Starting phenix.real_space_refine on Fri Mar 22 04:36:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4u_37270/03_2024/8w4u_37270_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4u_37270/03_2024/8w4u_37270.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4u_37270/03_2024/8w4u_37270_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4u_37270/03_2024/8w4u_37270_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4u_37270/03_2024/8w4u_37270_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4u_37270/03_2024/8w4u_37270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4u_37270/03_2024/8w4u_37270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4u_37270/03_2024/8w4u_37270_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w4u_37270/03_2024/8w4u_37270_neut_trim_updated.pdb" } resolution = 3.3 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 12 5.49 5 S 88 5.16 5 C 10460 2.51 5 N 2692 2.21 5 O 2892 1.98 5 F 4 1.80 5 H 15620 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 87": not complete - not flipped Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 212": "OD1" <-> "OD2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 87": not complete - not flipped Residue "B PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 172": "OD1" <-> "OD2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "B ASP 577": "OD1" <-> "OD2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "D PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 87": not complete - not flipped Residue "D PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D ASP 212": "OD1" <-> "OD2" Residue "D TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 322": "OE1" <-> "OE2" Residue "D TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 87": not complete - not flipped Residue "G PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 257": "OE1" <-> "OE2" Residue "G TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 322": "OE1" <-> "OE2" Residue "G PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 557": "OE1" <-> "OE2" Residue "H ASP 23": "OD1" <-> "OD2" Residue "H PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 120": "OE1" <-> "OE2" Residue "H GLU 141": "OE1" <-> "OE2" Residue "E PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 120": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31768 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5741 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5741 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5741 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "F" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5741 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'9MF': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'9MF': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'9MF': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'9MF': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.78, per 1000 atoms: 0.43 Number of scatterers: 31768 At special positions: 0 Unit cell: (128.34, 128.34, 125.55, 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 88 16.00 P 12 15.00 F 4 9.00 O 2892 8.00 N 2692 7.00 C 10460 6.00 H 15620 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: 25.40 Conformation dependent library (CDL) restraints added in 2.9 seconds 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 0 sheets defined 77.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 91 through 114 Processing helix chain 'A' and resid 119 through 149 removed outlier: 4.050A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 167 through 183 Processing helix chain 'A' and resid 196 through 212 removed outlier: 4.472A pdb=" N ASP A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 229 through 253 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 264 through 275 Processing helix chain 'A' and resid 288 through 347 removed outlier: 4.252A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) Proline residue: A 308 - end of helix Proline residue: A 335 - end of helix Processing helix chain 'A' and resid 357 through 366 removed outlier: 4.542A pdb=" N TYR A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 558 Processing helix chain 'A' and resid 564 through 599 Proline residue: A 597 - end of helix Processing helix chain 'B' and resid 71 through 85 Processing helix chain 'B' and resid 91 through 114 Processing helix chain 'B' and resid 119 through 149 removed outlier: 4.042A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY B 149 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 196 through 212 removed outlier: 4.475A pdb=" N ASP B 212 " --> pdb=" O MET B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 227 Processing