 3 through 6 removed outlier: 3.808A pdb=" N GLY P 180 " --> pdb=" O ALA P 168 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP P 166 " --> pdb=" O ILE P 182 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR P 184 " --> pdb=" O ALA P 164 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALA P 164 " --> pdb=" O TYR P 184 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'P' and resid 32 through 34 Processing sheet with id= O, first strand: chain 'P' and resid 169 through 172 Processing sheet with id= P, first strand: chain 'P' and resid 233 through 235 Processing sheet with id= Q, first strand: chain 'P' and resid 240 through 243 removed outlier: 3.628A pdb=" N TYR P 355 " --> pdb=" O GLN P 241 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N HIS P 243 " --> pdb=" O CYS P 353 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N CYS P 353 " --> pdb=" O HIS P 243 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'Q' and resid 42 through 48 1102 hydrogen bonds defined for protein. 3156 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: 7.43 Time building geometry restraints manager: 11.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.78: 26521 1.78 - 2.38: 302 2.38 - 2.99: 0 2.99 - 3.60: 0 3.60 - 4.20: 9 Bond restraints: 26832 Sorted by residual: bond pdb=" S4 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.233 4.205 -1.972 2.00e-02 2.50e+03 9.72e+03 bond pdb=" S4 F3S Q 303 " pdb="FE1 F3S Q 303 " ideal model delta sigma weight residual 2.233 4.203 -1.970 2.00e-02 2.50e+03 9.70e+03 bond pdb=" S4 F3S K 303 " pdb="FE1 F3S K 303 " ideal model delta sigma weight residual 2.233 4.181 -1.948 2.00e-02 2.50e+03 9.48e+03 bond pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " ideal model delta sigma weight residual 2.258 4.183 -1.925 2.00e-02 2.50e+03 9.26e+03 bond pdb=" S1 F3S Q 303 " pdb="FE4 F3S Q 303 " ideal model delta sigma weight residual 2.258 4.175 -1.917 2.00e-02 2.50e+03 9.19e+03 ... (remaining 26827 not shown) Histogram of bond angle deviations from ideal: 41.65 - 69.19: 18 69.19 - 96.73: 132 96.73 - 124.27: 35492 124.27 - 151.81: 782 151.81 - 179.35: 12 Bond angle restraints: 36436 Sorted by residual: angle pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " pdb=" S3 F3S B 303 " ideal model delta sigma weight residual 114.75 41.65 73.10 3.00e+00 1.11e-01 5.94e+02 angle pdb=" S1 F3S K 303 " pdb="FE4 F3S K 303 " pdb=" S3 F3S K 303 " ideal model delta sigma weight residual 114.75 41.82 72.93 3.00e+00 1.11e-01 5.91e+02 angle pdb=" S1 F3S Q 303 " pdb="FE4 F3S Q 303 " pdb=" S3 F3S Q 303 " ideal model delta sigma weight residual 114.75 41.84 72.91 3.00e+00 1.11e-01 5.91e+02 angle pdb=" S3 F3S B 303 " pdb="FE1 F3S B 303 " pdb=" S4 F3S B 303 " ideal model delta sigma weight residual 112.59 42.45 70.14 3.00e+00 1.11e-01 5.47e+02 angle pdb=" S3 F3S Q 303 " pdb="FE1 F3S Q 303 " pdb=" S4 F3S Q 303 " ideal model delta sigma weight residual 112.59 43.09 69.50 3.00e+00 1.11e-01 5.37e+02 ... (remaining 36431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.87: 15253 34.87 - 69.74: 545 69.74 - 104.61: 30 104.61 - 139.49: 1 139.49 - 174.36: 5 Dihedral angle restraints: 15834 sinusoidal: 6718 harmonic: 9116 Sorted by residual: dihedral pdb=" CA ASN K 37 " pdb=" C ASN K 37 " pdb=" N PRO K 38 " pdb=" CA PRO K 38 " ideal model delta harmonic sigma weight residual 180.00 149.08 30.92 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA GLY K 80 " pdb=" C GLY K 80 " pdb=" N VAL K 81 " pdb=" CA VAL K 81 " ideal model delta harmonic sigma weight residual -180.00 -149.26 -30.74 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CA GLY B 80 " pdb=" C GLY B 80 " pdb=" N VAL B 81 " pdb=" CA VAL B 81 " ideal model delta harmonic sigma weight residual -180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 15831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.335: 3927 1.335 - 2.669: 0 2.669 - 4.003: 0 4.003 - 5.338: 3 5.338 - 6.672: 3 Chirality restraints: 3933 Sorted by residual: chirality pdb=" S2 F3S Q 303 " pdb="FE1 F3S Q 303 " pdb="FE3 F3S Q 303 " pdb="FE4 F3S Q 303 " both_signs ideal model delta sigma weight residual False 10.77 4.10 6.67 2.00e-01 2.50e+01 1.11e+03 chirality pdb=" S2 F3S K 303 " pdb="FE1 F3S K 303 " pdb="FE3 F3S K 303 " pdb="FE4 F3S K 303 " both_signs ideal model delta sigma weight residual False 10.77 4.65 6.11 2.00e-01 2.50e+01 9.34e+02 chirality pdb=" S2 F3S B 303 " pdb="FE1 F3S B 303 " pdb="FE3 F3S B 303 " pdb="FE4 F3S B 303 " both_signs ideal model delta sigma weight residual False 10.77 4.73 6.04 2.00e-01 2.50e+01 9.11e+02 ... (remaining 3930 not shown) Planarity restraints: 4540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 MQ9 N 203 " -0.367 2.00e-02 2.50e+03 5.12e-01 3.28e+03 pdb=" C11 MQ9 N 203 " -0.275 2.00e-02 2.50e+03 pdb=" C7 MQ9 N 203 " -0.572 2.00e-02 2.50e+03 pdb=" C8 MQ9 N 203 " 0.746 2.00e-02 2.50e+03 pdb=" C9 MQ9 N 203 " 0.467 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 MQ9 H 204 " -0.282 2.00e-02 2.50e+03 3.17e-01 1.26e+03 pdb=" C13 MQ9 H 204 " 0.578 2.00e-02 2.50e+03 pdb=" C14 MQ9 H 204 " -0.296 2.00e-02 2.50e+03 pdb=" C15 MQ9 H 204 " 0.022 2.00e-02 2.50e+03 pdb=" C16 MQ9 H 204 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 MQ9 D 205 " -0.280 2.00e-02 2.50e+03 3.16e-01 