Starting phenix.real_space_refine on Fri Mar 22 20:33:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eat_27985/03_2024/8eat_27985.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eat_27985/03_2024/8eat_27985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eat_27985/03_2024/8eat_27985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eat_27985/03_2024/8eat_27985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eat_27985/03_2024/8eat_27985.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eat_27985/03_2024/8eat_27985.pdb" } resolution = 3.1 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= 0.005 sd= 0.194 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 96 5.16 5 C 11238 2.51 5 N 2769 2.21 5 O 3097 1.98 5 H 17463 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 22": "OE1" <-> "OE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 13": "OD1" <-> "OD2" Residue "F PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 98": "OD1" <-> "OD2" Residue "F ASP 106": "OD1" <-> "OD2" Residue "b ASP 213": "OD1" <-> "OD2" Residue "b ASP 248": "OD1" <-> "OD2" Residue "c PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c GLU 131": "OE1" <-> "OE2" Residue "d PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d ASP 155": "OD1" <-> "OD2" Residue "d TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d GLU 274": "OE1" <-> "OE2" Residue "d GLU 280": "OE1" <-> "OE2" Residue "g TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i ASP 48": "OD1" <-> "OD2" Residue "i TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j GLU 3": "OE1" <-> "OE2" Residue "j PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l ASP 157": "OD1" <-> "OD2" Residue "m GLU 3": "OE1" <-> "OE2" Residue "m TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n GLU 3": "OE1" <-> "OE2" Residue "n ASP 157": "OD1" <-> "OD2" Residue "o TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 34663 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1914 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1253 Classifications: {'peptide': 98} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 95 Chain: "F" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1598 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "b" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 730 Classifications: {'peptide': 46} Link IDs: {'TRANS': 45} Chain: "c" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3008 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 195} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "d" Number of atoms: 5233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5233 Classifications: {'peptide': 338} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 41 Chain: "g" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2334 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "h" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2334 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "i" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2334 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "j" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2334 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "k" Number of atoms: 2329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2329 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "l" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2302 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "m" Number of atoms: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2339 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "n" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2313 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "o" Number of atoms: 2308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2308 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 16.58, per 1000 atoms: 0.48 Number of scatterers: 34663 At special positions: 0 Unit cell: (155.53, 107.12, 95.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 O 3097 8.00 N 2769 7.00 C 11238 6.00 H 17463 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: 32.28 Conformation dependent library (CDL) restraints added in 3.9 seconds 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4190 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 3 sheets defined 79.9% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 15 through 50 removed outlier: 3.938A pdb=" N ARG A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLY A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP A 40 " --> pdb=" O LYS A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 removed outlier: 4.192A pdb=" N ASP A 54 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 137 Processing helix chain 'A' and resid 143 through 177 removed outlier: 3.717A pdb=" N ARG A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) Proline residue: A 158 - end of helix Processing helix chain 'B' and resid 7 through 19 removed outlier: 3.609A pdb=" N ASN B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 38 Processing helix chain 'B' and resid 41 through 53 Processing helix chain 'B' and resid 84 through 105 removed outlier: 3.667A pdb=" N GLU B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 24 Processing helix chain 'F' and resid 46 through 60 Processing helix chain 'F' and resid 71 through 77 Processing helix chain 'F' and resid 77 through 84 Processing helix chain 'F' and resid 102 through 105 Processing helix chain 'F' and resid 106 through 114 removed outlier: 