Starting phenix.real_space_refine on Sat Feb 24 20:48:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcw_14634/02_2024/7zcw_14634_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcw_14634/02_2024/7zcw_14634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcw_14634/02_2024/7zcw_14634.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcw_14634/02_2024/7zcw_14634.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcw_14634/02_2024/7zcw_14634_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcw_14634/02_2024/7zcw_14634_trim_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2189 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 162 5.16 5 C 14195 2.51 5 N 3867 2.21 5 O 4322 1.98 5 H 21746 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 367": "OD1" <-> "OD2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A ASP 438": "OD1" <-> "OD2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 26": "OD1" <-> "OD2" Residue "B ASP 41": "OD1" <-> "OD2" Residue "B PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B ASP 114": "OD1" <-> "OD2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 288": "OE1" <-> "OE2" Residue "B ASP 355": "OD1" <-> "OD2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B ASP 404": "OD1" <-> "OD2" Residue "B ASP 417": "OD1" <-> "OD2" Residue "C ASP 59": "OD1" <-> "OD2" Residue "C TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 109": "OD1" <-> "OD2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 227": "OD1" <-> "OD2" Residue "C TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 278": "OD1" <-> "OD2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D GLU 50": "OE1" <-> "OE2" Residue "E GLU 3": "OE1" <-> "OE2" Residue "E ASP 47": "OD1" <-> "OD2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 77": "OE1" <-> "OE2" Residue "E GLU 90": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 116": "OD1" <-> "OD2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E ASP 245": "OD1" <-> "OD2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 297": "OE1" <-> "OE2" Residue "E ASP 322": "OD1" <-> "OD2" Residue "E PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 423": "OE1" <-> "OE2" Residue "E GLU 429": "OE1" <-> "OE2" Residue "F ASP 26": "OD1" <-> "OD2" Residue "F TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 39": "OD1" <-> "OD2" Residue "F ASP 41": "OD1" <-> "OD2" Residue "F GLU 45": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F ASP 67": "OD1" <-> "OD2" Residue "F PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 108": "OE1" <-> "OE2" Residue "F ASP 118": "OD1" <-> "OD2" Residue "F GLU 157": "OE1" <-> "OE2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 224": "OD1" <-> "OD2" Residue "F GLU 288": "OE1" <-> "OE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 343": "OE1" <-> "OE2" Residue "F ASP 355": "OD1" <-> "OD2" Residue "F TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 404": "OD1" <-> "OD2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G ASP 74": "OD1" <-> "OD2" Residue "G PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 108": "OE1" <-> "OE2" Residue "G ASP 118": "OD1" <-> "OD2" Residue "G GLU 194": "OE1" <-> "OE2" Residue "G PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 328": "OE1" <-> "OE2" Residue "G GLU 343": "OE1" <-> "OE2" Residue "G GLU 383": "OE1" <-> "OE2" Residue "G GLU 405": "OE1" <-> "OE2" Residue "H GLU 3": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 123": "OE1" <-> "OE2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "H GLU 157": "OE1" <-> "OE2" Residue "H GLU 181": "OE1" <-> "OE2" Residue "H GLU 198": "OE1" <-> "OE2" Residue "H ASP 224": "OD1" <-> "OD2" Residue "H PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 421": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 44316 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 6658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 6658 Classifications: {'peptide': 430} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Chain: "B" Number of atoms: 6589 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 6588 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Conformer: "B" Number of residues, atoms: 426, 6588 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} bond proxies already assigned to first conformer: 6662 Chain: "C" Number of atoms: 4045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 4045 Classifications: {'peptide': 249} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 234} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 424 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 6635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 6635 Classifications: {'peptide': 428} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "F" Number of atoms: 6589 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 426, 6588 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Conformer: "A" Number of residues, atoms: 425, 6564 Classifications: {'peptide': 425} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 404} Chain breaks: 1 bond proxies already assigned to first conformer: 6637 Chain: "G" Number of atoms: 6589 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 426, 6588 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Conformer: "B" Number of residues, atoms: 426, 6588 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} bond proxies already assigned to first conformer: 6662 Chain: "H" Number of atoms: 6589 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 426, 6588 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Conformer: "A" Number of residues, atoms: 425, 6564 Classifications: {'peptide': 425} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 404} Chain breaks: 1 bond proxies already assigned to first conformer: 6637 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N BARG F 359 " occ=0.64 ... (22 atoms not shown) pdb="HH22BARG F 359 " occ=0.64 residue: pdb=" N BARG H 359 " occ=0.68 ... (22 atoms not shown) pdb="HH22BARG H 359 " occ=0.68 Time building chain proxies: 28.62, per 1000 atoms: 0.65 Number of scatterers: 44316 At special positions: 0 Unit cell: (129.076, 121.67, 167.164, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 162 16.00 P 18 15.00 Mg 6 11.99 O 4322 8.00 N 3867 7.00 C 14195 6.00 H 21746 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 33.96 Conformation dependent library (CDL) restraints added in 7.1 seconds 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5266 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 115 helices and 19 sheets defined 43.3% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.94 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.641A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 73 through 80 Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 112 through 127 removed outlier: 4.556A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 160 removed outlier: 4.159A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 removed outlier: 4.332A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 224 through 240 removed outlier: 3.613A pdb=" N ALA A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.558A pdb=" N ALA A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARG A 390 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.838A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 434 Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 42 through 45 No H-bonds generated for 'chain 'B' and resid 42 through 45' Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 71 through 78 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 181 through 192 removed outlier: 4.055A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 222 through 236 Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 286 through 293 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 323 through 336 removed outlier: 4.122A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 374 through 389 removed outlier: 4.314A pdb=" N PHE B 389 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.667A pdb=" N GLU B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 424 Processing helix chain 'C' and resid 60 through 73 Processing helix chain 'C' and resid 78 through 85 Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 139 through 152 Processing helix chain 'C' and resid 158 through 171 removed outlier: 4.897A pdb=" N GLY C 171 " --> pdb=" O TYR C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 239 removed outlier: 3.733A pdb=" N TYR C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 291 Processing helix chain 'D' and resid 27 through 52 Processing helix chain 'E' and resid 10 through 28 removed outlier: 3.712A pdb=" N ALA E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 51 removed outlier: 3.663A pdb=" N THR E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 51' Processing helix chain 'E' and resid 74 through 79 Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 115 through 128 removed outlier: 3.798A pdb=" N ARG E 121 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 160 removed outlier: 4.839A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 196 removed outlier: 4.369A pdb=" N HIS E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 215 Processing helix chain 'E' and resid 224 through 243 removed outlier: 5.197A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 256 Processing helix chain 'E' and resid 288 through 296 removed outlier: 3.771A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 309 No H-bonds generated for 'chain 'E' and resid 307 through 309' Processing helix chain 'E' and resid 325 through 336 Processing helix chain 'E' and resid 383 through 399 removed outlier: 4.413A pdb=" N ARG E 390 " --> pdb=" O ALA E 387 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TYR E 399 " --> pdb=" O ASP E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 411 Processing helix chain 'E' and resid 416 through 434 Processing helix chain 'F' and resid 10 through 28 removed outlier: 3.517A pdb=" N ASN F 14 " --> pdb=" O GLY F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 43 No H-bonds generated for 'chain 'F' and resid 41 through 43' Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 70 through 78 Processing helix chain 'F' and resid 87 through 89 No H-bonds generated for 'chain 'F' and resid 87 through 89' Processing helix chain 'F' and resid 109 through 124 removed outlier: 4.334A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N SER F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 158 removed outlier: 3.523A pdb=" N MET F 147 " --> pdb=" O THR F 143 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY F 148 " --> pdb=" O GLY F 144 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 192 removed outlier: 4.093A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 213 Processing helix chain 'F' and resid 222 through 236 Processing helix chain 'F' and resid 250 through 257 Processing helix chain 'F' and resid 286 through 294 removed outlier: 3.555A pdb=" N PHE F 294 " --> pdb=" O THR F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 307 No H-bonds generated for 'chain 'F' and resid 305 through 307' Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.778A pdb=" N GLN F 334 " --> pdb=" O MET F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 340 No H-bonds generated for 'chain 'F' and resid 338 through 340' Processing helix chain 'F' and resid 373 through 390 removed outlier: 3.641A pdb=" N ARG F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 401 removed outlier: 4.477A pdb=" N GLU F 401 " --> pdb=" O TRP F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 425 removed outlier: 4.272A pdb=" N TYR F 425 " --> pdb=" O GLU F 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 28 Processing helix chain 'G' and resid 41 through 45 Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 71 through 78 Processing helix chain 'G' and resid 87 through 89 No H-bonds generated for 'chain 'G' and resid 87 through 89' Processing helix chain 'G' and resid 113 through 125 Processing helix chain 'G' and resid 143 through 158 Processing helix chain 'G' and resid 181 through 192 removed outlier: 4.065A pdb=" N GLN G 191 " --> pdb=" O LEU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 213 Processing helix chain 'G' and resid 222 through 236 Processing helix chain 'G' and resid 238 through 240 No H-bonds generated for 'chain 'G' and resid 238 through 240' Processing helix chain 'G' and resid 250 through 257 Processing helix chain 'G' and resid 286 through 293 Processing helix chain 'G' and resid 296 through 298 No H-bonds generated for 'chain 'G' and resid 296 through 298' Processing helix chain 'G' and resid 305 through 307 No H-bonds generated for 'chain 'G' and resid 305 through 307' Processing helix chain 'G' and resid 323 through 336 removed outlier: 4.180A pdb=" N GLN G 334 " --> pdb=" O MET G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 340 No H-bonds generated for 'chain 'G' and resid 338 through 340' Processing helix chain 'G' and resid 372 through 389 removed outlier: 3.708A pdb=" N GLN G 375 " --> pdb=" O THR G 372 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG G 380 " --> pdb=" O LEU G 377 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE G 389 " --> pdb=" O THR G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 401 removed outlier: 4.126A pdb=" N GLU G 401 " --> pdb=" O TRP G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 425 removed outlier: 4.338A pdb=" N TYR G 425 " --> pdb=" O