1.25e+03 pdb=" C13 MQ9 D 205 " 0.571 2.00e-02 2.50e+03 pdb=" C14 MQ9 D 205 " -0.303 2.00e-02 2.50e+03 pdb=" C15 MQ9 D 205 " -0.041 2.00e-02 2.50e+03 pdb=" C16 MQ9 D 205 " 0.053 2.00e-02 2.50e+03 ... (remaining 4537 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 347 2.63 - 3.20: 23547 3.20 - 3.76: 39054 3.76 - 4.33: 57763 4.33 - 4.90: 97387 Nonbonded interactions: 218098 Sorted by model distance: nonbonded pdb=" O THR K 233 " pdb=" S4 F3S K 303 " model vdw 2.061 3.400 nonbonded pdb=" O ILE D 68 " pdb=" NH2 ARG D 78 " model vdw 2.086 2.520 nonbonded pdb=" OH TYR P 501 " pdb=" OE1 GLU Q 126 " model vdw 2.087 2.440 nonbonded pdb=" O PHE H 50 " pdb=" OG SER H 54 " model vdw 2.087 2.440 nonbonded pdb=" O PHE N 50 " pdb=" OG SER N 54 " model vdw 2.088 2.440 ... (remaining 218093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 5 or (resid 6 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 108 or (resid 109 and (name \ N or name CA or name C or name O or name CB )) or resid 110 through 121 or (resi \ d 122 and (name N or name CA or name C or name O or name CB )) or resid 123 thro \ ugh 130 or (resid 131 through 132 and (name N or name CA or name C or name O or \ name CB )) or resid 133 through 137 or (resid 138 and (name N or name CA or name \ C or name O or name CB )) or resid 139 through 170 or (resid 171 and (name N or \ name CA or name C or name O or name CB )) or resid 172 through 255 or (resid 25 \ 6 through 257 and (name N or name CA or name C or name O or name CB )) or resid \ 258 through 260 or (resid 261 and (name N or name CA or name C or name O or name \ CB )) or resid 262 through 268 or (resid 269 and (name N or name CA or name C o \ r name O or name CB )) or resid 270 through 275 or (resid 276 through 278 and (n \ ame N or name CA or name C or name O or name CB )) or resid 279 through 280 or ( \ resid 281 and (name N or name CA or name C or name O or name CB )) or resid 282 \ through 286 or (resid 287 and (name N or name CA or name C or name O or name CB \ )) or resid 288 through 296 or (resid 297 and (name N or name CA or name C or na \ me O or name CB )) or resid 298 through 300 or resid 347 through 426 or (resid 4 \ 27 and (name N or name CA or name C or name O or name CB )) or resid 428 through \ 429 or (resid 430 and (name N or name CA or name C or name O or name CB )) or r \ esid 431 through 440 or (resid 441 and (name N or name CA or name C or name O or \ name CB )) or resid 442 through 448 or (resid 449 and (name N or name CA or nam \ e C or name O or name CB )) or resid 450 through 468 or (resid 469 and (name N o \ r name CA or name C or name O or name CB )) or resid 470 through 531 or (resid 5 \ 32 and (name N or name CA or name C or name O or name CB )) or resid 533 through \ 569 or (resid 570 and (name N or name CA or name C or name O or name CB )) or r \ esid 571 through 577 or (resid 578 and (name N or name CA or name C or name O or \ name CB )) or resid 579 through 581 or resid 700)) selection = (chain 'J' and (resid 2 through 5 or (resid 6 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 108 or (resid 109 and (name \ N or name CA or name C or name O or name CB )) or resid 110 through 121 or (resi \ d 122 and (name N or name CA or name C or name O or name CB )) or resid 123 thro \ ugh 125 or (resid 126 through 127 and (name N or name CA or name C or name O or \ name CB )) or resid 128 through 130 or (resid 131 through 132 and (name N or nam \ e CA or name C or name O or name CB )) or resid 133 through 137 or (resid 138 an \ d (name N or name CA or name C or name O or name CB )) or resid 139 through 156 \ or (resid 157 and (name N or name CA or name C or name O or name CB )) or resid \ 158 through 170 or (resid 171 and (name N or name CA or name C or name O or name \ CB )) or resid 172 through 260 or (resid 261 and (name N or name CA or name C o \ r name O or name CB )) or resid 262 through 275 or (resid 276 through 278 and (n \ ame N or name CA or name C or name O or name CB )) or resid 279 through 280 or ( \ resid 281 and (name N or name CA or name C or name O or name CB )) or resid 282 \ through 286 or (resid 287 and (name N or name CA or name C or name O or name CB \ )) or resid 288 through 296 or (resid 297 and (name N or name CA or name C or na \ me O or name CB )) or resid 298 through 426 or (resid 427 and (name N or name CA \ or name C or name O or name CB )) or resid 428 or (resid 429 through 430 and (n \ ame N or name CA or name C or name O or name CB )) or resid 431 through 432 or ( \ resid 433 and (name N or name CA or name C or name O or name CB )) or resid 434 \ through 440 or (resid 441 and (name N or name CA or name C or name O or name CB \ )) or resid 442 through 448 or (resid 449 and (name N or name CA or name C or na \ me O or name CB )) or resid 450 through 468 or (resid 469 and (name N or name CA \ or name C or name O or name CB )) or resid 470 through 531 or (resid 532 and (n \ ame N or name CA or name C or name O or name CB )) or resid 533 through 569 or ( \ resid 570 and (name N or name CA or name C or name O or name CB )) or resid 571 \ through 577 or (resid 578 and (name N or name CA or name C or name O or name CB \ )) or resid 579 through 581 or resid 700)) selection = (chain 'P' and (resid 2 