helix chain 'B' and resid 229 through 253 Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'B' and resid 264 through 275 Processing helix chain 'B' and resid 288 through 347 removed outlier: 4.173A pdb=" N ILE B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) Proline residue: B 308 - end of helix Proline residue: B 335 - end of helix Processing helix chain 'B' and resid 357 through 366 removed outlier: 4.542A pdb=" N TYR B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 558 Processing helix chain 'B' and resid 564 through 599 Proline residue: B 597 - end of helix Processing helix chain 'C' and resid 7 through 20 Processing helix chain 'C' and resid 30 through 40 Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 66 through 74 Processing helix chain 'C' and resid 77 through 80 No H-bonds generated for 'chain 'C' and resid 77 through 80' Processing helix chain 'C' and resid 83 through 93 Processing helix chain 'C' and resid 103 through 111 removed outlier: 3.966A pdb=" N THR C 111 " --> pdb=" O ARG C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 129 Processing helix chain 'C' and resid 139 through 147 Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 91 through 114 Processing helix chain 'D' and resid 119 through 149 removed outlier: 3.953A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY D 149 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 167 through 183 Processing helix chain 'D' and resid 196 through 212 removed outlier: 4.486A pdb=" N ASP D 212 " --> pdb=" O MET D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 227 Processing helix chain 'D' and resid 229 through 253 Processing helix chain 'D' and resid 259 through 261 No H-bonds generated for 'chain 'D' and resid 259 through 261' Processing helix chain 'D' and resid 264 through 275 Processing helix chain 'D' and resid 288 through 347 removed outlier: 4.216A pdb=" N ILE D 300 " --> pdb=" O THR D 296 " (cutoff:3.500A) Proline residue: D 308 - end of helix Proline residue: D 335 - end of helix Processing helix chain 'D' and resid 357 through 366 removed outlier: 4.484A pdb=" N TYR D 362 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR D 363 " --> pdb=" O THR D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 558 Processing helix chain 'D' and resid 564 through 599 Proline residue: D 597 - end of helix Processing helix chain 'F' and resid 7 through 20 Processing helix chain 'F' and resid 30 through 40 Processing helix chain 'F' and resid 46 through 56 Processing helix chain 'F' and resid 66 through 74 Processing helix chain 'F' and resid 77 through 80 No H-bonds generated for 'chain 'F' and resid 77 through 80' Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'F' and resid 103 through 111 removed outlier: 3.976A pdb=" N THR F 111 " --> pdb=" O ARG F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 129 Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'G' and resid 71 through 85 Processing helix chain 'G' and resid 91 through 114 Processing helix chain 'G' and resid 119 through 149 removed outlier: 3.981A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLY G 149 " --> pdb=" O ILE G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 164 Processing helix chain 'G' and resid 167 through 183 Processing helix chain 'G' and resid 196 through 212 removed outlier: 4.513A pdb=" N ASP G 212 " --> pdb=" O MET G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 227 Processing helix chain 'G' and resid 229 through 253 Processing helix chain 'G' and resid 259 through 261 No H-bonds generated for 'chain 'G' and resid 259 through 261' Processing helix chain 'G' and resid 264 through 275 Processing helix chain 'G' and resid 288 through 347 removed outlier: 4.289A pdb=" N ILE G 300 " --> pdb=" O THR G 296 " (cutoff:3.500A) Proline residue: G 308 - end of helix Proline residue: G 335 - end of helix Processing helix chain 'G' and resid 357 through 366 removed outlier: 4.540A pdb=" N TYR G 362 " --> pdb=" O SER G 358 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR G 363 " --> pdb=" O THR G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 558 Processing helix chain 'G' and resid 564 through 599 Proline residue: G 597 - end of helix Processing helix chain 'H' and resid 7 through 20 Processing helix chain 'H' and resid 30 through 40 Processing helix chain 'H' and resid 46 through 56 Processing helix chain 'H' and resid 66 through 74 Processing helix chain 'H' and resid 77 through 80 No H-bonds generated for 'chain 'H' and resid 77 through 80' Processing helix chain 'H' and resid 83 through 93 Processing helix chain 'H' and resid 103 through 111 removed outlier: 3.985A pdb=" N THR H 111 " --> pdb=" O ARG