GLU G 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 28 Processing helix chain 'H' and resid 41 through 43 No H-bonds generated for 'chain 'H' and resid 41 through 43' Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 70 through 78 Processing helix chain 'H' and resid 108 through 125 removed outlier: 3.968A pdb=" N LEU H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N SER H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL H 116 " --> pdb=" O LEU H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 158 removed outlier: 3.823A pdb=" N THR H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 192 removed outlier: 4.040A pdb=" N GLN H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 213 Processing helix chain 'H' and resid 222 through 237 removed outlier: 3.983A pdb=" N THR H 237 " --> pdb=" O MET H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 257 Processing helix chain 'H' and resid 286 through 294 Processing helix chain 'H' and resid 305 through 307 No H-bonds generated for 'chain 'H' and resid 305 through 307' Processing helix chain 'H' and resid 324 through 336 removed outlier: 4.137A pdb=" N GLN H 334 " --> pdb=" O MET H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 340 No H-bonds generated for 'chain 'H' and resid 338 through 340' Processing helix chain 'H' and resid 372 through 389 removed outlier: 3.803A pdb=" N GLN H 375 " --> pdb=" O THR H 372 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE H 389 " --> pdb=" O THR H 386 " (cutoff:3.500A) Processing helix chain 'H' and resid 396 through 399 No H-bonds generated for 'chain 'H' and resid 396 through 399' Processing helix chain 'H' and resid 405 through 425 removed outlier: 3.634A pdb=" N THR H 409 " --> pdb=" O GLU H 405 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYR H 425 " --> pdb=" O GLU H 421 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 65 through 68 removed outlier: 9.040A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLY A 134 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ILE A 7 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU A 136 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL A 9 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE A 138 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'A' and resid 269 through 273 Processing sheet with id= D, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.401A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N VAL B 5 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE B 133 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ILE B 7 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU B 135 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ALA B 9 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N HIS B 137 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE B 163 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N LEU B 135 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASN B 165 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N HIS B 137 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE B 167 " --> pdb=" O HIS B 137 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 51 through 53 Processing sheet with id= F, first strand: chain 'B' and resid 349 through 354 removed outlier: 8.650A pdb=" N LYS B 350 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ALA B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N CYS B 354 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N PHE B 317 " --> pdb=" O CYS B 354 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASN B 370 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL B 313 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE B 368 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA B 315 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR B 366 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE B 317 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N SER B 364 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 205 through 207 removed outlier: 5.791A pdb=" N TYR C 185 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL C 243 " --> pdb=" O TYR C 185 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 65 through 68 removed outlier: 8.768A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE E 5 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE E 135 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE E 7 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL E 137 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL E 9 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER E 165 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL E 137 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU E 167 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N CYS E 200 " --> pdb=" O GLU E 168 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= J, first strand: chain 'E' and resid 351 through 354 removed outlier: 6.960A pdb=" N CYS E 315 " --> pdb=" O LYS E 352 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N GLY E 354 " --> pdb=" O CYS E 315 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU E 317 " --> pdb=" O GLY E 354 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 63 through 65 removed outlier: 8.425A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N VAL F 5 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE F 133 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE F 7 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU F 135 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS F 137 " --> pdb=" O PHE F 167 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 51 through 53 Processing sheet with id= M, first strand: chain 'F' and resid 199 through 201 Processing sheet with id= N, first strand: chain 'G' and resid 63 through 66 removed outlier: 8.442A pdb=" N ILE G 64 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N HIS G 6 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL G 66 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLN G 8 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N VAL G 5 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE G 133 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE G 7 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU G 135 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ALA G 9 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N HIS G 137 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS G 137 " --> pdb=" O PHE G 167 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 51 through 54 Processing sheet with id= P, first strand: chain 'G' and resid 349 through 354 removed outlier: 8.828A pdb=" N LYS G 350 " --> pdb=" O LEU G 311 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL G 313 " --> pdb=" O LYS G 350 