3.629A pdb=" N LYS F 110 " --> pdb=" O ASP F 106 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 246 Processing helix chain 'c' and resid 17 through 39 Processing helix chain 'c' and resid 41 through 45 Processing helix chain 'c' and resid 46 through 54 Processing helix chain 'c' and resid 55 through 91 removed outlier: 3.662A pdb=" N TRP c 59 " --> pdb=" O SER c 55 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 123 removed outlier: 4.410A pdb=" N LYS c 99 " --> pdb=" O ARG c 95 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE c 102 " --> pdb=" O THR c 98 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER c 103 " --> pdb=" O LYS c 99 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE c 104 " --> pdb=" O ASN c 100 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL c 110 " --> pdb=" O PHE c 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA c 111 " --> pdb=" O CYS c 107 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL c 120 " --> pdb=" O ILE c 116 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER c 123 " --> pdb=" O ILE c 119 " (cutoff:3.500A) Processing helix chain 'c' and resid 135 through 177 Processing helix chain 'c' and resid 177 through 206 removed outlier: 3.998A pdb=" N PHE c 181 " --> pdb=" O ASP c 177 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL c 182 " --> pdb=" O SER c 178 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS c 183 " --> pdb=" O ALA c 179 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE c 187 " --> pdb=" O LYS c 183 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU c 194 " --> pdb=" O PHE c 190 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY c 195 " --> pdb=" O GLY c 191 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 7 removed outlier: 4.339A pdb=" N ASN d 7 " --> pdb=" O GLY d 3 " (cutoff:3.500A) Processing helix chain 'd' and resid 10 through 23 Processing helix chain 'd' and resid 26 through 36 Processing helix chain 'd' and resid 38 through 47 Processing helix chain 'd' and resid 64 through 86 Processing helix chain 'd' and resid 89 through 116 removed outlier: 3.715A pdb=" N GLY d 101 " --> pdb=" O TYR d 97 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR d 102 " --> pdb=" O ILE d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 119 through 124 Processing helix chain 'd' and resid 135 through 140 removed outlier: 4.367A pdb=" N SER d 140 " --> pdb=" O LEU d 136 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 156 Processing helix chain 'd' and resid 158 through 163 removed outlier: 3.729A pdb=" N LYS d 163 " --> pdb=" O PRO d 160 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 200 Processing helix chain 'd' and resid 201 through 227 Processing helix chain 'd' and resid 234 through 242 Processing helix chain 'd' and resid 250 through 259 Processing helix chain 'd' and resid 261 through 271 Processing helix chain 'd' and resid 283 through 300 Processing helix chain 'd' and resid 306 through 333 removed outlier: 4.084A pdb=" N TRP d 310 " --> pdb=" O ILE d 306 " (cutoff:3.500A) Processing helix chain 'd' and resid 334 through 338 Processing helix chain 'g' and resid 8 through 44 removed outlier: 4.262A pdb=" N PHE g 12 " --> pdb=" O TYR g 8 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY g 13 " --> pdb=" O ALA g 9 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE g 21 " --> pdb=" O CYS g 17 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR g 24 " --> pdb=" O ALA g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 54 through 74 Processing helix chain 'g' and resid 83 through 122 removed outlier: 3.887A pdb=" N ARG g 117 " --> pdb=" O ASP g 113 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER g 120 " --> pdb=" O VAL g 116 " (cutoff:3.500A) Processing helix chain 'g' and resid 124 through 154 removed outlier: 4.262A pdb=" N GLY g 128 " --> pdb=" O ARG g 124 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU g 139 " --> pdb=" O PHE g 135 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY g 140 " --> pdb=" O ALA g 136 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU g 141 " --> pdb=" O GLU g 137 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL g 146 " --> pdb=" O TYR g 142 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA g 154 " --> pdb=" O LEU g 150 " (cutoff:3.500A) Processing helix chain 'h' and resid 8 through 43 removed outlier: 4.079A pdb=" N PHE h 12 " --> pdb=" O TYR h 8 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY h 13 " --> pdb=" O ALA h 9 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE h 21 " --> pdb=" O CYS h 17 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR h 24 " --> pdb=" O ALA h 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 46 through 48 No H-bonds generated for 'chain 'h' and resid 46 through 48' Processing helix chain 'h' and resid 49 through 54 Processing helix chain 'h' and resid 54 through 76 Processing helix chain 'h' and resid 83 through 122 removed outlier: 3.951A pdb=" N SER h 120 " --> pdb=" O VAL h 116 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN h 121 " --> pdb=" O ARG h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 124 through 154 removed outlier: 4.259A pdb=" N GLY h 128 " --> pdb=" O ARG h 124 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU h 139 " --> pdb=" O PHE h 135 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY h 140 " --> pdb=" O ALA h 136 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY h 143 " --> pdb=" O LEU h 139 " (cutoff:3.500A) Processing helix chain 'i' and resid 8 through 43 removed outlier: 4.071A pdb=" N PHE i 12 " --> pdb=" O TYR i 8 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY i 13 " --> pdb=" O ALA i 9 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE i 21 " --> pdb=" O CYS i 17 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR i 24 " --> pdb=" O ALA i 20 " (cutoff:3.500A) Processing helix chain 'i' and resid 46 through 48 No H-bonds generated for 'chain 'i' and resid 46 through 48' Processing helix chain 'i' and resid 49 through 54 Processing helix chain 'i' and resid 54 through 76 Processing helix chain 'i' and resid 83 through 122 removed outlier: 3.854A pdb=" N SER i 120 " --> pdb=" O VAL i 116 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN i 121 " --> pdb=" O ARG i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 125 through 155 removed outlier: 3.894A pdb=" N LEU i 139 " --> pdb=" O PHE i 135 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY i 140 " --> pdb=" O ALA i 136 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR i 155 " --> pdb=" O ASN i 151 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 44 removed outlier: 4.193A pdb=" N PHE j 12 " --> pdb=" O TYR j 8 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY j 13 " --> pdb=" O ALA j 9 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE j 21 " --> pdb=" O CYS j 17 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR j 24 " --> pdb=" O ALA j 20 " (cutoff:3.500A) Processing helix chain 'j' and resid 46 through 48 No H-bonds generated for 'chain 'j' and resid 46 through 48' Processing helix chain 'j' and resid 49 through 54 Processing helix chain 'j' and resid 54 through 77 Processing helix chain 'j' and resid 83 through 120 Processing helix chain 'j' and resid 124 through 153 removed outlier: 4.299A pdb=" N GLY j 128 " --> pdb=" O ARG j 124 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU j 139 " --> pdb=" O PHE j 135 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY j 140 " --> pdb=" O ALA j 136 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 43 removed outlier: 4.248A pdb=" N PHE k 12 " --> pdb=" O TYR k 8 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY k 13 " --> pdb=" O ALA k 9 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE k 23 " --> pdb=" O SER k 19 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR k 24 " --> pdb=" O ALA k 20 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 50 Processing helix chain 'k' and resid 54 through 78 Processing helix chain 'k' and resid 83 through 122 removed outlier: 3.805A pdb=" N GLN k 121 " --> pdb=" O ARG k 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 124 through 153 removed outlier: 4.234A pdb=" N GLY k 128 " --> pdb=" O ARG k 124 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU k 139 " --> pdb=" O PHE k 135 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY k 140 " --> pdb=" O ALA k 136 " (cutoff:3.500A) Processing helix chain 'l' and resid 8 through 43 removed outlier: 4.364A pdb=" N PHE l 12 " --> pdb=" O TYR l 8 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY l 13 " --> pdb=" O ALA l 9 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE l 21 " --> pdb=" O CYS l 17 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR l 24 " --> pdb=" O ALA l 20 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR l 30 " --> pdb=" O LEU l 26 " (cutoff:3.500A) Processing helix chain 'l' and resid 46 through 50 removed outlier: 3.551A pdb=" N LEU l 49 " --> pdb=" O ARG l 46 " (cutoff:3.500A) Processing helix chain 'l' and resid 54 through 77 Processing helix chain 'l' and resid 83 through 120 removed outlier: 3.615A pdb=" N SER l 120 " --> pdb=" O VAL l 116 " (cutoff:3.500A) Processing helix chain 'l' and resid 124 through 154 removed outlier: 4.115A pdb=" N GLY l 128 " --> pdb=" O ARG l 124 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY l 140 " --> pdb=" O ALA l 136 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU l 150 " --> pdb=" O VAL l 146 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA l 154 " --> pdb=" O LEU l 150 " (cutoff:3.500A) Processing helix chain 'm' and resid 8 through 43 removed outlier: 4.304A pdb=" N PHE m 12 " --> pdb=" O TYR m 8 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY m 13 " --> pdb=" O ALA m 9 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE m 21 " --> pdb=" O CYS m 17 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR m 24 " --> pdb=" O ALA m 20 " (cutoff:3.500A) Processing helix chain 'm' and resid 46 through 48 No H-bonds generated for 'chain 'm' and resid 46 through 48' Processing helix chain 'm' and resid 49 through 54 Processing helix chain 'm' and resid 54 through 76 removed outlier: 3.702A pdb=" N ILE m 63 " --> pdb=" O MET m 59 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA m 64 " --> pdb=" O ALA m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 83 through 120 removed outlier: 3.722A pdb=" N ALA m 103 " --> pdb=" O LEU m 99 " (cutoff:3.500A) Processing helix chain 'm' and resid 122 through 124 No H-bonds generated for 'chain 'm' and resid 122 through 124' Processing helix chain 'm' and resid 125 through 154 removed outlier: 3.913A pdb=" N LEU m 139 " --> pdb=" O PHE m 135 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY m 140 " --> pdb=" O ALA m 136 " (cutoff:3.500A) Processing helix chain 'n' and resid 8 through 44 removed outlier: 4.247A pdb=" N PHE n 12 " --> pdb=" O TYR n 8 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY n 13 " --> pdb=" O ALA n 9 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL n 44 " --> pdb=" O CYS n 40 " (cutoff:3.500A) Processing helix chain 'n' and resid 49 through 54 Processing helix chain 'n' and resid 54 through 78 Processing helix chain 'n' and resid 83 through 122 removed outlier: 3.872A pdb=" N ARG n 117 " --> pdb=" O ASP n 113 " (cutoff:3.500A) Processing helix chain 'n' and resid 125 through 154 removed outlier: 3.980A pdb=" N LEU n 139 " --> pdb=" O PHE n 135 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY n 140 " --> pdb=" O ALA n 136 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 48 removed outlier: 4.069A pdb=" N PHE o 18 " --> pdb=" O TYR o 14 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 51 No H-bonds generated for 'chain 'o' and resid 49 through 51' Processing helix chain 'o' and resid 60 through 83 Processing helix chain 'o' and resid 91 through 122 Processing helix chain 'o' and resid 130 through 132 No H-bonds generated for 'chain 'o' and resid 130 through 132' Processing helix chain 'o' and resid 133 through 164 removed outlier: 3.622A pdb=" N LEU o 139 " --> pdb=" O VAL o 135 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU o 147 " --> pdb=" O PHE o 143 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY o 148 " --> pdb=" O SER o 144 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY o 151 " --> pdb=" O LEU o 147 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR o 160 " --> pdb=" O LEU o 156 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 77 Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 40 Processing sheet with id=AA3, first strand: chain 'F' and resid 37 through 39 removed outlier: 6.441A pdb=" N LEU F 7 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE F 66 " --> pdb=" O LEU F 7 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA F 65 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU F 92 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU F 67 " --> pdb=" O LEU F 92 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE F 94 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE F 69 " --> pdb=" O ILE F 94 " (cutoff:3.500A) 1433 hydrogen bonds defined for protein. 4248 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: 14.09 Time building geometry restraints manager: 33.51 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: 17407 1.03 - 1.23: 126 1.23 - 1.42: 7036 1.42 - 1.62: 10258 1.62 - 1.81: 136 Bond restraints: 34963 Sorted by residual: bond pdb=" CB GLN n 82 " pdb=" CG GLN n 82 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.73e+00 bond pdb=" N GLY o 106 " pdb=" CA GLY o 106 " ideal model delta sigma weight residual 1.454 1.440 0.014 1.24e-02 6.50e+03 1.35e+00 bond pdb=" CB VAL o 105 " pdb=" CG2 VAL o 105 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.28e+00 bond pdb=" N PRO B 68 " pdb=" CA PRO B 68 " ideal model delta sigma weight residual 1.469 1.483 -0.014 1.28e-02 6.10e+03 1.20e+00 bond pdb=" N GLY o 117 " pdb=" CA GLY o 117 " ideal model delta sigma weight residual 1.454 1.441 0.013 1.24e-02 6.50e+03 1.11e+00 ... (remaining 34958 not shown) Histogram of bond angle deviations from ideal: 99.86 - 106.69: 358 106.69 - 113.52: 41902 113.52 - 120.35: 12010 120.35 - 127.17: 8924 127.17 - 134.00: 99 Bond angle restraints: 63293 Sorted by residual: angle pdb=" C ILE j 54 " pdb=" N VAL j 55 " pdb=" CA VAL j 55 " ideal model delta sigma weight residual 120.33 122.66 -2.33 8.00e-01 1.56e+00 8.48e+00 angle pdb=" N VAL l 146 " pdb=" CA VAL l 146 " pdb=" C VAL l 146 " ideal model delta sigma weight residual 111.91 109.40 2.51 8.90e-01 1.26e+00 7.97e+00 angle pdb=" N VAL m 55 " pdb=" CA VAL m 55 " pdb=" CB VAL m 55 " ideal model delta sigma weight residual 110.50 112.23 -1.73 6.30e-01 2.52e+00 7.52e+00 angle pdb=" C VAL m 55 " pdb=" CA VAL m 55 " pdb=" CB VAL m 55 " ideal model delta sigma weight residual 114.35 111.50 2.85 1.06e+00 8.90e-01 7.25e+00 angle pdb=" C VAL i 55 " pdb=" CA VAL i 55 " pdb=" CB VAL i 55 " ideal model delta sigma weight residual 114.00 110.62 3.38 1.31e+00 5.83e-01 6.65e+00 ... (remaining 63288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 14844 17.96 - 35.92: 933 35.92 - 53.87: 414 53.87 - 71.83: 222 71.83 - 89.79: 27 Dihedral angle restraints: 16440 sinusoidal: 8733 harmonic: 7707 Sorted by residual: dihedral pdb=" CA ASN A 49 " pdb=" C ASN A 49 " pdb=" N TYR A 50 " pdb=" CA TYR A 50 " ideal model delta harmonic sigma weight residual 180.00 157.21 22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLY o 123 " pdb=" C GLY o 123 " pdb=" N VAL o 124 " pdb=" CA VAL o 124 " ideal model delta harmonic sigma weight residual 180.00 161.06 18.94 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA VAL F 10 " pdb=" C VAL F 10 " pdb=" N ILE F 11 " pdb=" CA ILE F 11 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 16437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1715 0.026 - 0.051: 728 0.051 - 0.077: 313 0.077 - 0.103: 111 0.103 - 0.129: 33 Chirality restraints: 2900 Sorted by residual: chirality pdb=" CA ILE F 28 " pdb=" N ILE F 28 " pdb=" C ILE F 28 " pdb=" CB ILE F 28 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE F 69 " pdb=" N ILE F 69 " pdb=" C ILE F 69 " pdb=" CB ILE F 69 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA ILE d 200 " pdb=" N ILE d 200 " pdb=" C ILE d 200 " pdb=" CB ILE d 200 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 