H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 129 Processing helix chain 'H' and resid 139 through 147 Processing helix chain 'E' and resid 7 through 20 Processing helix chain 'E' and resid 30 through 40 Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 66 through 73 Processing helix chain 'E' and resid 77 through 80 No H-bonds generated for 'chain 'E' and resid 77 through 80' Processing helix chain 'E' and resid 83 through 93 Processing helix chain 'E' and resid 103 through 111 removed outlier: 3.876A pdb=" N THR E 111 " --> pdb=" O ARG E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 129 Processing helix chain 'E' and resid 139 through 147 1103 hydrogen bonds defined for protein. 3309 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: 10.89 Time building geometry restraints manager: 26.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15592 1.03 - 1.23: 47 1.23 - 1.42: 7001 1.42 - 1.62: 9300 1.62 - 1.81: 164 Bond restraints: 32104 Sorted by residual: bond pdb=" O11 PIO G 802 " pdb=" P1 PIO G 802 " ideal model delta sigma weight residual 1.510 1.459 0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" O41 PIO A 802 " pdb=" P4 PIO A 802 " ideal model delta sigma weight residual 1.510 1.459 0.051 2.00e-02 2.50e+03 6.54e+00 bond pdb=" O42 PIO G 802 " pdb=" P4 PIO G 802 " ideal model delta sigma weight residual 1.510 1.459 0.051 2.00e-02 2.50e+03 6.53e+00 bond pdb=" O11 PIO D 802 " pdb=" P1 PIO D 802 " ideal model delta sigma weight residual 1.510 1.459 0.051 2.00e-02 2.50e+03 6.49e+00 bond pdb=" O12 PIO A 802 " pdb=" P1 PIO A 802 " ideal model delta sigma weight residual 1.510 1.459 0.051 2.00e-02 2.50e+03 6.48e+00 ... (remaining 32099 not shown) Histogram of bond angle deviations from ideal: 99.01 - 115.09: 39505 115.09 - 131.17: 18098 131.17 - 147.25: 65 147.25 - 163.33: 0 163.33 - 179.41: 4 Bond angle restraints: 57672 Sorted by residual: angle pdb=" CB LYS F 31 " pdb=" CG LYS F 31 " pdb=" CD LYS F 31 " ideal model delta sigma weight residual 111.30 120.08 -8.78 2.30e+00 1.89e-01 1.46e+01 angle pdb=" N ARG A 213 " pdb=" CA ARG A 213 " pdb=" CB ARG A 213 " ideal model delta sigma weight residual 114.17 109.84 4.33 1.14e+00 7.69e-01 1.44e+01 angle pdb=" N ARG B 213 " pdb=" CA ARG B 213 " pdb=" CB ARG B 213 " ideal model delta sigma weight residual 114.17 109.94 4.23 1.14e+00 7.69e-01 1.38e+01 angle pdb=" CD2 TRP A 270 " pdb=" CE3 TRP A 270 " pdb=" CZ3 TRP A 270 " ideal model delta sigma weight residual 118.60 122.50 -3.90 1.30e+00 5.92e-01 9.01e+00 angle pdb=" CB MET F 125 " pdb=" CG MET F 125 " pdb=" SD MET F 125 " ideal model delta sigma weight residual 112.70 121.65 -8.95 3.00e+00 1.11e-01 8.89e+00 ... (remaining 57667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 14337 35.81 - 71.62: 531 71.62 - 107.43: 40 107.43 - 143.24: 4 143.24 - 179.05: 4 Dihedral angle restraints: 14916 sinusoidal: 7976 harmonic: 6940 Sorted by residual: dihedral pdb=" CD ARG B 87 " pdb=" NE ARG B 87 " pdb=" CZ ARG B 87 " pdb=" NH1 ARG B 87 " ideal model delta sinusoidal sigma weight residual 0.00 179.05 -179.05 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG A 87 " pdb=" NE ARG A 87 " pdb=" CZ ARG A 87 " pdb=" NH1 ARG A 87 " ideal model delta sinusoidal sigma weight residual 0.00 178.99 -178.99 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG G 87 " pdb=" NE ARG G 87 " pdb=" CZ ARG G 87 " pdb=" NH1 ARG G 87 " ideal model delta sinusoidal sigma weight residual 0.00 178.98 -178.98 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 14913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.999: 2452 0.999 - 1.998: 0 1.998 - 2.997: 0 2.997 - 3.997: 0 3.997 - 4.996: 4 Chirality restraints: 2456 Sorted by residual: chirality pdb=" C4 PIO D 802 " pdb=" C3 PIO D 802 " pdb=" C5 PIO D 802 " pdb=" O4 PIO D 802 " both_signs ideal model delta sigma weight residual False 2.50 -2.49 5.00 2.00e-01 2.50e+01 6.24e+02 chirality pdb=" C4 PIO A 802 " pdb=" C3 PIO A 802 " pdb=" C5 PIO A 802 " pdb=" O4 PIO A 802 " both_signs ideal model delta sigma weight residual False 2.50 -2.49 4.99 2.00e-01 2.50e+01 6.24e+02 chirality pdb=" C4 PIO G 802 " pdb=" C3 PIO G 802 " pdb=" C5 PIO G 802 " pdb=" O4 PIO G 802 " both_signs ideal model delta sigma weight residual False 2.50 -2.49 4.99 2.00e-01 2.50e+01 6.23e+02 ... (remaining 2453 not shown) Planarity restraints: 4716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN H 43 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.83e+00 pdb=" C ASN H 43 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN H 43 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO H 44 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 43 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.72e+00 