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )) or resid 158 through 268 or (resid 269 and (name N or \ name CA or name C or name O or name CB )) or resid 270 through 300 or resid 347 \ through 432 or (resid 433 and (name N or name CA or name C or name O or name CB \ )) or resid 434 through 581 or resid 700)) } ncs_group { reference = (chain 'B' and (resid 23 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 through 107 or (resid 108 and (name N or n \ ame CA or name C or name O or name CB )) or resid 109 through 111 or (resid 112 \ and (name N or name CA or name C or name O or name CB )) or resid 113 through 15 \ 6 or (resid 157 and (name N or name CA or name C or name O or name CB )) or resi \ d 158 through 159 or (resid 160 and (name N or name CA or name C or name O or na \ me CB )) or resid 161 through 211 or (resid 212 through 215 and (name N or name \ CA or name C or name O or name CB )) or resid 216 through 260 or resid 301 throu \ gh 303)) selection = (chain 'K' and (resid 23 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 through 107 or (resid 108 and (name N or n \ ame CA or name C or name O or name CB )) or resid 109 through 111 or (resid 112 \ and (name N or name CA or name C or name O or name CB )) or resid 113 through 15 \ 6 or (resid 157 and (name N or name CA or name C or name O or name CB )) or resi \ d 158 through 159 or (resid 160 and (name N or name CA or name C or name O or na \ me CB )) or resid 161 through 211 or (resid 212 through 215 and (name N or name \ CA or name C or name O or name CB )) or resid 216 through 260 or resid 301 throu \ gh 303)) selection = (chain 'Q' and (resid 23 through 260 or resid 301 through 303)) } ncs_group { reference = (chain 'C' and (resid 16 through 136 or resid 202)) selection = (chain 'G' and (resid 16 through 136 or resid 201)) selection = (chain 'M' and (resid 16 through 136 or resid 203)) } ncs_group { reference = (chain 'E' and resid 1 through 31) selection = chain 'I' selection = chain 'O' } ncs_group { reference = (chain 'H' and (resid 41 through 156 or resid 202 or resid 204)) selection = (chain 'N' and (resid 41 through 156 or resid 202 or resid 204)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.520 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 72.660 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.180 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:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 0.038 1.972 26832 Z= 2.488 Angle : 1.828 73.100 36436 Z= 0.839 Chirality : 0.232 6.672 3933 Planarity : 0.016 0.512 4540 Dihedral : 17.049 174.358 9990 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.77 % Favored : 90.07 % Rotamer: Outliers : 1.72 % Allowed : 5.38 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.13), residues: 3142 helix: -0.95 (0.12), residues: 1515 sheet: -2.05 (0.30), residues: 231 loop : -3.92 (0.12), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 102 HIS 0.008 0.001 HIS C 47 PHE 0.023 0.002 PHE O 5 TYR 0.021 0.002 TYR M 68 ARG 0.011 0.001 ARG K 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 428 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 MET cc_start: 0.8548 (ttt) cc_final: 0.8205 (ttt) REVERT: A 137 ASP cc_start: 0.7065 (t0) cc_final: 0.6766 (t0) REVERT: A 287 ARG cc_start: 0.6825 (mmt180) cc_final: 0.6499 (mpt-90) REVERT: J 448 ASN cc_start: 0.7023 (p0) cc_final: 0.6632 (p0) REVERT: K 47 ARG cc_start: 0.7378 (ttm-80) cc_final: 0.7128 (mtm180) REVERT: P 410 ARG cc_start: 0.7261 (mtp85) cc_final: 0.6826 (mtm-85) REVERT: Q 47 ARG cc_start: 0.7319 (ttm110) cc_final: 0.6950 (pmt170) REVERT: Q 87 MET cc_start: 0.7842 (mtt) cc_final: 0.7635 (mtt) REVERT: Q 104 MET cc_start: 0.3783 (mtm) cc_final: 0.2897 (ppp) outliers start: 44 outliers final: 4 residues processed: 464 average time/residue: 1.4478 time to fit residues: 774.9883 Evaluate side-chains 350 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 346 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain N residue 54 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 20.0000 chunk 235 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 243 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 282 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS C 87 HIS D 30 HIS A 57 ASN A 114 GLN A 141 HIS A 195 HIS ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN A 421 ASN A 459 GLN A 465 ASN B 79 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN G 33 HIS G 47 HIS G 87 HIS G 109 GLN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 459 GLN J 460 GLN J 464 ASN J 477 GLN J 557 GLN K 90 ASN K 132 ASN K 160 GLN K 245 GLN M 33 HIS M 87 HIS M 132 HIS N 123 ASN ** P 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 62 ASN ** P 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 241 GLN P 267 ASN P 405 ASN P 459 GLN P 465 ASN P 527 ASN P 557 GLN Q 93 ASN Q 132 ASN Q 245 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 26832 Z= 0.256 Angle : 1.157 85.472 36436 Z= 0.450 Chirality : 0.054 1.390 3933 Planarity : 0.005 0.051 4540 Dihedral : 14.881 167.337 4388 Min Nonbonded Distance : 1.563 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.89 % Allowed : 12.80 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.14), residues: 3142 helix: 0.41 (0.13), residues: 1509 sheet: -1.48 (0.32), residues: 215 loop : -3.36 (0.13), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 48 HIS 0.006 0.001 HIS P 43 PHE 0.014 0.001 PHE O 19 TYR 0.019 0.001 TYR J 569 ARG 0.008 0.000 ARG M 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 372 time to evaluate : 3.