2897 not shown) Planarity restraints: 5232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS o 52 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO o 53 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO o 53 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO o 53 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE d 192 " -0.019 2.00e-02 2.50e+03 1.29e-02 4.96e+00 pdb=" CG PHE d 192 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE d 192 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE d 192 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE d 192 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE d 192 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE d 192 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE d 192 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE d 192 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE d 192 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE d 192 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE d 192 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP c 77 " -0.013 2.00e-02 2.50e+03 1.10e-02 4.85e+00 pdb=" CG TRP c 77 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP c 77 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP c 77 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP c 77 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP c 77 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP c 77 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP c 77 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP c 77 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP c 77 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP c 77 " -0.008 2.00e-02 2.50e+03 pdb=" HE1 TRP c 77 " -0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP c 77 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP c 77 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP c 77 " -0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP c 77 " -0.000 2.00e-02 2.50e+03 ... (remaining 5229 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 517 2.08 - 2.71: 60505 2.71 - 3.34: 112190 3.34 - 3.97: 139754 3.97 - 4.60: 226135 Nonbonded interactions: 539101 Sorted by model distance: nonbonded pdb="HE22 GLN n 82 " pdb=" OE1 GLN n 90 " model vdw 1.454 1.850 nonbonded pdb=" O ASN c 132 " pdb="HD21 ASN c 138 " model vdw 1.526 1.850 nonbonded pdb=" OD2 ASP d 217 " pdb=" HH TYR d 275 " model vdw 1.639 1.850 nonbonded pdb="HD22 ASN c 138 " pdb=" OXT GLN c 213 " model vdw 1.663 1.850 nonbonded pdb=" O ASP d 298 " pdb=" HG1 THR d 301 " model vdw 1.672 1.850 ... (remaining 539096 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 'g' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name HA )) or resid 3 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 44 or (resid 45 through 4 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 47 or (resid 48 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 49 through 121 or (resid 122 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 123 or (resi \ d 124 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 125 through 159)) selection = (chain 'h' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name HA )) or resid 3 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 44 or (resid 45 through 4 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 47 or (resid 48 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 49 through 121 or (resid 122 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 123 or (resi \ d 124 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 125 through 159)) selection = (chain 'i' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name HA )) or resid 3 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 44 or (resid 45 through 4 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 47 or (resid 48 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 49 through 121 or (resid 122 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 123 or (resi \ d 124 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 125 through 159)) selection = (chain 'j' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name HA )) or resid 3 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 44 or (resid 45 through 4 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 47 or (resid 48 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 49 through 121 or (resid 122 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 123 or (resi \ d 124 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 125 through 159)) selection = (chain 'k' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name HA )) or resid 3 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 44 or (resid 45 through 4 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 47 through 121 or (resid 122 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 123 or (resid 124 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 125 throug \ h 159)) selection = (chain 'l' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name HA )) or resid 3 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 44 or (resid 45 through 4 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 47 through 159)) selection = (chain 'm' and (resid 2 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 44 or (resid 45 through 4 \ 6 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 47 or (resid 48 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 49 through 121 or (resid 