pdb=" C ASN F 43 " 0.041 2.00e-02 2.50e+03 pdb=" O ASN F 43 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO F 44 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN H 43 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO H 44 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO H 44 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 44 " -0.024 5.00e-02 4.00e+02 ... (remaining 4713 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1263 2.13 - 2.75: 58941 2.75 - 3.36: 97515 3.36 - 3.98: 114365 3.98 - 4.60: 180943 Nonbonded interactions: 453027 Sorted by model distance: nonbonded pdb="HE22 GLN A 341 " pdb=" O LEU E 113 " model vdw 1.512 1.850 nonbonded pdb=" OE1 GLU C 46 " pdb=" H GLU C 46 " model vdw 1.524 1.850 nonbonded pdb="HE22 GLN D 341 " pdb=" O LEU F 113 " model vdw 1.546 1.850 nonbonded pdb="HE22 GLN G 341 " pdb=" O LEU H 113 " model vdw 1.550 1.850 nonbonded pdb="HE22 GLN B 341 " pdb=" O LEU C 113 " model vdw 1.564 1.850 ... (remaining 453022 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.460 Extract box with map and model: 4.580 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 95.970 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.160 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16484 Z= 0.254 Angle : 0.646 8.946 22200 Z= 0.342 Chirality : 0.204 4.996 2456 Planarity : 0.005 0.058 2780 Dihedral : 18.556 179.049 5952 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.60 % Allowed : 25.78 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.19), residues: 1956 helix: 1.82 (0.13), residues: 1560 sheet: None (None), residues: 0 loop : 0.23 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 288 HIS 0.002 0.001 HIS G 575 PHE 0.016 0.001 PHE C 13 TYR 0.010 0.001 TYR G 362 ARG 0.013 0.001 ARG D 588 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 268 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 258 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 73 MET cc_start: 0.6470 (mmm) cc_final: 0.4870 (mmm) REVERT: H 31 LYS cc_start: 0.8493 (mmmt) cc_final: 0.8210 (mppt) REVERT: E 31 LYS cc_start: 0.8514 (mmmt) cc_final: 0.8144 (mppt) REVERT: E 87 ARG cc_start: 0.9006 (mmm-85) cc_final: 0.8770 (mmm-85) outliers start: 10 outliers final: 9 residues processed: 263 average time/residue: 0.8027 time to fit residues: 289.9994 Evaluate side-chains 227 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 218 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 571 TYR Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 571 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 6.9990 chunk 148 optimal weight: 0.9980 chunk 82 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 177 optimal weight: 20.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 GLN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16484 Z= 0.223 Angle : 0.546 8.154 22200 Z= 0.294 Chirality : 0.034 0.164 2456 Planarity : 0.004 0.042 2780 Dihedral : 12.053 178.529 2246 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.91 % Allowed : 24.82 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.19), residues: 1956 helix: 1.89 (0.13), residues: 1560 sheet: None (None), residues: 0 loop : 0.16 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 288 HIS 0.004 0.001 HIS B 96 PHE 0.016 0.001 PHE E 13 TYR 0.008 0.001 TYR G 362 ARG 0.006 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 226 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: B 109 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6654 (tp) REVERT: B 546 MET cc_start: 0.8561 (tpt) cc_final: 0.8303 (tpt) REVERT: G 546 MET cc_start: 0.8599 (tpt) cc_final: 0.8398 (tpt) REVERT: H 31 LYS cc_start: 0.8338 (mmmt) cc_final: 0.8101 (mppt) REVERT: E 23 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7530 (t0) REVERT: E 31 LYS cc_start: 0.8464 (mmmt) cc_final: 0.8201 (mppt) outliers start: 32 outliers final: 21 residues processed: 248 average time/residue: 0.7362 time to fit residues: 258.8748 Evaluate side-chains 243 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 220 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 571 TYR Chi-restraints excluded: chain F residue 9 GLN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 571 TYR Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 92 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 121 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 178 optimal weight: 9.9990 chunk 192 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 176 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16484 Z= 0.239 Angle : 0.525 5.336 22200 Z= 0.290 Chirality : 0.033 0.162 2456 Planarity : 0.004 0.043 2780 Dihedral : 11.817 178.635 2242 