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ALA G 352 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA G 315 " --> pdb=" O ALA G 352 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N CYS G 354 " --> pdb=" O ALA G 315 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE G 317 " --> pdb=" O CYS G 354 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASN G 370 " --> pdb=" O LEU G 311 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL G 313 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE G 368 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA G 315 " --> pdb=" O THR G 366 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N THR G 366 " --> pdb=" O ALA G 315 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE G 317 " --> pdb=" O SER G 364 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER G 364 " --> pdb=" O PHE G 317 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 63 through 66 removed outlier: 8.445A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL H 66 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLN H 8 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL H 5 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE H 133 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE H 7 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU H 135 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ALA H 9 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N HIS H 137 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE H 163 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LEU H 135 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ASN H 165 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N HIS H 137 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE H 167 " --> pdb=" O HIS H 137 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU H 198 " --> pdb=" O THR H 166 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N SER H 168 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N TYR H 200 " --> pdb=" O SER H 168 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 51 through 53 Processing sheet with id= S, first strand: chain 'H' and resid 349 through 354 removed outlier: 8.766A pdb=" N LYS H 350 " --> pdb=" O LEU H 311 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL H 313 " --> pdb=" O LYS H 350 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ALA H 352 " --> pdb=" O VAL H 313 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA H 315 " --> pdb=" O ALA H 352 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N CYS H 354 " --> pdb=" O ALA H 315 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE H 317 " --> pdb=" O CYS H 354 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASN H 370 " --> pdb=" O LEU H 311 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL H 313 " --> pdb=" O ILE H 368 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE H 368 " --> pdb=" O VAL H 313 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA H 315 " --> pdb=" O THR H 366 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N THR H 366 " --> pdb=" O ALA H 315 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N PHE H 317 " --> pdb=" O SER H 364 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER H 364 " --> pdb=" O PHE H 317 " (cutoff:3.500A) 826 hydrogen bonds defined for protein. 2232 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: 18.22 Time building geometry restraints manager: 35.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.03: 21689 1.03 - 1.24: 2366 1.24 - 1.44: 7754 1.44 - 1.65: 12742 1.65 - 1.86: 280 Bond restraints: 44831 Sorted by residual: bond pdb=" C2' G2P H 501 " pdb=" C3' G2P H 501 " ideal model delta sigma weight residual 1.528 1.243 0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C2' G2P B 501 " pdb=" C3' G2P B 501 " ideal model delta sigma weight residual 1.528 1.243 0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C2' G2P G 501 " pdb=" C3' G2P G 501 " ideal model delta sigma weight residual 1.528 1.243 0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C2' G2P F 501 " pdb=" C3' G2P F 501 " ideal model delta sigma weight residual 1.528 1.245 0.283 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C3' G2P F 501 " pdb=" C4' G2P F 501 " ideal model delta sigma weight residual 1.526 1.665 -0.139 2.00e-02 2.50e+03 4.84e+01 ... (remaining 44826 not shown) Histogram of bond angle deviations from ideal: 98.63 - 109.09: 24550 109.09 - 119.55: 38099 119.55 - 130.01: 17870 130.01 - 140.46: 176 140.46 - 150.92: 4 Bond angle restraints: 80699 Sorted by residual: angle pdb=" C1' G2P B 501 " pdb=" N9 G2P B 501 " pdb=" C8 G2P B 501 " ideal model delta sigma weight residual 127.92 102.01 25.91 3.00e+00 1.11e-01 7.46e+01 angle pdb=" C1' G2P G 501 " pdb=" N9 G2P G 501 " pdb=" C8 G2P G 501 " ideal model delta sigma weight residual 127.92 102.13 25.79 3.00e+00 1.11e-01 7.39e+01 angle pdb=" C1' G2P B 501 " pdb=" N9 G2P B 501 " pdb=" C4 G2P B 501 " ideal model delta sigma weight residual 125.17 150.92 -25.75 3.00e+00 1.11e-01 7.37e+01 angle pdb=" C1' G2P F 501 " pdb=" N9 G2P F 501 " pdb=" C8 G2P F 501 " ideal model delta sigma weight residual 127.92 102.35 25.57 3.00e+00 1.11e-01 7.27e+01 angle pdb=" C1' G2P H 501 " pdb=" N9 G2P H 501 " pdb=" C8 G2P H 501 " ideal model delta sigma weight residual 127.92 102.36 25.56 3.00e+00 1.11e-01 7.26e+01 ... (remaining 80694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 20494 35.38 - 70.75: 816 70.75 - 106.13: 27 106.13 - 141.51: 4 141.51 - 176.88: 4 Dihedral angle restraints: 21345 sinusoidal: 11589 harmonic: 9756 Sorted by residual: dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -113.85 -176.88 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -133.58 -157.15 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" O5' GTP E 501 " pdb=" O3A GTP E 501 " pdb=" PA GTP E 501 " pdb=" PB GTP E 501 " ideal model delta sinusoidal sigma weight residual 274.12 123.63 150.50 1 2.00e+01 2.50e-03 4.49e+01 ... (remaining 21342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2911 0.062 - 0.125: 426 0.125 - 0.187: 56 0.187 - 0.250: 5 0.250 - 0.312: 4 Chirality restraints: 3402 Sorted by residual: chirality pdb=" C3' G2P H 501 " pdb=" C2' G2P H 501 " pdb=" C4' G2P H 501 " pdb=" O3' G2P H 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.39 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C3' G2P F 501 " pdb=" C2' G2P F 501 " pdb=" C4' G2P F 501 " pdb=" O3' G2P F 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.41 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C3' G2P G 501 " pdb=" C2' G2P G 501 " pdb=" C4' G2P G 501 " pdb=" O3' G2P G 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.41 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 3399 not shown) Planarity