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 ARG cc_start: 0.7535 (mtp85) cc_final: 0.7305 (mtp-110) REVERT: E 30 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7617 (t70) REVERT: A 137 ASP cc_start: 0.6899 (t0) cc_final: 0.6644 (t0) REVERT: A 272 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.6517 (ttp-170) REVERT: A 281 ILE cc_start: 0.7048 (OUTLIER) cc_final: 0.6823 (pp) REVERT: A 287 ARG cc_start: 0.6712 (mmt180) cc_final: 0.6455 (mpt-90) REVERT: I 30 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7516 (m-30) REVERT: J 448 ASN cc_start: 0.6971 (p0) cc_final: 0.6602 (p0) REVERT: K 29 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7827 (ttmt) REVERT: O 1 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.6074 (tmt) REVERT: P 410 ARG cc_start: 0.7182 (mtp85) cc_final: 0.6733 (mtm-85) REVERT: Q 104 MET cc_start: 0.3065 (mtm) cc_final: 0.2643 (ppp) REVERT: Q 144 LYS cc_start: 0.8160 (mmtm) cc_final: 0.7900 (mtpm) outliers start: 74 outliers final: 30 residues processed: 414 average time/residue: 1.3204 time to fit residues: 632.6274 Evaluate side-chains 370 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 334 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain J residue 245 THR Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain J residue 493 THR Chi-restraints excluded: chain J residue 539 ASP Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 29 LYS Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain P residue 463 ASP Chi-restraints excluded: chain P residue 539 ASP Chi-restraints excluded: chain Q residue 209 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 156 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 305 optimal weight: 0.9990 chunk 251 optimal weight: 8.9990 chunk 280 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 226 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 215 ASN J 423 ASN J 465 ASN ** J 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 ASN ** P 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 354 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 26832 Z= 0.286 Angle : 1.085 84.975 36436 Z= 0.428 Chirality : 0.057 1.499 3933 Planarity : 0.005 0.049 4540 Dihedral : 13.980 166.917 4387 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.43 % Allowed : 15.29 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.14), residues: 3142 helix: 0.75 (0.13), residues: 1523 sheet: -1.23 (0.32), residues: 219 loop : -3.05 (0.14), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 48 HIS 0.006 0.001 HIS P 43 PHE 0.015 0.001 PHE C 43 TYR 0.014 0.001 TYR J 540 ARG 0.009 0.000 ARG C 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 369 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 ARG cc_start: 0.7482 (mtp85) cc_final: 0.7279 (mtp-110) REVERT: E 30 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7626 (t70) REVERT: A 137 ASP cc_start: 0.6937 (t0) cc_final: 0.6684 (t0) REVERT: A 281 ILE cc_start: 0.7047 (OUTLIER) cc_final: 0.6845 (pp) REVERT: J 448 ASN cc_start: 0.6978 (p0) cc_final: 0.6616 (p0) REVERT: K 29 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7836 (ttmt) REVERT: O 1 MET cc_start: 0.6770 (OUTLIER) cc_final: 0.6140 (tmt) REVERT: P 9 VAL cc_start: 0.7871 (OUTLIER) cc_final: 0.7634 (m) REVERT: P 294 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.7267 (ttp) REVERT: P 410 ARG cc_start: 0.7176 (mtp85) cc_final: 0.6703 (mtm-85) REVERT: Q 32 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6856 (mmm160) REVERT: Q 103 ASP cc_start: 0.3931 (OUTLIER) cc_final: 0.3713 (p0) REVERT: Q 144 LYS cc_start: 0.8141 (mmtm) cc_final: 0.7898 (mtpm) outliers start: 88 outliers final: 37 residues processed: 421 average time/residue: 1.3220 time to fit residues: 647.5564 Evaluate side-chains 385 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 340 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 403 ASP Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain J residue 493 THR Chi-restraints excluded: chain J residue 539 ASP Chi-restraints excluded: chain K residue 29 LYS Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 289 ILE Chi-restraints excluded: chain P residue 294 MET Chi-restraints excluded: chain P residue 463 ASP Chi-restraints excluded: chain Q residue 32 ARG Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 103 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 279 optimal weight: 7.9990 chunk 212 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 135 optimal weight: 0.4980 chunk 189 optimal weight: 2.9990 chunk 283 optimal weight: 20.0000 chunk 300 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 269 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN J 48 GLN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 423 ASN ** J 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 ASN P 57 ASN P 114 GLN P 150 ASN Q 93 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 26832 Z= 0.324 Angle : 1.091 83.827 36436 Z= 0.432 Chirality : 0.058 1.459 3933 Planarity : 0.005 0.048 4540 Dihedral : 13.648 170.436 4387 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.82 % Allowed : 17.21 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.15), residues: 3142 helix: 0.89 (0.13), residues: 1503 sheet: -0.98 (0.32), residues: 223 loop : -2.91 (0.14), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 102 HIS 0.006 0.001 HIS P 43 PHE 0.016 0.002 PHE J 407 TYR 0.015 0.001 TYR M 68 ARG 0.009 0.000 ARG Q 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 365 time to evaluate : 2.947 Fit side-chains revert: symmetry clash REVERT: E 30 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7661 (t70) REVERT: A 137 ASP cc_start: 0.6915 (t0) cc_final: 0.6696 (t0) REVERT: A 281 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6691 (pp) REVERT: J 448 ASN cc_start: 0.7005 (p0) cc_final: 0.6628 (p0) REVERT: K 29 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7797 (ttmt) REVERT: O 1 MET cc_start: 0.6792 (OUTLIER) cc_final: 0.6153 (tmt) REVERT: P 9 VAL cc_start: 0.7792 (OUTLIER) cc_final: 0.7562 (m) REVERT: P 77 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7226 (tt) REVERT: P 166 ASP cc_start: 0.5767 (t70) cc_final: 0.5520 (t70) REVERT: P 410 ARG cc_start: 0.7200 (mtp85) cc_final: 0.6717 (mtm-85) REVERT: Q 32 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6854 (mmm160) REVERT: Q 144 LYS cc_start: 0.8162 (mmtm) cc_final: 0.7894 (mtpm) REVERT: Q 238 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7495 (pp20) outliers start: 98 outliers final: 46 residues processed: 429 average time/residue: 1.3184 time to fit residues: 659.2383 Evaluate side-chains 403 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 349 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 219 LEU Chi-restraints excluded: chain J residue 245 THR Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain J residue 493 THR Chi-restraints excluded: chain J residue 539 ASP Chi-restraints excluded: chain K residue 29 LYS Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 289 ILE Chi-restraints excluded: chain Q residue 32 ARG Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 103 ASP Chi-restraints excluded: chain Q residue 209 SER Chi-restraints excluded: chain Q residue 238 GLU Chi-restraints excluded: chain Q residue 244 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 250 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 223 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 256 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 269 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN B 112 GLN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 423 ASN ** J 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 HIS P 372 ASN P 527 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 26832 Z= 0.349 Angle : 1.102 84.100 36436 Z= 0.438 Chirality : 0.059 1.453 3933 Planarity : 0.005 0.050 4540 Dihedral : 13.479 174.680 4387 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 3.86 % Allowed : 18.38 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.15), residues: 3142 helix: 0.88 (0.13), residues: 1502 sheet: -0.84 (0.33), residues: 223 loop : -2.80 (0.15), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 102 HIS 0.006 0.001 HIS P 43 PHE 0.017 0.002 PHE I 5 TYR 0.018 0.002 TYR M 68 ARG 0.010 0.000 ARG Q 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 360 time to evaluate : 2.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 86 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7080 (mt-10) REVERT: E 30 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7661 (t70) REVERT: A 137 ASP cc_start: 0.6914 (t0) cc_final: 0.6692 (t0) REVERT: A 281 ILE cc_start: 0.6934 (OUTLIER) cc_final: 0.6715 (pp) REVERT: J 448 ASN cc_start: 0.7025 (p0) cc_final: 0.6635 (p0) REVERT: K 29 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7788 (ttmt) REVERT: O 1 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6263 (tmt) REVERT: P 9 VAL cc_start: 0.7802 (OUTLIER) cc_final: 0.7553 (m) REVERT: P 77 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7238 (tt) REVERT: P 410 ARG cc_start: 0.7203 (mtp85) cc_final: 0.6703 (mtm-85) REVERT: P 463 ASP cc_start: 0.6712 (OUTLIER) cc_final: 0.6439 (p0) REVERT: Q 32 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6848 (mmm160) REVERT: Q 47 ARG cc_start: 0.7245 (ttm110) cc_final: 0.6778 (pmt170) REVERT: Q 144 LYS cc_start: 0.8117 (mmtm) cc_final: 0.7843 (mtpm) REVERT: Q 238 GLU cc_start: 0.7819 (pp20) cc_final: 0.7545 (pp20) outliers start: 99 outliers final: 51 residues processed: 424 average time/residue: 1.3340 time to fit residues: 656.7246 Evaluate side-chains 407 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 347 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 219 LEU Chi-restraints excluded: chain J residue 245 THR Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain J residue 493 THR Chi-restraints excluded: chain J residue 539 ASP Chi-restraints excluded: chain K residue 29 LYS Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 220 THR Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 289 ILE Chi-restraints excluded: chain P residue 463 ASP Chi-restraints excluded: chain P residue 485 LEU Chi-restraints excluded: chain P residue 539 ASP Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 32 ARG Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 103 ASP Chi-restraints excluded: chain Q residue 209 SER Chi-restraints excluded: chain Q residue 244 ILE Chi-restraints excluded: chain Q residue 247 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 101 optimal weight: 4.9990 chunk 270 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 300 optimal weight: 7.9990 chunk 249 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 157 optimal weight: 0.0670 overall best weight: 0.