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.51 % Allowed : 23.51 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.19), residues: 1956 helix: 1.89 (0.13), residues: 1560 sheet: None (None), residues: 0 loop : 0.19 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 288 HIS 0.004 0.001 HIS A 96 PHE 0.011 0.001 PHE E 13 TYR 0.008 0.001 TYR D 251 ARG 0.007 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 225 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: B 109 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6688 (tp) REVERT: B 183 LEU cc_start: -0.0586 (OUTLIER) cc_final: -0.0889 (tp) REVERT: H 31 LYS cc_start: 0.8333 (mmmt) cc_final: 0.8118 (mppt) REVERT: H 73 MET cc_start: 0.8273 (mmm) cc_final: 0.7389 (mmm) REVERT: E 23 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7490 (t0) REVERT: E 31 LYS cc_start: 0.8474 (mmmt) cc_final: 0.8219 (mppt) outliers start: 42 outliers final: 26 residues processed: 255 average time/residue: 0.7875 time to fit residues: 282.4411 Evaluate side-chains 238 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 209 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 571 TYR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 92 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 189 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16484 Z= 0.261 Angle : 0.536 5.797 22200 Z= 0.297 Chirality : 0.034 0.169 2456 Planarity : 0.004 0.043 2780 Dihedral : 11.749 178.573 2238 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.74 % Allowed : 23.03 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.19), residues: 1956 helix: 1.83 (0.13), residues: 1560 sheet: None (None), residues: 0 loop : 0.14 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 288 HIS 0.004 0.001 HIS B 96 PHE 0.010 0.001 PHE E 13 TYR 0.008 0.001 TYR D 251 ARG 0.007 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 221 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6685 (tp) REVERT: B 183 LEU cc_start: -0.0523 (OUTLIER) cc_final: -0.0827 (tp) REVERT: B 546 MET cc_start: 0.8660 (tpt) cc_final: 0.8422 (tpt) REVERT: F 9 GLN cc_start: 0.4725 (OUTLIER) cc_final: 0.4334 (mp10) REVERT: F 73 MET cc_start: 0.6298 (mmm) cc_final: 0.5648 (mmm) REVERT: H 31 LYS cc_start: 0.8371 (mmmt) cc_final: 0.8171 (mppt) REVERT: H 73 MET cc_start: 0.7741 (mmm) cc_final: 0.7407 (mmm) REVERT: E 14 LYS cc_start: 0.8853 (tppt) cc_final: 0.8373 (mmtm) REVERT: E 23 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7505 (t0) REVERT: E 31 LYS cc_start: 0.8450 (mmmt) cc_final: 0.8192 (mppt) outliers start: 46 outliers final: 37 residues processed: 255 average time/residue: 0.7283 time to fit residues: 260.7273 Evaluate side-chains 254 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 213 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 571 TYR Chi-restraints excluded: chain F residue 9 GLN Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 96 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 170 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 overall best weight: 6.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 16484 Z= 0.439 Angle : 0.625 6.379 22200 Z= 0.357 Chirality : 0.039 0.217 2456 Planarity : 0.004 0.043 2780 Dihedral : 11.835 178.768 2238 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.46 % Allowed : 23.03 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.19), residues: 1956 helix: 1.36 (0.13), residues: 1556 sheet: None (None), residues: 0 loop : -0.02 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 344 HIS 0.005 0.001 HIS B 228 PHE 0.016 0.002 PHE A 104 TYR 0.014 0.002 TYR D 251 ARG 0.009 0.001 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 275 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 217 time to evaluate : 2.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: B 109 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6793 (tp) REVERT: B 183 LEU cc_start: -0.0521 (OUTLIER) cc_final: -0.0795 (tp) REVERT: H 31 LYS cc_start: 0.8485 (mmmt) cc_final: 0.8272 (mppt) REVERT: E 23 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7222 (t0) REVERT: E 31 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8300 (mppt) REVERT: E 43 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7742 (t0) outliers start: 58 outliers final: 45 residues processed: 256 average time/residue: 0.7001 time to fit residues: 253.8545 Evaluate side-chains 260 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 211 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 571 TYR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 571 TYR Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 96 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 189 