restraints: 6770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 286 " -0.068 5.00e-02 4.00e+02 9.90e-02 1.57e+01 pdb=" N PRO H 287 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO H 287 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO H 287 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 31 " -0.049 5.00e-02 4.00e+02 7.41e-02 8.78e+00 pdb=" N PRO G 32 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO G 32 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO G 32 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 320 " 0.214 9.50e-02 1.11e+02 7.17e-02 6.22e+00 pdb=" NE ARG H 320 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG H 320 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG H 320 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG H 320 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG H 320 " -0.007 2.00e-02 2.50e+03 pdb="HH12 ARG H 320 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG H 320 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 320 " -0.000 2.00e-02 2.50e+03 ... (remaining 6767 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 6310 2.26 - 2.85: 96679 2.85 - 3.43: 113945 3.43 - 4.02: 155722 4.02 - 4.60: 241759 Nonbonded interactions: 614415 Sorted by model distance: nonbonded pdb=" OE1 GLN F 279 " pdb="HH12 ARG F 282 " model vdw 1.678 1.850 nonbonded pdb=" O LYS H 252 " pdb="HD22 ASN H 256 " model vdw 1.704 1.850 nonbonded pdb=" OE2 GLU B 27 " pdb="HH22 ARG B 318 " model vdw 1.712 1.850 nonbonded pdb=" OD1 ASN A 186 " pdb=" HH TYR A 408 " model vdw 1.713 1.850 nonbonded pdb=" O GLY A 142 " pdb="HD22 ASN A 186 " model vdw 1.715 1.850 ... (remaining 614410 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 437 or resid 501 through 502)) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 1 through 358 or resid 361 through 426 or resid 501 throug \ h 502)) selection = (chain 'F' and (resid 1 through 358 or resid 361 through 426 or resid 501 throug \ h 502)) selection = (chain 'G' and (resid 1 through 358 or resid 361 through 426 or resid 501 throug \ h 502)) selection = (chain 'H' and (resid 1 through 358 or resid 361 through 426 or resid 501 throug \ h 502)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.280 Construct map_model_manager: 0.740 Extract box with map and model: 4.070 Check model and map are aligned: 0.670 Set scattering table: 0.410 Process input model: 149.300 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.285 23085 Z= 0.501 Angle : 1.014 25.907 31328 Z= 0.477 Chirality : 0.048 0.312 3402 Planarity : 0.006 0.099 4073 Dihedral : 17.262 176.884 8574 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.21 % Allowed : 12.83 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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: -1.14 (0.15), residues: 2819 helix: 0.51 (0.14), residues: 1226 sheet: -1.79 (0.24), residues: 413 loop : -1.69 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 67 HIS 0.021 0.002 HIS H 190 PHE 0.019 0.002 PHE H 212 TYR 0.026 0.002 TYR H 310 ARG 0.019 0.001 ARG F 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 68 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 464 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 459 time to evaluate : 3.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 265 LYS cc_start: 0.7878 (mmmt) cc_final: 0.7672 (tmmt) REVERT: C 270 ASN cc_start: 0.7379 (t0) cc_final: 0.6720 (p0) REVERT: D 50 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6935 (mt-10) REVERT: F 262 ARG cc_start: 0.7941 (ttm-80) cc_final: 0.7710 (mtt90) REVERT: G 383 GLU cc_start: 0.7704 (tp30) cc_final: 0.7471 (tm-30) REVERT: G 412 GLU cc_start: 0.8129 (tp30) cc_final: 0.7851 (tm-30) REVERT: H 252 LYS cc_start: 0.5102 (mmtt) cc_final: 0.4833 (mmtt) REVERT: H 415 MET cc_start: 0.8224 (mmp) cc_final: 0.7785 (mmm) outliers start: 5 outliers final: 3 residues processed: 459 average time/residue: 0.9035 time to fit residues: 611.5995 Evaluate side-chains 445 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 442 time to evaluate : 3.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain F residue 178 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 235 optimal weight: 10.0000 chunk 211 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 218 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 162 optimal weight: 7.9990 chunk 253 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 HIS E 15 GLN E 61 HIS F 396 HIS G 329 GLN G 416 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.0738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23085 Z= 0.219 Angle : 0.524 6.235 31328 Z= 0.268 Chirality : 0.040 0.142 3402 Planarity : 0.004 0.067 4073 Dihedral : 9.862 177.099 3250 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.32 % Allowed : 12.96 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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: 2819 helix: 0.76 (0.15), residues: 1236 sheet: -1.89 (0.23), residues: 443 loop : -1.53 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 21 HIS 0.005 0.001 HIS H 190 PHE 0.017 0.001 PHE B 81 TYR 0.012 0.001 TYR H 310 ARG 0.005 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 68 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 465 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 433 time to evaluate : 3.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 262 ARG cc_start: 0.7931 (ttm-80) cc_final: 0.7684 (mtt90) REVERT: G 159 TYR cc_start: 0.8103 (m-80) cc_final: 0.7881 (m-80) REVERT: G 329 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6399 (tp40) REVERT: G 383 GLU cc_start: 0.7756 (tp30) cc_final: 0.7516 (tm-30) REVERT: H 252 LYS cc_start: 0.4985 (mmtt) cc_final: 0.4717 (mmtt) REVERT: H 288 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7355 (mt-10) REVERT: H 415 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7732 (tpp) outliers start: 32 outliers final: 25 residues processed: 443 average time/residue: 0.9398 time to fit residues: 614.5835 Evaluate side-chains 446 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 419 time to evaluate : 3.