Starting phenix.real_space_refine on Sun Feb 18 21:23:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmf_22924/02_2024/7kmf_22924_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmf_22924/02_2024/7kmf_22924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmf_22924/02_2024/7kmf_22924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmf_22924/02_2024/7kmf_22924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmf_22924/02_2024/7kmf_22924_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmf_22924/02_2024/7kmf_22924_updated.pdb" } resolution = 2.91 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 117 5.16 5 C 14575 2.51 5 N 3997 2.21 5 O 4184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 149": "OE1" <-> "OE2" Residue "C PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ASP 301": "OD1" <-> "OD2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C ASP 347": "OD1" <-> "OD2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D GLU 157": "OE1" <-> "OE2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 228": "NH1" <-> "NH2" Residue "D PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 304": "OE1" <-> "OE2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 209": "NH1" <-> "NH2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "F ASP 305": "OD1" <-> "OD2" Residue "F ARG 306": "NH1" <-> "NH2" Residue "F ARG 321": "NH1" <-> "NH2" Residue "F ARG 321": "NH1" <-> "NH2" Residue "F TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 368": "OE1" <-> "OE2" Residue "F ARG 374": "NH1" <-> "NH2" Residue "F ARG 417": "NH1" <-> "NH2" Residue "F ARG 483": "NH1" <-> "NH2" Residue "F TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 503": "OE1" <-> "OE2" Residue "E PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 301": "NH1" <-> "NH2" Residue "E TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 321": "NH1" <-> "NH2" Residue "E ASP 331": "OD1" <-> "OD2" Residue "E GLU 348": "OE1" <-> "OE2" Residue "E ARG 355": "NH1" <-> "NH2" Residue "E ARG 374": "NH1" <-> "NH2" Residue "E ARG 417": "NH1" <-> "NH2" Residue "E ARG 446": "NH1" <-> "NH2" Residue "E ASP 459": "OD1" <-> "OD2" Residue "E ARG 467": "NH1" <-> "NH2" Residue "E ARG 483": "NH1" <-> "NH2" Residue "E TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "H ARG 147": "NH1" <-> "NH2" Residue "H TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 198": "OE1" <-> "OE2" Residue "H ARG 237": "NH1" <-> "NH2" Residue "H PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 136": "NH1" <-> "NH2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G ASP 180": "OD1" <-> "OD2" Residue "G ARG 237": "NH1" <-> "NH2" Residue "G PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 133": "OD1" <-> "OD2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 270": "OD1" <-> "OD2" Residue "B TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 329": "OD1" <-> "OD2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "I ARG 54": "NH1" <-> "NH2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I ASP 139": "OD1" <-> "OD2" Residue "I GLU 187": "OE1" <-> "OE2" Residue "I PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 270": "OD1" <-> "OD2" Residue "I TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 428": "NH1" <-> "NH2" Residue "J TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 22875 Number of models: 1 Model: "" Number of chains: 19 Chain: "C" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2468 Classifications: {'peptide': 315} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 300} Chain breaks: 1 Chain: "D" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2440 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 300} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "F" Number of atoms: 2414 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 325, 2406 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 309} Chain breaks: 4 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 325, 2406 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 309} Chain breaks: 4 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 2438 Chain: "E" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2466 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 314} Chain breaks: 4 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 63 Chain: "H" Number of atoms: 2151 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 280, 2140 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 270} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 280, 2140 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 270} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 2160 Chain: "G" Number of atoms: 2201 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 287, 2190 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 277} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Conformer: "B" Number of residues, atoms: 287, 2190 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 277} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 bond proxies already assigned to first conformer: 2212 Chain: "B" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3165 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 70 Chain: "I" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3192 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 18, 'TRANS': 397} Chain breaks: 2 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "J" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1159 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain breaks: 8 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 66 Chain: "K" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1169 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 4, 'TRANS': 158} Chain breaks: 8 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'F6P': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'F6P': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG H 136 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG H 136 " occ=0.50 residue: pdb=" N AARG G 136 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG G 136 " occ=0.50 Time building chain proxies: 15.39, per 1000 atoms: 0.67 Number of scatterers: 22875 At special positions: 0 Unit cell: (165.36, 144.56, 113.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 117 16.00 P 2 15.00 O 4184 8.00 N 3997 7.00 C 14575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS F 465 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.71 Conformation dependent library (CDL) restraints added in 6.2 seconds 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5740 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 119 helices and 36 sheets defined 36.6% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.13 Creating SS restraints... Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 31 through 48 Processing helix chain 'C' and resid 54 through 71 Processing helix chain 'C' and resid 76 through 94 removed outlier: 3.542A pdb=" N MET C 81 " --> pdb=" O THR C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 143 removed outlier: 4.314A pdb=" N ILE C 133 " --> pdb=" O GLN C 130 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL C 142 " --> pdb=" O GLU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 158 removed outlier: 4.356A pdb=" N GLN C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLU C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS C 158 " --> pdb=" O GLN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 Processing helix chain 'C' and resid 201 through 209 removed outlier: 3.732A pdb=" N ASN C 206 " --> pdb=" O GLU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 228 removed outlier: 3.508A pdb=" N ARG C 228 " --> pdb=" O VAL C 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 225 through 228' Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 297 through 299 No H-bonds generated for 'chain 'C' and resid 297 through 299' Processing helix chain 'C' and resid 301 through 304 Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 333 through 341 removed outlier: 5.653A pdb=" N TYR C 337 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 348 No H-bonds generated for 'chain 'C' and resid 346 through 348' Processing helix chain 'D' and resid 10 through 24 Processing helix chain 'D' and resid 31 through 48 Processing helix chain 'D' and resid 54 through 71 Processing helix chain 'D' and resid 76 through 92 Processing helix chain 'D' and resid 129 through 143 removed outlier: 3.861A pdb=" N ILE D 134 " --> pdb=" O GLN D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 4.017A pdb=" N GLN D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 180 Processing helix chain 'D' and resid 200 through 209 Processing helix chain 'D' and resid 251 through 260 removed outlier: 3.627A pdb=" N ALA D 257 " --> pdb=" O THR D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 293 No H-bonds generated for 'chain 'D' and resid 291 through 293' Processing helix chain 'D' and resid 297 through 299 No H-bonds generated for 'chain 'D' and resid 297 through 299' Processing helix chain 'D' and resid 301 through 304 Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 333 through 341 removed outlier: 5.135A pdb=" N TYR D 337 " --> pdb=" O SER D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 348 No H-bonds generated for 'chain 'D' and resid 346 through 348' Processing helix chain 'F' and resid 205 through 216 Processing helix chain 'F' and resid 222 through 238 Processing helix chain 'F' and resid 249 through 266 removed outlier: 3.705A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 271 through 286 Processing helix chain 'F' and resid 295 through 312 removed outlier: 3.511A pdb=" N ASP F 305 " --> pdb=" O ARG F 301 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU F 310 " --> pdb=" O ARG F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 325 removed outlier: 3.921A pdb=" N GLN F 325 " --> pdb=" O ARG F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 351 Processing helix chain 'F' and resid 369 through 379 removed outlier: 3.728A pdb=" N SER F 375 " --> pdb=" O HIS F 371 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA F 379 " --> pdb=" O SER F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 394 removed outlier: 4.461A pdb=" N SER F 392 " --> pdb=" O PRO F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 429 Processing helix chain 'F' and resid 440 through 442 No H-bonds generated for 'chain 'F' and resid 440 through 442' Processing helix chain 'F' and resid 460 through 462 No H-bonds generated for 'chain 'F' and resid 460 through 462' Processing helix chain 'F' and resid 512 through 518 Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 222 through 232 removed outlier: 3.635A pdb=" N CYS E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 239 removed outlier: 3.750A pdb=" N GLN E 238 " --> pdb=" O GLN E 234 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP E 239 " --> pdb=" O GLN E 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 234 through 239' Processing helix chain 'E' and resid 249 through 266 removed outlier: 3.746A pdb=" N ASN E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS E 257 " --> pdb=" O VAL E 253 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 271 through 286 Processing helix chain 'E' and resid 293 through 324 removed outlier: 3.542A pdb=" N ARG E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP E 305 " --> pdb=" O ARG E 301 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N LEU E 314 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ALA E 315 " --> pdb=" O LYS E 311 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA E 316 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG E 321 " --> pdb=" O GLN E 317 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 377 removed outlier: 3.766A pdb=" N SER E 375 " --> pdb=" O HIS E 371 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU E 376 " --> pdb=" O THR E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 391 Processing helix chain 'E' and resid 395 through 397 No H-bonds generated for 'chain 'E' and resid 395 through 397' Processing helix chain 'E' and resid 418 through 429 removed outlier: 3.959A pdb=" N ALA E 421 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN E 422 " --> pdb=" O GLY E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 463 Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 494 through 496 No H-bonds generated for 'chain 'E' and resid 494 through 496' Processing helix chain 'E' and resid 512 through 518 removed outlier: 3.511A pdb=" N ARG E 517 " --> pdb=" O PRO E 513 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 16 Processing helix chain 'H' and resid 22 through 34 Processing helix chain 'H' and resid 45 through 59 Processing helix chain 'H' and resid 63 through 75 removed outlier: 3.947A pdb=" N GLU H 70 " --> pdb=" O SER H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 104 Processing helix chain 'H' and resid 107 through 118 removed outlier: 4.579A pdb=" N THR H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 143 Processing helix chain 'H' and resid 160 through 171 removed outlier: 4.393A pdb=" N HIS H 170 " --> pdb=" O LYS H 166 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU H 171 " --> pdb=" O ALA H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 186 No H-bonds generated for 'chain 'H' and resid 183 through 186' Processing helix chain 'H' and resid 212 through 221 Processing helix chain 'H' and resid 232 through 234 No H-bonds generated for 'chain 'H' and resid 232 through 234' Processing helix chain 'H' and resid 248 through 251 No H-bonds generated for 'chain 'H' and resid 248 through 251' Processing helix chain 'H' and resid 278 through 280 No H-bonds generated for 'chain 'H' and resid 278 through 280' Processing helix chain 'H' and resid 293 through 301 removed outlier: 3.764A pdb=" N SER H 297 " --> pdb=" O SER H 294 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASP H 298 " --> pdb=" O ALA H 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'G' and resid 44 through 60 removed outlier: 3.765A pdb=" N VAL G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 75 removed outlier: 4.060A pdb=" N GLU G 70 " --> pdb=" O SER G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 82 removed outlier: 3.590A pdb=" N GLU G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 104 removed outlier: 3.874A pdb=" N LEU G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 118 removed outlier: 4.646A pdb=" N THR G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N PHE G 118 " --> pdb=" O LEU G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 143 Processing helix chain 'G' and resid 160 through 171 removed outlier: 4.358A pdb=" N HIS G 170 " --> pdb=" O LYS G 166 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU G 171 " --> pdb=" O ALA G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 189 removed outlier: 4.994A pdb=" N GLU G 188 " --> pdb=" O GLY G 184 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LYS G 189 " --> pdb=" O TYR G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 222 Processing helix chain 'G' and resid 232 through 234 No H-bonds generated for 'chain 'G' and resid 232 through 234' Processing helix chain 'G' and resid 248 through 251 No H-bonds generated