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 99 optimal weight: 0.6980 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16484 Z= 0.303 Angle : 0.566 6.747 22200 Z= 0.317 Chirality : 0.036 0.199 2456 Planarity : 0.004 0.044 2780 Dihedral : 11.715 178.914 2238 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.52 % Allowed : 24.22 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.19), residues: 1956 helix: 1.49 (0.13), residues: 1560 sheet: None (None), residues: 0 loop : -0.06 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 288 HIS 0.003 0.001 HIS D 575 PHE 0.011 0.001 PHE A 104 TYR 0.010 0.001 TYR B 251 ARG 0.007 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 222 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: B 109 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6699 (tp) REVERT: B 183 LEU cc_start: -0.0512 (OUTLIER) cc_final: -0.0798 (tp) REVERT: G 560 ARG cc_start: 0.8470 (mmm160) cc_final: 0.8150 (ttp80) REVERT: H 31 LYS cc_start: 0.8464 (mmmt) cc_final: 0.8257 (mppt) REVERT: E 23 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7401 (t0) REVERT: E 31 LYS cc_start: 0.8532 (mmmt) cc_final: 0.8298 (mppt) outliers start: 59 outliers final: 48 residues processed: 264 average time/residue: 0.7142 time to fit residues: 268.0030 Evaluate side-chains 266 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 215 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 571 TYR Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 96 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16484 Z= 0.266 Angle : 0.560 6.999 22200 Z= 0.311 Chirality : 0.036 0.198 2456 Planarity : 0.004 0.044 2780 Dihedral : 11.465 178.939 2236 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.46 % Allowed : 24.52 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.19), residues: 1956 helix: 1.59 (0.13), residues: 1560 sheet: None (None), residues: 0 loop : -0.06 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 288 HIS 0.003 0.001 HIS A 96 PHE 0.010 0.001 PHE F 69 TYR 0.009 0.001 TYR B 251 ARG 0.008 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 282 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 224 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: B 109 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6750 (tp) REVERT: B 183 LEU cc_start: -0.0492 (OUTLIER) cc_final: -0.0802 (tp) REVERT: B 268 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9026 (mp) REVERT: F 72 MET cc_start: 0.8476 (tmm) cc_final: 0.8268 (tmm) REVERT: G 560 ARG cc_start: 0.8460 (mmm160) cc_final: 0.8170 (ttp80) REVERT: E 23 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7513 (t0) REVERT: E 31 LYS cc_start: 0.8530 (mmmt) cc_final: 0.8287 (mppt) outliers start: 58 outliers final: 52 residues processed: 264 average time/residue: 0.7054 time to fit residues: 264.3742 Evaluate side-chains 274 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 218 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 571 TYR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 363 TYR Chi-restraints excluded: chain G residue 571 TYR Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 96 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 7.9990 chunk 75 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 128 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16484 Z= 0.349 Angle : 0.587 6.785 22200 Z= 0.330 Chirality : 0.037 0.201 2456 Planarity : 0.004 0.044 2780 Dihedral : 11.439 179.045 2236 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.94 % Allowed : 24.22 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.19), residues: 1956 helix: 1.50 (0.13), residues: 1560 sheet: None (None), residues: 0 loop : -0.09 (0.36), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 344 HIS 0.003 0.001 HIS B 228 PHE 0.014 0.001 PHE E 142 TYR 0.010 0.001 TYR B 251 ARG 0.009 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 289 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 223 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: B 109 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6729 (tp) REVERT: B 183 LEU cc_start: -0.0517 (OUTLIER) cc_final: -0.0796 (tp) REVERT: B 268 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9054 (mp) REVERT: G 560 ARG cc_start: 0.8487 (mmm160) cc_final: 0.8264 (ttp80) REVERT: E 23 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7346 (t0) REVERT: E 31 LYS cc_start: 0.8561 (mmmt) cc_final: 0.8331 (mppt) outliers start: 66 outliers final: 57 residues processed: 269 average time/residue: 0.6869 time to fit residues: 262.5001 Evaluate side-chains 282 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 221 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 571 