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 209 ASP Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 329 GLN Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 415 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 140 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 210 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 253 optimal weight: 9.9990 chunk 274 optimal weight: 2.9990 chunk 226 optimal weight: 8.9990 chunk 251 optimal weight: 9.9990 chunk 86 optimal weight: 50.0000 chunk 203 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 414 ASN H 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23085 Z= 0.310 Angle : 0.553 5.911 31328 Z= 0.286 Chirality : 0.042 0.166 3402 Planarity : 0.004 0.058 4073 Dihedral : 9.853 178.892 3250 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.02 % Allowed : 13.57 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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: -0.97 (0.16), residues: 2819 helix: 0.70 (0.15), residues: 1233 sheet: -1.85 (0.23), residues: 437 loop : -1.58 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 21 HIS 0.006 0.001 HIS F 37 PHE 0.013 0.001 PHE G 385 TYR 0.014 0.001 TYR H 281 ARG 0.006 0.000 ARG F 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 68 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 486 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 437 time to evaluate : 3.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8132 (p0) REVERT: B 417 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7671 (t0) REVERT: C 270 ASN cc_start: 0.7353 (t0) cc_final: 0.6823 (p0) REVERT: G 159 TYR cc_start: 0.8206 (m-80) cc_final: 0.7955 (m-80) REVERT: G 383 GLU cc_start: 0.7670 (tp30) cc_final: 0.7447 (tm-30) REVERT: H 91 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8104 (p) REVERT: H 252 LYS cc_start: 0.4995 (mmtt) cc_final: 0.4774 (mmtt) REVERT: H 288 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7368 (mt-10) REVERT: H 415 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7788 (tpp) outliers start: 49 outliers final: 34 residues processed: 459 average time/residue: 0.9160 time to fit residues: 616.4943 Evaluate side-chains 463 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 425 time to evaluate : 3.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 147 MET Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 415 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 250 optimal weight: 8.9990 chunk 190 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 254 optimal weight: 0.9980 chunk 269 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 241 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 416 ASN E 301 GLN F 298 ASN ** G 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23085 Z= 0.244 Angle : 0.515 5.898 31328 Z= 0.265 Chirality : 0.041 0.143 3402 Planarity : 0.004 0.050 4073 Dihedral : 9.737 179.266 3250 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.89 % Allowed : 13.78 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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: -0.92 (0.16), residues: 2819 helix: 0.78 (0.15), residues: 1241 sheet: -1.89 (0.23), residues: 452 loop : -1.58 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 21 HIS 0.005 0.001 HIS F 37 PHE 0.012 0.001 PHE A 395 TYR 0.015 0.001 TYR C 117 ARG 0.004 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 68 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 484 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 438 time to evaluate : 4.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8114 (p0) REVERT: A 386 GLU cc_start: 0.8165 (tp30) cc_final: 0.7778 (tp30) REVERT: A 432 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.6074 (t80) REVERT: B 417 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7797 (t0) REVERT: C 270 ASN cc_start: 0.7347 (t0) cc_final: 0.6821 (p0) REVERT: E 161 TYR cc_start: 0.8626 (m-80) cc_final: 0.8422 (m-80) REVERT: E 219 ILE cc_start: 0.8619 (mm) cc_final: 0.8228 (tp) REVERT: G 159 TYR cc_start: 0.8207 (m-80) cc_final: 0.7922 (m-80) REVERT: G 383 GLU cc_start: 0.7645 (tp30) cc_final: 0.7416 (tm-30) REVERT: H 91 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8132 (p) REVERT: H 252 LYS cc_start: 0.5019 (mmtt) cc_final: 0.4263 (mmtm) REVERT: H 288 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7351 (mt-10) REVERT: H 415 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7834 (tpp) outliers start: 46 outliers final: 34 residues processed: 461 average time/residue: 0.9248 time to fit residues: 625.1055 Evaluate side-chains 464 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 425 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain H residue 415 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 224 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 186 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 242 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 423 GLN C 170 ASN ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 416 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 23085 Z= 0.438 Angle : 0.606 5.918 31328 Z= 0.318 Chirality : 0.044 0.162 3402 Planarity : 0.005 0.048 4073 Dihedral : 10.142 172.912 3248 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.51 % Allowed : 14.56 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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: -1.34 (0.15), residues: 2819 helix: 0.35 (0.14), residues: 1240 sheet: -1.97 (0.24), residues: 450 loop : -1.76 (0.17), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 21 HIS 0.007 0.001 HIS A 88 PHE 0.020 0.002 PHE G 385 TYR 0.021 0.002 TYR H 281 ARG 0.008 0.001 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 68 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 491 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 430 time to evaluate : 3.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8235 (p0) REVERT: A 386 GLU cc_start: 0.8102 (tp30) cc_final: 0.7617 (tp30) REVERT: A 432 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.6201 (t80) REVERT: B 417 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7717 (t0) REVERT: C 270 ASN cc_start: 0.7371 (t0) cc_final: 0.6957 (p0) REVERT: E 168 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7766 (mm-30) REVERT: F 147 MET cc_start: 0.8973 (ttp) cc_final: 0.8664 (ttt) REVERT: G 159 TYR cc_start: 0.8380 (m-80) cc_final: 0.8135 (m-80) REVERT: H 252 LYS cc_start: 0.5183 (mmtt) cc_final: 0.4321 (mmtp) REVERT: H 415 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7830 (tpp) outliers start: 61 outliers final: 45 residues processed: 465 average time/residue: 0.9226 time to fit residues: 631.4954 Evaluate side-chains 471 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 421 time to evaluate : 3.