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 367 GLN J 423 ASN ** J 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 267 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 26832 Z= 0.236 Angle : 1.060 83.805 36436 Z= 0.415 Chirality : 0.058 1.462 3933 Planarity : 0.004 0.050 4540 Dihedral : 12.889 179.926 4387 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 3.20 % Allowed : 19.35 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.89 (0.15), residues: 3142 helix: 1.16 (0.13), residues: 1502 sheet: -0.54 (0.34), residues: 215 loop : -2.68 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 48 HIS 0.005 0.001 HIS P 43 PHE 0.014 0.001 PHE E 19 TYR 0.020 0.001 TYR J 540 ARG 0.007 0.000 ARG Q 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 375 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 30 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7563 (t70) REVERT: A 281 ILE cc_start: 0.6911 (OUTLIER) cc_final: 0.6708 (pp) REVERT: J 448 ASN cc_start: 0.7019 (p0) cc_final: 0.6638 (p0) REVERT: K 29 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7791 (ttmt) REVERT: K 54 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6955 (t0) REVERT: P 77 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7103 (tt) REVERT: P 410 ARG cc_start: 0.7144 (mtp85) cc_final: 0.6775 (mmm-85) REVERT: P 463 ASP cc_start: 0.6561 (OUTLIER) cc_final: 0.6250 (OUTLIER) REVERT: Q 32 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6836 (mmm160) REVERT: Q 144 LYS cc_start: 0.8091 (mmtm) cc_final: 0.7851 (mtpm) REVERT: Q 223 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7103 (tm-30) REVERT: Q 238 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7540 (pp20) outliers start: 82 outliers final: 41 residues processed: 425 average time/residue: 1.3171 time to fit residues: 651.6719 Evaluate side-chains 395 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 347 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 245 THR Chi-restraints excluded: chain J residue 493 THR Chi-restraints excluded: chain J residue 539 ASP Chi-restraints excluded: chain K residue 29 LYS Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 220 THR Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 463 ASP Chi-restraints excluded: chain P residue 485 LEU Chi-restraints excluded: chain Q residue 32 ARG Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 103 ASP Chi-restraints excluded: chain Q residue 238 GLU Chi-restraints excluded: chain Q residue 244 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 290 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 170 optimal weight: 0.7980 chunk 253 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 299 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN J 57 ASN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 527 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 26832 Z= 0.352 Angle : 1.107 84.647 36436 Z= 0.441 Chirality : 0.059 1.424 3933 Planarity : 0.005 0.052 4540 Dihedral : 12.997 174.976 4385 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 3.28 % Allowed : 20.37 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.99 (0.15), residues: 3142 helix: 1.02 (0.13), residues: 1505 sheet: -0.65 (0.33), residues: 223 loop : -2.66 (0.15), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 102 HIS 0.006 0.001 HIS P 43 PHE 0.019 0.002 PHE I 5 TYR 0.024 0.002 TYR J 540 ARG 0.012 0.000 ARG Q 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 351 time to evaluate : 3.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7653 (t70) REVERT: A 137 ASP cc_start: 0.6910 (t0) cc_final: 0.6556 (t0) REVERT: J 448 ASN cc_start: 0.7036 (p0) cc_final: 0.6643 (p0) REVERT: K 29 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7795 (ttmt) REVERT: P 77 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7063 (tt) REVERT: P 410 ARG cc_start: 0.7181 (mtp85) cc_final: 0.6699 (mtm-85) REVERT: P 463 ASP cc_start: 0.6595 (OUTLIER) cc_final: 0.6246 (OUTLIER) REVERT: Q 32 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6923 (mmm160) REVERT: Q 144 LYS cc_start: 0.8113 (mmtm) cc_final: 0.7866 (mtpm) REVERT: Q 238 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7567 (pp20) outliers start: 84 outliers final: 57 residues processed: 407 average time/residue: 1.3004 time to fit residues: 617.4028 Evaluate side-chains 408 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 346 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 219 LEU Chi-restraints excluded: chain J residue 245 THR Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 434 MET Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain J residue 493 THR Chi-restraints excluded: chain J residue 539 ASP