TYR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 363 TYR Chi-restraints excluded: chain G residue 571 TYR Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 96 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.8980 chunk 180 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 chunk 176 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16484 Z= 0.178 Angle : 0.540 7.937 22200 Z= 0.290 Chirality : 0.034 0.190 2456 Planarity : 0.004 0.044 2780 Dihedral : 11.004 179.258 2236 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.45 % Allowed : 25.48 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.19), residues: 1956 helix: 1.78 (0.13), residues: 1588 sheet: None (None), residues: 0 loop : -0.20 (0.38), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 344 HIS 0.003 0.001 HIS A 96 PHE 0.013 0.001 PHE E 142 TYR 0.008 0.001 TYR A 251 ARG 0.007 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 270 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 229 time to evaluate : 2.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LEU cc_start: 0.8674 (mm) cc_final: 0.8426 (mm) REVERT: A 268 LEU cc_start: 0.8875 (tt) cc_final: 0.8447 (mt) REVERT: B 109 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6710 (tp) REVERT: B 183 LEU cc_start: -0.0639 (OUTLIER) cc_final: -0.0937 (tp) REVERT: D 171 ILE cc_start: 0.7249 (mt) cc_final: 0.7000 (tt) REVERT: G 268 LEU cc_start: 0.8913 (tt) cc_final: 0.8476 (mt) REVERT: G 560 ARG cc_start: 0.8471 (mmm160) cc_final: 0.8238 (ttp80) REVERT: H 8 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8486 (pm20) REVERT: E 14 LYS cc_start: 0.8817 (mmmt) cc_final: 0.8578 (mmtm) outliers start: 41 outliers final: 36 residues processed: 258 average time/residue: 0.7716 time to fit residues: 283.0476 Evaluate side-chains 258 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 219 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 571 TYR Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 96 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 129 optimal weight: 0.7980 chunk 195 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 chunk 155 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16484 Z= 0.203 Angle : 0.546 9.726 22200 Z= 0.296 Chirality : 0.034 0.189 2456 Planarity : 0.004 0.053 2780 Dihedral : 10.904 179.227 2236 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.51 % Allowed : 25.72 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.19), residues: 1956 helix: 1.84 (0.13), residues: 1588 sheet: None (None), residues: 0 loop : -0.18 (0.38), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 344 HIS 0.004 0.001 HIS A 96 PHE 0.009 0.001 PHE C 93 TYR 0.016 0.001 TYR B 264 ARG 0.011 0.000 ARG C 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 262 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 220 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6714 (tp) REVERT: B 183 LEU cc_start: -0.0540 (OUTLIER) cc_final: -0.0840 (tp) REVERT: D 171 ILE cc_start: 0.7251 (mt) cc_final: 0.6990 (tt) REVERT: G 268 LEU cc_start: 0.8926 (tt) cc_final: 0.8496 (mt) REVERT: G 560 ARG cc_start: 0.8466 (mmm160) cc_final: 0.8219 (ttp80) REVERT: E 14 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8583 (mmtm) REVERT: E 31 LYS cc_start: 0.8541 (mmmt) cc_final: 0.8334 (mppt) REVERT: E 125 MET cc_start: 0.9196 (mmm) cc_final: 0.8932 (mmm) outliers start: 42 outliers final: 37 residues processed: 250 average time/residue: 0.7181 time to fit residues: 253.6698 Evaluate side-chains 259 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 220 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain D residue 571 TYR Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 363 TYR Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 96 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.144706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.098603 restraints weight = 112881.606| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.06 r_work: 0.3422 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16484 Z= 0.207 Angle : 0.547 8.802 22200 Z= 0.297 Chirality : 0.034 0.184 2456 Planarity : 0.004 0.044 2780 Dihedral : 10.854 179.464 2236 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.45 % Allowed : 25.95 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.19), residues: 1956 helix: 1.95 (0.13), residues: 1564 sheet: None (None), residues: 0 loop : 0.00 (0.37), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 344 HIS 0.003 0.001 HIS B 96 PHE 0.009 0.001 PHE H 142 TYR 0.022 0.001 TYR B 264 ARG 0.009 0.000 ARG D 560 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6821.18 seconds wall clock time: 121 minutes 8.71 seconds (7268.71 seconds total)