for 'chain 'G' and resid 248 through 251' Processing helix chain 'G' and resid 278 through 280 No H-bonds generated for 'chain 'G' and resid 278 through 280' Processing helix chain 'G' and resid 293 through 303 removed outlier: 4.319A pdb=" N SER G 297 " --> pdb=" O PRO G 293 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP G 298 " --> pdb=" O SER G 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 62 No H-bonds generated for 'chain 'B' and resid 59 through 62' Processing helix chain 'B' and resid 75 through 86 removed outlier: 3.540A pdb=" N GLU B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 106 Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.536A pdb=" N THR B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 303 through 314 Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 75 through 86 removed outlier: 3.628A pdb=" N THR I 79 " --> pdb=" O LEU I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 107 Processing helix chain 'I' and resid 110 through 112 No H-bonds generated for 'chain 'I' and resid 110 through 112' Processing helix chain 'I' and resid 131 through 136 Processing helix chain 'I' and resid 163 through 173 Processing helix chain 'I' and resid 254 through 262 Processing helix chain 'I' and resid 269 through 277 Processing helix chain 'I' and resid 303 through 314 Processing helix chain 'I' and resid 319 through 321 No H-bonds generated for 'chain 'I' and resid 319 through 321' Processing helix chain 'I' and resid 323 through 325 No H-bonds generated for 'chain 'I' and resid 323 through 325' Processing helix chain 'I' and resid 339 through 341 No H-bonds generated for 'chain 'I' and resid 339 through 341' Processing helix chain 'J' and resid 37 through 46 Processing helix chain 'J' and resid 89 through 92 No H-bonds generated for 'chain 'J' and resid 89 through 92' Processing helix chain 'J' and resid 114 through 122 Processing helix chain 'J' and resid 184 through 189 Processing helix chain 'J' and resid 229 through 235 removed outlier: 3.913A pdb=" N VAL J 233 " --> pdb=" O ILE J 229 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG J 234 " --> pdb=" O PRO J 230 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 42 Processing helix chain 'K' and resid 89 through 92 No H-bonds generated for 'chain 'K' and resid 89 through 92' Processing helix chain 'K' and resid 114 through 120 removed outlier: 4.388A pdb=" N VAL K 118 " --> pdb=" O HIS K 115 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP K 119 " --> pdb=" O GLU K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 189 Processing helix chain 'K' and resid 211 through 216 removed outlier: 3.603A pdb=" N MET K 216 " --> pdb=" O VAL K 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 229 through 235 removed outlier: 3.609A pdb=" N VAL K 233 " --> pdb=" O ILE K 229 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG K 234 " --> pdb=" O PRO K 230 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 165 through 167 removed outlier: 6.255A pdb=" N THR C 215 " --> pdb=" O VAL C 191 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 231 through 234 removed outlier: 7.722A pdb=" N ILE C 234 " --> pdb=" O PRO C 264 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE C 266 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU C 323 " --> pdb=" O VAL C 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'C' and resid 245 through 248 Processing sheet with id= D, first strand: chain 'D' and resid 164 through 167 removed outlier: 6.404A pdb=" N HIS D 188 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR D 167 " --> pdb=" O HIS D 188 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE D 190 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU D 213 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL D 191 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N THR D 215 " --> pdb=" O VAL D 191 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'D' and resid 231 through 234 removed outlier: 7.620A pdb=" N ILE D 234 " --> pdb=" O PRO D 264 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE D 266 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU D 323 " --> pdb=" O VAL D 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'D' and resid 245 through 248 Processing sheet with id= G, first strand: chain 'F' and resid 332 through 336 removed outlier: 6.522A pdb=" N ARG F 357 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL F 335 " --> pdb=" O ARG F 357 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL F 359 " --> pdb=" O VAL F 335 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL F 360 " --> pdb=" O PRO F 382 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N SER F 384 " --> pdb=" O VAL F 360 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ASP F 362 " --> pdb=" O SER F 384 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU F 386 " --> pdb=" O ASP F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'F' and resid 400 through 404 removed outlier: 7.554A pdb=" N LEU F 403 " --> pdb=" O PRO F 433 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU F 435 " --> pdb=" O LEU F 403 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU F 499 " --> pdb=" O VAL F 436 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'F' and resid 414 through 417 Processing sheet with id= J, first strand: chain 'E' and resid 332 through 336 removed outlier: 6.313A pdb=" N ARG E 357 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL E 335 " --> pdb=" O ARG E 357 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL E 359 " --> pdb=" O VAL E 335 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 400 through 404 removed outlier: 7.915A pdb=" N LEU E 403 " --> pdb=" O PRO E 433 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU E 435 " --> pdb=" O LEU E 403 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU E 499 " --> pdb=" O VAL E 436 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 414 through 416 Processing sheet with id= M, first strand: chain 'H' and resid 225 through 228 removed outlier: 4.031A pdb=" N LEU H 192 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR H 153 " --> pdb=" O THR H 127 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL H 152 " --> pdb=" O PRO H 174 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N THR H 176 " --> pdb=" O VAL H 152 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 206 through 209 Processing sheet with id= O, first strand: chain 'H' and resid 284 through 286 removed outlier: 3.610A pdb=" N THR H 286 " --> pdb=" O GLY H 289 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY H 289 " --> pdb=" O THR H 286 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 225 through 228 removed outlier: 4.063A pdb=" N LEU G 192 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL G 152 " --> pdb=" O PRO G 174 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N THR G 176 " --> pdb=" O VAL G 152 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 206 through 209 Processing sheet with id= R, first strand: chain 'G' and resid 284 through 286 removed outlier: 3.561A pdb=" N THR G 286 " --> pdb=" O GLY G 289 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY G 289 " --> pdb=" O THR G 286 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 148 through 151 removed outlier: 7.017A pdb=" N GLN B 44 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL B 151 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL B 46 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 181 through 186 Processing sheet with id= U, first strand: chain 'B' and resid 239 through 241 removed outlier: 6.712A pdb=" N ASP B 206 