Chi-restraints excluded: chain K residue 29 LYS Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 220 THR Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 289 ILE Chi-restraints excluded: chain P residue 453 ASP Chi-restraints excluded: chain P residue 463 ASP Chi-restraints excluded: chain P residue 485 LEU Chi-restraints excluded: chain Q residue 32 ARG Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 103 ASP Chi-restraints excluded: chain Q residue 209 SER Chi-restraints excluded: chain Q residue 210 ARG Chi-restraints excluded: chain Q residue 238 GLU Chi-restraints excluded: chain Q residue 244 ILE Chi-restraints excluded: chain Q residue 247 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 185 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 235 optimal weight: 6.9990 chunk 272 optimal weight: 5.9990 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 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN B 79 HIS G 132 HIS ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 26832 Z= 0.234 Angle : 1.067 84.145 36436 Z= 0.419 Chirality : 0.058 1.468 3933 Planarity : 0.004 0.052 4540 Dihedral : 12.508 164.045 4385 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.04 % Allowed : 21.15 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.76 (0.15), residues: 3142 helix: 1.24 (0.13), residues: 1503 sheet: -0.42 (0.34), residues: 215 loop : -2.59 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 48 HIS 0.005 0.001 HIS P 43 PHE 0.014 0.001 PHE E 19 TYR 0.025 0.001 TYR J 540 ARG 0.014 0.000 ARG Q 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 365 time to evaluate : 2.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 30 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7547 (t70) REVERT: J 448 ASN cc_start: 0.7014 (p0) cc_final: 0.6626 (p0) REVERT: J 580 MET cc_start: 0.6834 (pmt) cc_final: 0.6608 (pmm) REVERT: K 29 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7789 (ttmt) REVERT: P 77 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7055 (tt) REVERT: P 100 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7173 (pmm) REVERT: P 410 ARG cc_start: 0.7163 (mtp85) cc_final: 0.6786 (mmm-85) REVERT: P 463 ASP cc_start: 0.6534 (OUTLIER) cc_final: 0.6289 (t0) REVERT: Q 32 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.6935 (mmm160) REVERT: Q 144 LYS cc_start: 0.8094 (mmtm) cc_final: 0.7844 (mtpm) REVERT: Q 238 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7552 (pp20) outliers start: 78 outliers final: 48 residues processed: 417 average time/residue: 1.3064 time to fit residues: 640.0565 Evaluate side-chains 396 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 341 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 219 LEU Chi-restraints excluded: chain J residue 245 THR Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain J residue 493 THR Chi-restraints excluded: chain J residue 539 ASP Chi-restraints excluded: chain K residue 29 LYS Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain P residue 220 THR Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 289 ILE Chi-restraints excluded: chain P residue 453 ASP Chi-restraints excluded: chain P residue 463 ASP Chi-restraints excluded: chain P residue 485 LEU Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 32 ARG Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 103 ASP Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain Q residue 210 ARG Chi-restraints excluded: chain Q residue 238 GLU Chi-restraints excluded: chain Q residue 244 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 287 optimal weight: 7.9990 chunk 262 optimal weight: 30.0000 chunk 279 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 121 optimal weight: 0.6980 chunk 219 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 252 optimal weight: 6.9990 chunk 264 optimal weight: 0.2980 chunk 278 optimal weight: 0.9980 chunk 183 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 26832 Z= 0.230 Angle : 1.066 84.274 36436 Z= 0.419 Chirality : 0.057 1.471 3933 Planarity : 0.004 0.056 4540 Dihedral : 12.241 156.505 4385 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.42 % Allowed : 22.01 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.66 (0.15), residues: 3142 helix: 1.31 (0.13), residues: 1503 sheet: -0.28 (0.34), residues: 215 loop : -2.53 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 48 HIS 0.005 0.001 HIS P 43 PHE 0.013 0.001 PHE E 19 TYR 0.025 0.001 TYR J 540 ARG 0.014 0.000 ARG Q 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 350 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 76 MET cc_start: 0.7680 (mtp) cc_final: 0.7450 (mtt) REVERT: E 30 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7481 (t70) REVERT: A 499 LYS cc_start: 0.8713 (ttmm) cc_final: 0.8415 (ttpt) REVERT: J 448 ASN cc_start: 0.7010 (p0) cc_final: 0.6626 (p0) REVERT: J 580 MET cc_start: 0.6827 (pmt) cc_final: 0.6615 (pmm) REVERT: K 54 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6932 (t0) REVERT: M 119 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6923 (mm) REVERT: P 77 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7061 (tt) REVERT: P 410 ARG cc_start: 0.7156 (mtp85) cc_final: 0.6778 (mmm-85) REVERT: P 463 ASP cc_start: 0.6487 (OUTLIER) cc_final: 