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 413 MET Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 415 MET Chi-restraints excluded: chain H residue 422 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 90 optimal weight: 4.9990 chunk 242 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 269 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 141 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN F 298 ASN F 307 HIS ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 416 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 23085 Z= 0.235 Angle : 0.522 5.948 31328 Z= 0.268 Chirality : 0.041 0.154 3402 Planarity : 0.004 0.046 4073 Dihedral : 9.902 177.123 3248 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.18 % Allowed : 14.93 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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: -1.06 (0.16), residues: 2819 helix: 0.64 (0.15), residues: 1239 sheet: -1.91 (0.24), residues: 455 loop : -1.64 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 21 HIS 0.005 0.001 HIS F 37 PHE 0.012 0.001 PHE A 395 TYR 0.015 0.001 TYR C 117 ARG 0.005 0.000 ARG G 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 68 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 495 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 442 time to evaluate : 3.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8139 (p0) REVERT: A 386 GLU cc_start: 0.8149 (tp30) cc_final: 0.7654 (tp30) REVERT: A 432 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.6135 (t80) REVERT: B 417 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7795 (t0) REVERT: B 422 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.6057 (t80) REVERT: C 270 ASN cc_start: 0.7330 (t0) cc_final: 0.7099 (p0) REVERT: F 147 MET cc_start: 0.8913 (ttp) cc_final: 0.8562 (ttt) REVERT: F 158 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6624 (mp0) REVERT: G 159 TYR cc_start: 0.8280 (m-80) cc_final: 0.7987 (m-80) REVERT: H 91 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8142 (p) REVERT: H 252 LYS cc_start: 0.5131 (mmtt) cc_final: 0.4732 (mmtm) REVERT: H 415 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7847 (tpp) outliers start: 53 outliers final: 38 residues processed: 472 average time/residue: 0.9130 time to fit residues: 635.0729 Evaluate side-chains 475 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 430 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 298 ASN Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 415 MET Chi-restraints excluded: chain H residue 422 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 260 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 153 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 227 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 chunk 268 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN F 298 ASN H 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23085 Z= 0.185 Angle : 0.505 5.996 31328 Z= 0.258 Chirality : 0.040 0.163 3402 Planarity : 0.004 0.043 4073 Dihedral : 9.722 178.933 3248 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.89 % Allowed : 15.63 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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: -0.88 (0.16), residues: 2819 helix: 0.81 (0.15), residues: 1241 sheet: -1.80 (0.24), residues: 455 loop : -1.58 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 21 HIS 0.004 0.001 HIS F 37 PHE 0.010 0.001 PHE H 212 TYR 0.014 0.001 TYR C 117 ARG 0.012 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 68 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 483 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 437 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.8172 (p0) REVERT: A 386 GLU cc_start: 0.8151 (tp30) cc_final: 0.7652 (tp30) REVERT: A 432 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.6109 (t80) REVERT: B 282 ARG cc_start: 0.7634 (mtp-110) cc_final: 0.7428 (mtp-110) REVERT: B 417 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7860 (t0) REVERT: B 422 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.6152 (t80) REVERT: C 270 ASN cc_start: 0.7428 (t0) cc_final: 0.7021 (p0) REVERT: E 219 ILE cc_start: 0.8675 (mm) cc_final: 0.8279 (tp) REVERT: F 147 MET cc_start: 0.8892 (ttp) cc_final: 0.8295 (ttt) REVERT: F 158 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6536 (mp0) REVERT: G 422 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.6504 (t80) REVERT: H 91 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8123 (p) REVERT: H 252 LYS cc_start: 0.5109 (mmtt) cc_final: 0.4690 (mmtt) REVERT: H 415 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7837 (tpp) outliers start: 46 outliers final: 33 residues processed: 463 average time/residue: 0.9369 time to fit residues: 639.4301 Evaluate side-chains 471 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 430 time to evaluate : 3.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 415 MET Chi-restraints excluded: chain H residue 422 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 166 optimal weight: 6.9990 chunk 107 optimal weight: 30.0000 chunk 160 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 170 optimal weight: 0.6980 chunk 183 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 211 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN G 165 ASN G 416 ASN H 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23085 Z= 0.201 Angle : 0.505 6.014 31328 Z= 0.258 Chirality : 0.040 0.158 3402 Planarity : 0.004 0.042 4073 Dihedral : 9.574 179.404 3248 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.93 % Allowed : 15.71 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % 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: -0.79 (0.16), residues: 2819 helix: 0.89 (0.15), residues: 1241 sheet: -1.73 (0.24), residues: 455 loop : -1.55 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 21 HIS 0.004 0.001 HIS F 37 PHE 0.009 0.001 PHE A 395 TYR 0.015 0.001 TYR C 117 ARG 0.007 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 68 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 487 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 440 time to evaluate : 3.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8183 (p0) REVERT: A 386 GLU cc_start: 0.8150 (tp30) cc_final: 0.7641 (tp30) REVERT: A 432 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.6131 (t80) REVERT: B 412 GLU cc_start: 0.8006 (tp30) cc_final: 0.7804 (tp30) REVERT: B 417 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7875 (t0) REVERT: B 422 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.6251 (t80) REVERT: C 270 ASN cc_start: 0.7387 (t0) cc_final: 0.6985 (p0) REVERT: F 147 MET cc_start: 0.8888 (ttp) cc_final: 0.8307 (ttt) REVERT: F 158 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6557 (mp0) REVERT: F 298 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7988 (t0) REVERT: G 422 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.6559 (t80) REVERT: H 252 LYS cc_start: 0.5105 (mmtt) cc_final: 0.4279 (mmtm) REVERT: H 330 MET cc_start: 0.7454 (mmm) cc_final: 0.7164 (mmm) REVERT: H 415 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7859 (tpp) outliers start: 47 outliers final: 37 residues processed: 467 average time/residue: 0.9421 time to fit residues: 642.2826 Evaluate side-chains 475 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 430 time to evaluate : 3.