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL B 212 " --> pdb=" O ASP B 206 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 335 through 337 removed outlier: 3.543A pdb=" N THR B 336 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 344 " --> pdb=" O THR B 336 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'B' and resid 373 through 375 Processing sheet with id= X, first strand: chain 'I' and resid 44 through 48 removed outlier: 6.415A pdb=" N GLU I 90 " --> pdb=" O ALA I 45 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU I 47 " --> pdb=" O GLU I 90 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE I 92 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 155 through 157 Processing sheet with id= Z, first strand: chain 'I' and resid 182 through 186 removed outlier: 7.004A pdb=" N HIS I 288 " --> pdb=" O MET I 183 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N PHE I 185 " --> pdb=" O HIS I 288 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N HIS I 290 " --> pdb=" O PHE I 185 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'I' and resid 239 through 241 Processing sheet with id= AB, first strand: chain 'I' and resid 335 through 337 removed outlier: 3.657A pdb=" N ARG I 344 " --> pdb=" O THR I 336 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'I' and resid 373 through 375 removed outlier: 3.733A pdb=" N LEU I 391 " --> pdb=" O PHE I 373 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'I' and resid 400 through 402 removed outlier: 7.109A pdb=" N ALA I 417 " --> pdb=" O ARG I 401 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'I' and resid 411 through 413 removed outlier: 6.752A pdb=" N SER I 429 " --> pdb=" O LEU I 412 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'J' and resid 3 through 7 removed outlier: 6.436A pdb=" N ASP J 100 " --> pdb=" O GLN J 4 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL J 6 " --> pdb=" O ASP J 100 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LEU J 102 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU J 204 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU J 131 " --> pdb=" O LEU J 204 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 194 through 197 Processing sheet with id= AH, first strand: chain 'K' and resid 4 through 6 Processing sheet with id= AI, first strand: chain 'K' and resid 128 through 131 Processing sheet with id= AJ, first strand: chain 'K' and resid 194 through 197 701 hydrogen bonds defined for protein. 1935 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: 7.46 Time building geometry restraints manager: 9.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6961 1.33 - 1.45: 3723 1.45 - 1.57: 12396 1.57 - 1.69: 6 1.69 - 1.81: 176 Bond restraints: 23262 Sorted by residual: bond pdb=" CB VAL F 332 " pdb=" CG2 VAL F 332 " ideal model delta sigma weight residual 1.521 1.435 0.086 3.30e-02 9.18e+02 6.85e+00 bond pdb=" CG LEU D 254 " pdb=" CD1 LEU D 254 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.46e+00 bond pdb=" CB ILE B 408 " pdb=" CG2 ILE B 408 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.35e+00 bond pdb=" CB VAL E 381 " pdb=" CG1 VAL E 381 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.58e+00 bond pdb=" CB VAL E 434 " pdb=" CG1 VAL E 434 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.52e+00 ... (remaining 23257 not shown) Histogram of bond angle deviations from ideal: 95.05 - 103.67: 303 103.67 - 112.28: 12142 112.28 - 120.90: 12369 120.90 - 129.51: 6622 129.51 - 138.13: 164 Bond angle restraints: 31600 Sorted by residual: angle pdb=" C THR C 218 " pdb=" N ASP C 219 " pdb=" CA ASP C 219 " ideal model delta sigma weight residual 126.32 138.13 -11.81 1.74e+00 3.30e-01 4.60e+01 angle pdb=" N PHE K 121 " pdb=" CA PHE K 121 " pdb=" C PHE K 121 " ideal model delta sigma weight residual 114.56 108.37 6.19 1.27e+00 6.20e-01 2.38e+01 angle pdb=" N ILE C 151 " pdb=" CA ILE C 151 " pdb=" C ILE C 151 " ideal model delta sigma weight residual 111.58 106.42 5.16 1.06e+00 8.90e-01 2.37e+01 angle pdb=" CB MET G 187 " pdb=" CG MET G 187 " pdb=" SD MET G 187 " ideal model delta sigma weight residual 112.70 98.19 14.51 3.00e+00 1.11e-01 2.34e+01 angle pdb=" CA LEU E 346 " pdb=" CB LEU E 346 " pdb=" CG LEU E 346 " ideal model delta sigma weight residual 116.30 132.31 -16.01 3.50e+00 8.16e-02 2.09e+01 ... (remaining 31595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 12795 17.81 - 35.62: 1050 35.62 - 53.42: 162 53.42 - 71.23: 45 71.23 - 89.04: 25 Dihedral angle restraints: 14077 sinusoidal: 5290 harmonic: 8787 Sorted by residual: dihedral pdb=" CB CYS C 198 " pdb=" SG CYS C 198 " pdb=" SG CYS F 465 " pdb=" CB CYS F 465 " ideal model delta sinusoidal sigma weight residual 93.00 155.40 -62.40 1 1.00e+01 1.00e-02 5.15e+01 dihedral pdb=" CA HIS G 128 " pdb=" C HIS G 128 " pdb=" N ALA G 129 " pdb=" CA ALA G 129 " ideal model delta harmonic sigma weight residual -180.00 -147.31 -32.69 0 5.00e+00 4.00e-02 4.28e+01 dihedral pdb=" CA THR I 208 " pdb=" C THR I 208 " pdb=" N THR I 209 " pdb=" CA THR I 209 " ideal model delta harmonic sigma weight residual 180.00 150.34 29.66 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 14074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3336 0.095 - 0.189: 412 0.189 - 0.284: 33 0.284 - 0.378: 5 0.378 - 0.473: 4 Chirality restraints: 3790 Sorted by residual: chirality pdb=" CB THR G 124 " pdb=" CA THR G 124 " pdb=" OG1 THR G 124 " pdb=" CG2 THR G 124 " both_signs ideal model delta sigma weight residual False 2.55 2.08 0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" CB ILE I 374 " pdb=" CA ILE I 374 " pdb=" CG1 ILE I 374 " pdb=" CG2 ILE I 374 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" CB THR H 124 " pdb=" CA THR H 124 " pdb=" OG1 THR H 124 " pdb=" CG2 THR H 124 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.44 2.00e-01 2.50e+01 4.80e+00 ... (remaining 3787 not shown) Planarity restraints: 4011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY I 380 " -0.089 5.00e-02 4.00e+02 1.35e-01 2.91e+01 pdb=" N PRO I 381 " 0.233 5.00e-02 4.00e+02 pdb=" CA PRO I 381 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO I 381 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 183 " 0.078 5.00e-02 4.00e+02 1.17e-01 2.19e+01 pdb=" N PRO E 184 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO E 184 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO E 184 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 300 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C VAL B 300 " 0.058 2.00e-02 2.50e+03 pdb=" O VAL B 300 " -0.022 2.00e-02 2.50e+03 pdb=" N SER B 301 " -0.019 2.00e-02 2.50e+03 ... (remaining 4008 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2461 2.74 - 3.28: 22760 3.28 - 3.82: 38761 3.82 - 4.36: 46903 4.36 - 4.90: 81598 Nonbonded interactions: 192483 Sorted by model distance: nonbonded pdb=" OG1 THR C 76 " pdb=" OG1 THR C 238 " model vdw 2.199 2.440 nonbonded pdb=" OG1 THR D 76 " pdb=" OG1 THR D 238 " model vdw 2.220 2.440 nonbonded pdb=" OD1 ASN E 223 " pdb=" OH TYR E 441 " model vdw 2.229 2.440 nonbonded pdb=" O GLY G 196 " pdb=" OD1 ASN G 208 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLU D 193 " pdb=" NE2 HIS D 201 " model vdw 2.285 2.520 ... (remaining 192478 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 41 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 218 or (resid 219 and (name N o \ r name CA or name C or name O or name CB )) or resid 220 or (resid 221 through 2 \ 23 and (name N or name CA or name C or name O or name CB )) or resid 224 through \ 456 or (resid 457 through 458 and (name N or name CA or name C or name O or nam \ e