0.6269 (t0) REVERT: Q 32 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6884 (mmm160) REVERT: Q 51 LEU cc_start: 0.7809 (tm) cc_final: 0.7563 (tt) REVERT: Q 144 LYS cc_start: 0.8066 (mmtm) cc_final: 0.7823 (mtpm) REVERT: Q 238 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7538 (pp20) outliers start: 62 outliers final: 44 residues processed: 390 average time/residue: 1.3321 time to fit residues: 605.8628 Evaluate side-chains 384 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 333 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 219 LEU Chi-restraints excluded: chain J residue 245 THR Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain J residue 493 THR Chi-restraints excluded: chain J residue 539 ASP Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 220 THR Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 453 ASP Chi-restraints excluded: chain P residue 463 ASP Chi-restraints excluded: chain P residue 485 LEU Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 32 ARG Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain Q residue 210 ARG Chi-restraints excluded: chain Q residue 238 GLU Chi-restraints excluded: chain Q residue 244 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 295 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 309 optimal weight: 0.5980 chunk 285 optimal weight: 8.9990 chunk 246 optimal weight: 20.0000 chunk 25 optimal weight: 0.8980 chunk 190 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 195 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 26832 Z= 0.253 Angle : 1.073 84.578 36436 Z= 0.423 Chirality : 0.058 1.462 3933 Planarity : 0.004 0.052 4540 Dihedral : 12.213 156.076 4384 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.22 % Allowed : 22.47 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.66 (0.15), residues: 3142 helix: 1.30 (0.13), residues: 1498 sheet: -0.34 (0.34), residues: 219 loop : -2.51 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 48 HIS 0.005 0.001 HIS P 43 PHE 0.014 0.001 PHE C 43 TYR 0.027 0.001 TYR J 540 ARG 0.008 0.000 ARG Q 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 339 time to evaluate : 2.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 76 MET cc_start: 0.7717 (mtp) cc_final: 0.7490 (mtt) REVERT: E 30 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7547 (t70) REVERT: A 499 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8426 (ttpt) REVERT: J 448 ASN cc_start: 0.7014 (p0) cc_final: 0.6626 (p0) REVERT: J 580 MET cc_start: 0.6879 (pmt) cc_final: 0.6658 (pmm) REVERT: K 54 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6933 (t0) REVERT: P 77 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7092 (tt) REVERT: P 100 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7586 (pmm) REVERT: P 365 ASN cc_start: 0.7306 (t0) cc_final: 0.6996 (t0) REVERT: P 410 ARG cc_start: 0.7154 (mtp85) cc_final: 0.6767 (mmm-85) REVERT: Q 32 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6896 (mmm160) REVERT: Q 51 LEU cc_start: 0.7855 (tm) cc_final: 0.7604 (tt) REVERT: Q 144 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7841 (mtpm) REVERT: Q 238 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7568 (pp20) outliers start: 57 outliers final: 42 residues processed: 376 average time/residue: 1.2889 time to fit residues: 566.8771 Evaluate side-chains 389 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 341 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 219 LEU Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain J residue 493 THR Chi-restraints excluded: chain J residue 539 ASP Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain P residue 220 THR Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 453 ASP Chi-restraints excluded: chain P residue 485 LEU Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 32 ARG Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 210 ARG Chi-restraints excluded: chain Q residue 238 GLU Chi-restraints excluded: chain Q residue 244 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 68 optimal weight: 0.0870 chunk 247 optimal weight: 6.9990 chunk 103 optimal weight: 0.3980 chunk 253 optimal weight: 0.0270 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN A 267 ASN A 399 ASN B 34 ASN ** H 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 114 GLN J 574 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.174331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126789 restraints weight = 28294.794| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.01 r_work: 0.3246 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 26832 Z= 0.205 Angle : 1.052 83.821 36436 Z= 0.411 Chirality : 0.057 1.456 3933 Planarity : 0.004 0.054 4540 Dihedral : 11.799 155.538 4384 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.95 % Allowed : 23.10 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.15), residues: 3142 helix: 1.49 (0.13), residues: 1496 sheet: -0.09 (0.34), residues: 214 loop : -2.46 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 48 HIS 0.005 0.001 HIS P 43 PHE 0.013 0.001 PHE G 118 TYR 0.025 0.001 TYR J 540 ARG 0.015 0.000 ARG Q 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10179.40 seconds wall clock time: 182 minutes 0.36 seconds (10920.36 seconds total)