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 298 ASN Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 48 ASN Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 415 MET Chi-restraints excluded: chain H residue 422 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 257 optimal weight: 7.9990 chunk 235 optimal weight: 9.9990 chunk 250 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 196 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 226 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 ASN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 ASN G 335 ASN H 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.345 23085 Z= 0.392 Angle : 0.737 59.197 31328 Z= 0.456 Chirality : 0.044 0.917 3402 Planarity : 0.004 0.154 4073 Dihedral : 9.575 179.141 3248 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.93 % Allowed : 15.84 % Favored : 82.23 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.22 % 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: -0.79 (0.16), residues: 2819 helix: 0.88 (0.15), residues: 1241 sheet: -1.73 (0.24), residues: 455 loop : -1.56 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 21 HIS 0.004 0.001 HIS F 37 PHE 0.013 0.001 PHE B 81 TYR 0.012 0.001 TYR C 117 ARG 0.004 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 68 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 478 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 431 time to evaluate : 3.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8190 (p0) REVERT: A 386 GLU cc_start: 0.8158 (tp30) cc_final: 0.7646 (tp30) REVERT: A 432 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.6151 (t80) REVERT: B 412 GLU cc_start: 0.8015 (tp30) cc_final: 0.7811 (tp30) REVERT: B 417 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7879 (t0) REVERT: B 422 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.6271 (t80) REVERT: C 270 ASN cc_start: 0.7387 (t0) cc_final: 0.6984 (p0) REVERT: F 147 MET cc_start: 0.8874 (ttp) cc_final: 0.8285 (ttt) REVERT: F 158 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6564 (mp0) REVERT: G 159 TYR cc_start: 0.8197 (m-80) cc_final: 0.7904 (m-80) REVERT: G 422 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.6565 (t80) REVERT: H 252 LYS cc_start: 0.5116 (mmtt) cc_final: 0.4290 (mmtm) REVERT: H 330 MET cc_start: 0.7463 (mmm) cc_final: 0.7174 (mmm) REVERT: H 415 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7867 (tpp) outliers start: 47 outliers final: 39 residues processed: 458 average time/residue: 0.9263 time to fit residues: 619.9096 Evaluate side-chains 478 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 432 time to evaluate : 3.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 415 MET Chi-restraints excluded: chain H residue 422 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 264 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 277 optimal weight: 10.0000 chunk 255 optimal weight: 0.4980 chunk 221 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 170 optimal weight: 0.0670 chunk 135 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.345 23085 Z= 0.392 Angle : 0.737 59.197 31328 Z= 0.456 Chirality : 0.044 0.917 3402 Planarity : 0.004 0.154 4073 Dihedral : 9.575 179.141 3248 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.89 % Allowed : 15.88 % Favored : 82.23 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.22 % 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: -0.79 (0.16), residues: 2819 helix: 0.88 (0.15), residues: 1241 sheet: -1.73 (0.24), residues: 455 loop : -1.56 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 21 HIS 0.004 0.001 HIS F 37 PHE 0.013 0.001 PHE B 81 TYR 0.012 0.001 TYR C 117 ARG 0.004 0.000 ARG B 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5638 Ramachandran restraints generated. 2819 Oldfield, 0 Emsley, 2819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 48 is missing expected H atoms. Skipping. Residue MET 68 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 478 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 432 time to evaluate : 3.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8190 (p0) REVERT: A 386 GLU cc_start: 0.8158 (tp30) cc_final: 0.7646 (tp30) REVERT: A 432 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.6151 (t80) REVERT: B 412 GLU cc_start: 0.8016 (tp30) cc_final: 0.7811 (tp30) REVERT: B 417 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7879 (t0) REVERT: B 422 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.6271 (t80) REVERT: C 270 ASN cc_start: 0.7385 (t0) cc_final: 0.6984 (p0) REVERT: F 147 MET cc_start: 0.8874 (ttp) cc_final: 0.8285 (ttt) REVERT: F 158 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6564 (mp0) REVERT: G 422 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.6565 (t80) REVERT: H 252 LYS cc_start: 0.5116 (mmtt) cc_final: 0.4290 (mmtm) REVERT: H 330 MET cc_start: 0.7463 (mmm) cc_final: 0.7174 (mmm) REVERT: H 415 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7867 (tpp) outliers start: 46 outliers final: 39 residues processed: 458 average time/residue: 0.9157 time to fit residues: 613.3648 Evaluate side-chains 479 residues out of total 2442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 433 time to evaluate : 3.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 422 TYR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 415 MET Chi-restraints excluded: chain H residue 422 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 235 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 204 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 221 optimal weight: 0.5980 chunk 92 optimal weight: 20.0000 chunk 227 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.145627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115655 restraints weight = 82839.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.121037 restraints weight = 39746.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.123087 restraints weight = 20562.900| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.345 23085 Z= 0.392 Angle : 0.737 59.197 31328 Z= 0.456 Chirality : 0.044 0.917 3402 Planarity : 0.004 0.154 4073 Dihedral : 9.575 179.141 3248 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.89 % Allowed : 15.88 % Favored : 82.23 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.22 % 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: -0.79 (0.16), residues: 2819 helix: 0.88 (0.15), residues: 1241 sheet: -1.73 (0.24), residues: 455 loop : -1.56 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 21 HIS 0.004 0.001 HIS F 37 PHE 0.013 0.001 PHE B 81 TYR 0.012 0.001 TYR C 117 ARG 0.004 0.000 ARG B 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10544.18 seconds wall clock time: 187 minutes 28.80 seconds (11248.80 seconds total)