CB )) or resid 459 through 464)) selection = (chain 'I' and (resid 41 through 176 or (resid 177 through 178 and (name N or na \ me CA or name C or name O or name CB )) or resid 179 through 196 or (resid 197 a \ nd (name N or name CA or name C or name O or name CB )) or resid 198 through 231 \ or resid 238 through 279 or (resid 285 and (name N or name CA or name C or name \ O or name CB )) or resid 286 through 433 or (resid 434 and (name N or name CA o \ r name C or name O or name CB )) or resid 435 through 459 or (resid 460 through \ 461 and (name N or name CA or name C or name O or name CB )) or resid 462 throug \ h 464)) } ncs_group { reference = (chain 'C' and (resid 9 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 26 or resid 29 through 138 or (resi \ d 139 and (name N or name CA or name C or name O or name CB )) or resid 140 thro \ ugh 142 or (resid 143 and (name N or name CA or name C or name O or name CB )) o \ r resid 144 or (resid 145 and (name N or name CA or name C or name O or name CB \ )) or resid 146 through 148 or (resid 149 and (name N or name CA or name C or na \ me O or name CB )) or resid 150 through 281 or (resid 282 through 283 and (name \ N or name CA or name C or name O or name CB )) or resid 284 through 351)) selection = (chain 'D' and (resid 9 through 97 or resid 126 through 351)) } ncs_group { reference = (chain 'E' and (resid 179 through 180 or (resid 181 and (name N or name CA or na \ me C or name O or name CB )) or resid 182 through 185 or (resid 186 and (name N \ or name CA or name C or name O or name CB )) or resid 187 or (resid 192 through \ 198 and (name N or name CA or name C or name O or name CB )) or resid 199 throug \ h 202 or (resid 203 and (name N or name CA or name C or name O or name CB )) or \ resid 204 through 240 or (resid 241 and (name N or name CA or name C or name O o \ r name CB )) or resid 242 through 256 or (resid 257 and (name N or name CA or na \ me C or name O or name CB )) or resid 258 through 263 or (resid 264 through 265 \ and (name N or name CA or name C or name O or name CB )) or resid 266 through 28 \ 9 or (resid 294 through 300 and (name N or name CA or name C or name O or name C \ B )) or resid 301 through 320 or resid 322 through 339 or (resid 340 and (name N \ or name CA or name C or name O or name CB )) or resid 341 through 452 or (resid \ 453 through 454 and (name N or name CA or name C or name O or name CB )) or res \ id 455 through 457 or (resid 458 and (name N or name CA or name C or name O or n \ ame CB )) or resid 459 through 460 or (resid 461 and (name N or name CA or name \ C or name O or name CB )) or resid 462 through 466 or resid 471 through 520)) selection = (chain 'F' and (resid 179 through 214 or (resid 215 and (name N or name CA or na \ me C or name O or name CB )) or resid 216 through 320 or resid 322 through 327 o \ r (resid 328 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 29 through 449 or (resid 450 through 454 and (name N or name CA or name C or nam \ e O or name CB )) or resid 455 through 477 or (resid 478 and (name N or name CA \ or name C or name O or name CB )) or resid 479 through 518 or (resid 519 and (na \ me N or name CA or name C or name O or name CB )) or resid 520)) } ncs_group { reference = (chain 'G' and (resid 3 through 36 or (resid 42 and (name N or name CA or name C \ or name O or name CB )) or resid 43 through 53 or (resid 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 through 80 or resid 88 through \ 94 or (resid 95 and (name N or name CA or name C or name O or name CB )) or res \ id 96 through 135 or resid 137 through 304 or resid 401)) selection = (chain 'H' and (resid 3 through 36 or resid 42 through 135 or resid 137 through \ 254 or (resid 266 and (name N or name CA or name C or name O or name CB )) or re \ sid 267 through 304 or resid 401)) } ncs_group { reference = (chain 'J' and (resid 1 through 44 or resid 48 through 53 or resid 75 through 78 \ or resid 87 through 95 or (resid 96 through 99 and (name N or name CA or name C \ or name O or name CB )) or resid 100 through 212 or (resid 213 through 214 and \ (name N or name CA or name C or name O or name CB )) or resid 226 through 233 or \ (resid 234 through 235 and (name N or name CA or name C or name O or name CB )) \ or resid 236 through 267)) selection = (chain 'K' and (resid 1 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB )) or resid 48 through 50 or (resid 51 and (name N or name \ CA or name C or name O or name CB )) or resid 52 through 98 or (resid 99 and (n \ ame N or name CA or name C or name O or name CB )) or resid 100 through 113 or ( \ resid 114 and (name N or name CA or name C or name O or name CB )) or resid 115 \ through 116 or (resid 117 and (name N or name CA or name C or name O or name CB \ )) or resid 118 through 171 or resid 174 through 214 or resid 226 or (resid 227 \ through 229 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 0 through 236 or (resid 237 through 240 and (name N or name CA or name C or name \ O or name CB )) or resid 241 through 243 or resid 260 through 267)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.790 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 66.910 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.170 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:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.009 0.086 23262 Z= 0.615 Angle : 1.055 16.008 31600 Z= 0.554 Chirality : 0.064 0.473 3790 Planarity : 0.007 0.135 4011 Dihedral : 14.190 89.040 8334 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.21 % Allowed : 0.59 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.57 (0.14), residues: 2920 helix: -1.75 (0.13), residues: 1168 sheet: -1.55 (0.27), residues: 365 loop : -1.59 (0.16), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 51 HIS 0.010 0.001 HIS G 128 PHE 0.032 0.003 PHE G 239 TYR 0.041 0.003 TYR G 9 ARG 0.016 0.001 ARG F 428 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 2.510 Fit side-chains REVERT: C 16 GLU cc_start: 0.7613 (mp0) cc_final: 0.7394 (mp0) REVERT: C 130 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8518 (tm-30) REVERT: D 16 GLU cc_start: 0.7825 (mp0) cc_final: 0.7547 (mp0) REVERT: D 128 GLN cc_start: 0.8590 (pm20) cc_final: 0.8342 (pm20) REVERT: F 363 SER cc_start: 0.8830 (p) cc_final: 0.8425 (t) REVERT: F 415 MET cc_start: 0.8397 (ttp) cc_final: 0.7942 (ttm) REVERT: F 459 ASP cc_start: 0.7588 (p0) cc_final: 0.7260 (p0) REVERT: F 506 MET cc_start: 0.8846 (mtm) cc_final: 0.8548 (mtm) REVERT: E 300 LEU cc_start: 0.8278 (mm) cc_final: 0.8043 (mm) REVERT: E 415 MET cc_start: 0.8251 (ttp) cc_final: 0.7849 (ttm) REVERT: G 48 ASN cc_start: 0.8344 (m110) cc_final: 0.8143 (m110) REVERT: J 263 ILE cc_start: 0.6825 (mt) cc_final: 0.6595 (mt) REVERT: K 100 ASP cc_start: 0.7444 (m-30) cc_final: 0.7029 (m-30) REVERT: K 192 ARG cc_start: 0.8641 (mtp180) cc_final: 0.8026 (mtp180) outliers start: 0 outliers final: 1 residues processed: 318 average time/residue: 1.2958 time to fit residues: 472.7201 Evaluate side-chains 233 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 329 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.5980 chunk 225 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 151 optimal weight: 0.6980 chunk 120 optimal weight: 7.9990 chunk 232 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 141 optimal weight: 0.0050 chunk 173 optimal weight: 0.8980 chunk 269 optimal weight: 3.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 154 GLN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 130 GLN ** D 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23262 Z= 0.205 Angle : 0.634 10.910 31600 Z= 0.320 Chirality : 0.045 0.220 3790 Planarity : 0.005 0.092 4011 Dihedral : 6.122 42.934 3265 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.22 % Allowed : 9.73 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.83 (0.15), residues: 2920 helix: -0.75 (0.15), residues: 1168 sheet: -1.69 (0.25), residues: 409 loop : -1.36 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.004 0.001 HIS G 128 PHE 0.029 0.001 PHE B 264 TYR 0.018 0.001 TYR F 240 ARG 0.008 0.000 ARG J 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 265 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 130 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8522 (tm-30) REVERT: C 219 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8241 (p0) REVERT: D 43 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7645 (ttm-80) REVERT: D 128 GLN cc_start: 0.8632 (pm20) cc_final: 0.8341 (pm20) REVERT: F 459 ASP cc_start: 0.7472 (p0) cc_final: 0.7271 (p0) REVERT: F 506 MET cc_start: 0.8812 (mtm) cc_final: 0.8598 (mtm) REVERT: E 192 LEU cc_start: 0.7695 (tp) cc_final: 0.7476 (tp) REVERT: G 48 ASN cc_start: 0.8388 (m110) cc_final: 0.8176 (m110) REVERT: I 177 ASN cc_start: 0.7401 (m-40) cc_final: 0.7119 (m-40) REVERT: I 266 TYR cc_start: 0.7402 (m-80) cc_final: 0.7179 (m-80) REVERT: I 276 LEU cc_start: 0.7810 (tt) cc_final: 0.7607 (tm) REVERT: K 100 ASP cc_start: 0.7460 (m-30) cc_final: 0.7086 (m-30) outliers start: 24 outliers final: 7 residues processed: 280 average time/residue: 1.2111 time to fit residues: 394.1046 Evaluate side-chains 244 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 235 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain J residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 291 optimal weight: 0.9980 chunk 240 optimal weight: 1.9990 chunk 267 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 216 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN E 455 ASN ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23262 Z= 0.264 Angle : 0.616 10.850 31600 Z= 0.311 Chirality : 0.046 0.226 3790 Planarity : 0.005 0.067 4011 Dihedral : 5.464 35.603 3263 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.05 % Allowed : 13.29 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.50 (0.15), residues: 2920 helix: -0.32 (0.15), residues: 1183 sheet: -1.53 (0.26), residues: 379 loop : -1.36 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 350 HIS 0.005 0.001 HIS G 128 PHE 0.016 0.001 PHE D 272 TYR 0.012 0.001 TYR G 9 ARG 0.010 0.000 ARG J 234 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 248 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 130 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8497 (tm-30) REVERT: C 219 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8240 (p0) REVERT: D 43 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7629 (ttm-80) REVERT: D 128 GLN cc_start: 0.8657 (pm20) cc_final: 0.8359 (pm20) REVERT: F 306 ARG cc_start: 0.7064 (mtm-85) cc_final: 0.6702 (ttm110) REVERT: F 506 MET cc_start: 0.8798 (mtm) cc_final: 0.8592 (mtm) REVERT: G 48 ASN cc_start: 0.8432 (m110) cc_final: 0.8207 (m110) REVERT: I 177 ASN cc_start: 0.7526 (m-40) cc_final: 0.7246 (m-40) REVERT: J 8 MET cc_start: 0.7485 (mmm) cc_final: 0.7010 (mmm) REVERT: K 100 ASP cc_start: 0.7452 (m-30) cc_final: 0.7078 (m-30) outliers start: 44 outliers final: 15 residues processed: 274 average time/residue: 1.2061 time to fit residues: 382.9145 Evaluate side-chains 251 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 234 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain G residue 89 CYS Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 336 THR Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 3.9990 chunk 203 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 287 optimal weight: 0.4980 chunk 141 optimal weight: 0.8980 chunk 256 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 431 ASN E 329 ASN ** H 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23262 Z= 0.221 Angle : 0.586 10.735 31600 Z= 0.296 Chirality : 0.044 0.209 3790 Planarity : 0.004 0.057 4011 Dihedral : 5.018 25.358 3263 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.26 % Allowed : 15.47 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.18 (0.16), residues: 2920 helix: 0.02 (0.15), residues: 1174 sheet: -1.45 (0.26), residues: 373 loop : -1.22 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 111 HIS 0.005 0.001 HIS G 128 PHE 0.021 0.001 PHE I 264 TYR 0.016 0.001 TYR F 240 ARG 0.009 0.000 ARG J 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 255 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 130 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8535 (tm-30) REVERT: C 331 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.8241 (p0) REVERT: D 128 GLN cc_start: 0.8642 (pm20) cc_final: 0.8284 (pm20) REVERT: D 184 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8629 (mptt) REVERT: F 306 ARG cc_start: 0.7121 (mtm-85) cc_final: 0.6787 (ttm110) REVERT: F 506 MET cc_start: 0.8783 (mtm) cc_final: 0.8580 (mtm) REVERT: G 48 ASN cc_start: 0.8438 (m110) cc_final: 0.8234 (m110) REVERT: G 164 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7210 (ttp) REVERT: B 183 MET cc_start: 0.8115 (mtp) cc_final: 0.7816 (mtp) REVERT: I 177 ASN cc_start: 0.7520 (m-40) cc_final: 0.7203 (m-40) REVERT: J 8 MET cc_start: 0.7428 (mmm) cc_final: 0.6873 (mmm) REVERT: K 100 ASP cc_start: 0.7462 (m-30) cc_final: 0.7000 (m-30) REVERT: K 121 PHE cc_start: 0.7299 (t80) cc_final: 0.7070 (t80) outliers start: 49 outliers final: 23 residues processed: 287 average time/residue: 1.2402 time to fit residues: 412.6932 Evaluate side-chains 260 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 234 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain G residue 89 CYS Chi-restraints excluded: chain G residue 164 MET Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 336 THR Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain K residue 262 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 4.9990 chunk 162 optimal weight: 0.0980 chunk 4 optimal weight: 0.9980 chunk 213 optimal weight: 0.2980 chunk 118 optimal weight: 0.0570 chunk 244 optimal weight: 0.8980 chunk 198 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 0.7980 chunk 257 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 overall best weight: 0.2698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN G 13 GLN B 105 HIS I 288 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 23262 Z= 0.160 Angle : 0.556 10.449 31600 Z= 0.281 Chirality : 0.043 0.202 3790 Planarity : 0.004 0.061 4011 Dihedral : 4.580 23.294 3263 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.81 % Allowed : 16.02 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.91 (0.16), residues: 2920 helix: 0.33 (0.16), residues: 1170 sheet: -1.39 (0.27), residues: 374 loop : -1.12 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 111 HIS 0.004 0.000 HIS B 337 PHE 0.019 0.001 PHE D 272 TYR 0.016 0.001 TYR G 9 ARG 0.011 0.000 ARG J 234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 284 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 130 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8538 (tm-30) REVERT: D 128 GLN cc_start: 0.8619 (pm20) cc_final: 0.8324 (pm20) REVERT: F 306 ARG cc_start: 0.7083 (mtm-85) cc_final: 0.6731 (ttm110) REVERT: F 311 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8527 (mttp) REVERT: H 91 LYS cc_start: 0.8928 (mmpt) cc_final: 0.8439 (mptt) REVERT: B 183 MET cc_start: 0.8173 (mtp) cc_final: 0.7841 (mtp) REVERT: B 384 HIS cc_start: 0.7927 (m-70) cc_final: 0.7684 (t70) REVERT: I 152 TYR cc_start: 0.7726 (t80) cc_final: 0.7462 (t80) REVERT: I 177 ASN cc_start: 0.7644 (m-40) cc_final: 0.7308 (m-40) REVERT: J 8 MET cc_start: 0.7307 (mmm) cc_final: 0.6771 (mmm) REVERT: K 100 ASP cc_start: 0.7481 (m-30) cc_final: 0.6905 (m-30) REVERT: K 121 PHE cc_start: 0.7214 (t80) cc_final: 0.6973 (t80) outliers start: 62 outliers final: 24 residues processed: 326 average time/residue: 1.0538 time to fit residues: 405.6499 Evaluate side-chains 270 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 245 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain K residue 262 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 7.9990 chunk 258 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 287 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 95 optimal weight: 0.0370 chunk 150 optimal weight: 3.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN G 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23262 Z= 0.243 Angle : 0.591 10.564 31600 Z= 0.296 Chirality : 0.045 0.206 3790 Planarity : 0.004 0.060 4011 Dihedral : 4.602 21.536 3263 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.14 % Allowed : 16.98 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.83 (0.16), residues: 2920 helix: 0.42 (0.16), residues: 1171 sheet: -1.32 (0.26), residues: 392 loop : -1.11 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 350 HIS 0.005 0.001 HIS G 128 PHE 0.019 0.001 PHE I 264 TYR 0.016 0.001 TYR F 240 ARG 0.009 0.000 ARG J 234 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 245 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.7526 (pp20) cc_final: 0.7149 (pp20) REVERT: C 331 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8290 (p0) REVERT: D 43 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.7644 (ttm-80) REVERT: D 128 GLN cc_start: 0.8622 (pm20) cc_final: 0.8292 (pm20) REVERT: D 184 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8640 (mptt) REVERT: F 306 ARG cc_start: 0.7086 (mtm-85) cc_final: 0.6800 (ttm110) REVERT: F 311 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8544 (mttp) REVERT: H 91 LYS cc_start: 0.8933 (mmpt) cc_final: 0.8437 (mptt) REVERT: B 183 MET cc_start: 0.8159 (mtp) cc_final: 0.7830 (mtp) REVERT: B 457 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: I 177 ASN cc_start: 0.7636 (m-40) cc_final: 0.7340 (m-40) REVERT: I 183 MET cc_start: 0.7475 (mtp) cc_final: 0.7210 (mtp) REVERT: J 8 MET cc_start: 0.7367 (mmm) cc_final: 0.6848 (mmm) REVERT: K 44 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.5942 (pt0) REVERT: K 100 ASP cc_start: 0.7497 (m-30) cc_final: 0.6939 (m-30) REVERT: K 155 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.7069 (mtp-110) REVERT: K 183 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7895 (mtpm) outliers start: 70 outliers final: 32 residues processed: 294 average time/residue: 1.2172 time to fit residues: 415.4789 Evaluate side-chains 271 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 231 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 183 LYS Chi-restraints excluded: chain K residue 262 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 209 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 241 optimal weight: 7.9990 chunk 160 optimal weight: 0.7980 chunk 286 optimal weight: 6.9990 chunk 179 optimal weight: 0.0070 chunk 174 optimal weight: 1.9990 chunk 132 optimal weight: 0.3980 overall best weight: 0.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN G 13 GLN B 393 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23262 Z= 0.223 Angle : 0.587 10.595 31600 Z= 0.293 Chirality : 0.044 0.195 3790 Planarity : 0.004 0.059 4011 Dihedral : 4.567 22.491 3263 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.27 % Allowed : 17.15 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.72 (0.16), residues: 2920 helix: 0.51 (0.16), residues: 1162 sheet: -1.27 (0.27), residues: 388 loop : -1.04 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 97 HIS 0.004 0.001 HIS G 128 PHE 0.035 0.001 PHE B 264 TYR 0.013 0.001 TYR E 240 ARG 0.010 0.000 ARG J 234 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 241 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 130 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8518 (tm-30) REVERT: D 128 GLN cc_start: 0.8621 (pm20) cc_final: 0.8290 (pm20) REVERT: D 184 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8643 (mptt) REVERT: F 306 ARG cc_start: 0.7003 (mtm-85) cc_final: 0.6765 (ttm110) REVERT: F 311 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8543 (mttp) REVERT: E 207 MET cc_start: 0.7131 (mmt) cc_final: 0.6925 (mmt) REVERT: H 91 LYS cc_start: 0.8921 (mmpt) cc_final: 0.8446 (mptt) REVERT: G 215 MET cc_start: 0.8619 (ttm) cc_final: 0.8387 (ttm) REVERT: B 183 MET cc_start: 0.8149 (mtp) cc_final: 0.7843 (mtp) REVERT: B 457 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: I 177 ASN cc_start: 0.7707 (m-40) cc_final: 0.7405 (m-40) REVERT: I 183 MET cc_start: 0.7558 (mtp) cc_final: 0.7177 (mtp) REVERT: K 44 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.5925 (pt0) REVERT: K 100 ASP cc_start: 0.7455 (m-30) cc_final: 0.6963 (m-30) REVERT: K 155 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.7028 (mtp-110) REVERT: K 183 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7868 (mtpm) outliers start: 73 outliers final: 42 residues processed: 288 average time/residue: 1.1481 time to fit residues: 386.1195 Evaluate side-chains 282 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 234 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain E residue 329 ASN Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 89 CYS Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 302 ASN Chi-restraints excluded: chain I residue 336 THR Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain K residue 44 GLU Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 183 LYS Chi-restraints excluded: chain K residue 262 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 0.0980 chunk 114 optimal weight: 0.3980 chunk 170 optimal weight: 0.0050 chunk 86 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 chunk 55 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 225 optimal weight: 1.9990 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23262 Z= 0.162 Angle : 0.568 10.436 31600 Z= 0.285 Chirality : 0.043 0.194 3790 Planarity : 0.004 0.060 4011 Dihedral : 4.398 21.156 3263 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.85 % Allowed : 17.74 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.56 (0.16), residues: 2920 helix: 0.67 (0.16), residues: 1158 sheet: -1.17 (0.27), residues: 389 loop : -0.98 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 97 HIS 0.004 0.000 HIS B 337 PHE 0.019 0.001 PHE D 272 TYR 0.019 0.001 TYR F 240 ARG 0.011 0.000 ARG J 234 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 275 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.7483 (pp20) cc_final: 0.7110 (pp20) REVERT: C 130 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8523 (tm-30) REVERT: D 128 GLN cc_start: 0.8565 (pm20) cc_final: 0.8253 (pm20) REVERT: D 184 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8564 (mptt) REVERT: F 311 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8559 (mttp) REVERT: E 207 MET cc_start: 0.7088 (mmt) cc_final: 0.6785 (mmt) REVERT: E 366 TRP cc_start: 0.8241 (m100) cc_final: 0.7932 (m-90) REVERT: H 91 LYS cc_start: 0.8897 (mmpt) cc_final: 0.8407 (mptt) REVERT: G 89 CYS cc_start: 0.7113 (t) cc_final: 0.6906 (m) REVERT: G 215 MET cc_start: 0.8586 (ttm) cc_final: 0.8370 (ttm) REVERT: B 175 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: B 183 MET cc_start: 0.8138 (mtp) cc_final: 0.7841 (mtp) REVERT: I 177 ASN cc_start: 0.7817 (m-40) cc_final: 0.7488 (m-40) REVERT: I 183 MET cc_start: 0.7365 (mtp) cc_final: 0.7003 (mtp) REVERT: I 305 MET cc_start: 0.8248 (tpt) cc_final: 0.8031 (tpp) REVERT: J 132 MET cc_start: 0.6909 (mmt) cc_final: 0.6417 (mmt) REVERT: K 100 ASP cc_start: 0.7485 (m-30) cc_final: 0.7054 (m-30) REVERT: K 155 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.7022 (mtp-110) REVERT: K 183 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7908 (mtpm) outliers start: 63 outliers final: 35 residues processed: 315 average time/residue: 1.1349 time to fit residues: 418.3570 Evaluate side-chains 285 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 245 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 336 THR Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 183 LYS Chi-restraints excluded: chain K residue 262 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 8.9990 chunk 274 optimal weight: 0.8980 chunk 250 optimal weight: 0.7980 chunk 266 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 209 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 241 optimal weight: 7.9990 chunk 252 optimal weight: 9.9990 chunk 265 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23262 Z= 0.226 Angle : 0.592 10.454 31600 Z= 0.294 Chirality : 0.045 0.209 3790 Planarity : 0.004 0.059 4011 Dihedral : 4.449 22.762 3263 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.60 % Allowed : 18.49 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.60 (0.16), residues: 2920 helix: 0.65 (0.16), residues: 1160 sheet: -1.15 (0.26), residues: 397 loop : -1.04 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 350 HIS 0.004 0.001 HIS H 128 PHE 0.023 0.001 PHE B 264 TYR 0.018 0.001 TYR G 9 ARG 0.011 0.000 ARG G 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 243 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 43 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7577 (ttm-80) REVERT: D 128 GLN cc_start: 0.8570 (pm20) cc_final: 0.8259 (pm20) REVERT: D 184 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8647 (mptt) REVERT: F 306 ARG cc_start: 0.6777 (ttm110) cc_final: 0.6350 (ttp-110) REVERT: F 311 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8604 (mttp) REVERT: E 207 MET cc_start: 0.7147 (mmt) cc_final: 0.6815 (mmt) REVERT: E 366 TRP cc_start: 0.8236 (m100) cc_final: 0.7914 (m-90) REVERT: H 91 LYS cc_start: 0.8897 (mmpt) cc_final: 0.8409 (mptt) REVERT: G 89 CYS cc_start: 0.6950 (t) cc_final: 0.6712 (m) REVERT: G 215 MET cc_start: 0.8632 (ttm) cc_final: 0.8376 (ttm) REVERT: B 183 MET cc_start: 0.8164 (mtp) cc_final: 0.7865 (mtp) REVERT: I 177 ASN cc_start: 0.7792 (m-40) cc_final: 0.7484 (m-40) REVERT: I 183 MET cc_start: 0.7428 (mtp) cc_final: 0.7049 (mtp) REVERT: I 305 MET cc_start: 0.8356 (tpt) cc_final: 0.8086 (tpp) REVERT: J 8 MET cc_start: 0.7295 (mmm) cc_final: 0.6708 (mmm) REVERT: K 100 ASP cc_start: 0.7496 (m-30) cc_final: 0.7014 (m-30) REVERT: K 155 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.7044 (mtp-110) REVERT: K 183 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7892 (mtpm) outliers start: 57 outliers final: 38 residues processed: 282 average time/residue: 1.1779 time to fit residues: 386.8029 Evaluate side-chains 277 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 234 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 302 ASN Chi-restraints excluded: chain I residue 336 THR Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 262 ASP Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 183 LYS Chi-restraints excluded: chain K residue 262 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.6980 chunk 282 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 295 optimal weight: 0.7980 chunk 272 optimal weight: 6.9990 chunk 235 optimal weight: 0.9990 chunk 24 optimal weight: 0.0980 chunk 181 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23262 Z= 0.206 Angle : 0.592 10.468 31600 Z= 0.294 Chirality : 0.044 0.216 3790 Planarity : 0.004 0.059 4011 Dihedral : 4.425 22.852 3263 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.43 % Allowed : 18.95 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.58 (0.16), residues: 2920 helix: 0.64 (0.16), residues: 1163 sheet: -1.09 (0.27), residues: 387 loop : -1.02 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 97 HIS 0.004 0.001 HIS G 128 PHE 0.021 0.001 PHE C 272 TYR 0.019 0.001 TYR G 9 ARG 0.011 0.000 ARG J 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5840 Ramachandran restraints generated. 2920 Oldfield, 0 Emsley, 2920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 246 time to evaluate : 2.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 13 GLU cc_start: 0.7492 (pp20) cc_final: 0.7137 (pp20) REVERT: C 219 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.8092 (p0) REVERT: D 43 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7570 (ttm-80) REVERT: D 128 GLN cc_start: 0.8556 (pm20) cc_final: 0.8246 (pm20) REVERT: D 184 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8646 (mptt) REVERT: F 311 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8595 (mttp) REVERT: E 207 MET cc_start: 0.7090 (mmt) cc_final: 0.6811 (mmt) REVERT: H 91 LYS cc_start: 0.8890 (mmpt) cc_final: 0.8401 (mptt) REVERT: G 89 CYS cc_start: 0.6966 (t) cc_final: 0.6733 (m) REVERT: G 215 MET cc_start: 0.8633 (ttm) cc_final: 0.8388 (ttm) REVERT: B 183 MET cc_start: 0.8144 (mtp) cc_final: 0.7826 (mtp) REVERT: I 177 ASN cc_start: 0.7794 (m-40) cc_final: 0.7500 (m-40) REVERT: I 183 MET cc_start: 0.7381 (mtp) cc_final: 0.6981 (mtp) REVERT: I 305 MET cc_start: 0.8325 (tpt) cc_final: 0.8057 (tpp) REVERT: J 8 MET cc_start: 0.7300 (mmm) cc_final: 0.6661 (mmm) REVERT: K 100 ASP cc_start: 0.7497 (m-30) cc_final: 0.7011 (m-30) REVERT: K 155 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.7010 (mtp-110) REVERT: K 183 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7895 (mtpm) outliers start: 53 outliers final: 34 residues processed: 283 average time/residue: 1.1783 time to fit residues: 392.2814 Evaluate side-chains 276 residues out of total 2626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 236 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 492 THR Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 336 THR Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain K residue 155 ARG Chi-restraints excluded: chain K residue 183 LYS Chi-restraints excluded: chain K residue 262 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 0.9980 chunk 250 optimal weight: 0.6980 chunk 72 optimal weight: 9.9990 chunk 217 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 235 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 242 optimal weight: 0.0870 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.126104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.089673 restraints weight = 73730.505| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.73 r_work: 0.3146 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23262 Z= 0.187 Angle : 0.588 10.310 31600 Z= 0.292 Chirality : 0.044 0.274 3790 Planarity : 0.004 0.060 4011 Dihedral : 4.369 22.696 3263 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.43 % Allowed : 19.20 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.49 (0.16), residues: 2920 helix: 0.73 (0.16), residues: 1154 sheet: -1.02 (0.27), residues: 376 loop : -0.97 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 97 HIS 0.003 0.000 HIS B 337 PHE 0.025 0.001 PHE C 272 TYR 0.019 0.001 TYR G 9 ARG 0.011 0.000 ARG J 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7683.71 seconds wall clock time: 137 minutes 43.85 seconds (8263.85 seconds total)