122 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 123 or (resi \ d 124 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 125 through 159)) selection = (chain 'n' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name HA )) or resid 3 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 49 through 121 or (resid \ 122 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 123 or (resid 124 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 125 through 159)) } 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: 4.430 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: 0.590 Extract box with map and model: 9.030 Check model and map are aligned: 0.570 Set scattering table: 0.370 Process input model: 115.860 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.140 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:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 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 0.040 17500 Z= 0.268 Angle : 0.544 5.899 23787 Z= 0.329 Chirality : 0.037 0.129 2900 Planarity : 0.004 0.104 2969 Dihedral : 12.777 89.789 6002 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.17), residues: 2313 helix: 0.31 (0.12), residues: 1705 sheet: -0.66 (0.92), residues: 30 loop : -0.37 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP c 77 HIS 0.003 0.001 HIS d 78 PHE 0.038 0.001 PHE d 192 TYR 0.023 0.001 TYR d 185 ARG 0.005 0.000 ARG d 181 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 17 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 233 is missing expected H atoms. Skipping. Residue THR 2 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.7618 time to fit residues: 260.9087 Evaluate side-chains 198 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN l 121 GLN n 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17500 Z= 0.239 Angle : 0.526 7.287 23787 Z= 0.288 Chirality : 0.037 0.129 2900 Planarity : 0.004 0.082 2969 Dihedral : 4.150 52.857 2496 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.63 % Allowed : 3.37 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.61 (0.17), residues: 2313 helix: 1.56 (0.12), residues: 1738 sheet: -0.93 (0.90), residues: 30 loop : -0.28 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP d 312 HIS 0.003 0.001 HIS B 38 PHE 0.029 0.001 PHE c 80 TYR 0.013 0.001 TYR A 50 ARG 0.006 0.000 ARG F 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 17 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 233 is missing expected H atoms. Skipping. Residue THR 2 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 202 time to evaluate : 2.748 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: A 49 ASN cc_start: 0.7868 (m-40) cc_final: 0.7605 (m110) REVERT: g 113 ASP cc_start: 0.7871 (t0) cc_final: 0.7641 (t0) REVERT: n 129 MET cc_start: 0.7094 (ttp) cc_final: 0.6647 (ttp) outliers start: 11 outliers final: 8 residues processed: 207 average time/residue: 0.6724 time to fit residues: 211.9997 Evaluate side-chains 203 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 195 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain b residue 247 LEU Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 151 ASN Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain o residue 89 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 169 optimal weight: 0.0370 chunk 138 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN k 82 GLN o 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17500 Z= 0.213 Angle : 0.480 5.402 23787 Z= 0.265 Chirality : 0.036 0.128 2900 Planarity : 0.004 0.069 2969 Dihedral : 4.040 51.287 2496 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.46 % Allowed : 5.02 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.93 (0.17), residues: 2313 helix: 1.79 (0.12), residues: 1732 sheet: -1.01 (0.89), residues: 30 loop : -0.09 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP c 77 HIS 0.002 0.001 HIS B 38 PHE 0.024 0.001 PHE c 80 TYR 0.012 0.001 TYR A 50 ARG 0.008 0.000 ARG F 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 17 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 233 is missing expected H atoms. Skipping. Residue THR 2 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 204 time to evaluate : 2.682 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: A 49 ASN cc_start: 0.7792 (m-40) cc_final: 0.7590 (m-40) REVERT: g 59 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7578 (mtt) REVERT: j 35 SER cc_start: 0.8805 (t) cc_final: 0.8503 (m) REVERT: n 129 MET cc_start: 0.6982 (ttp) cc_final: 0.6656 (ttp) outliers start: 8 outliers final: 6 residues processed: 209 average time/residue: 0.6873 time to fit residues: 222.3155 Evaluate side-chains 203 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 196 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain h residue 151 ASN Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain o residue 89 ASP Chi-restraints excluded: chain o residue 159 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 216 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 193 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17500 Z= 0.229 Angle : 0.476 5.346 23787 Z= 0.263 Chirality : 0.036 0.128 2900 Planarity : 0.003 0.063 2969 Dihedral : 4.027 50.396 2496 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.74 % Allowed : 5.59 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.99 (0.17), residues: 2313 helix: 1.83 (0.12), residues: 1733 sheet: -1.09 (0.88), residues: 30 loop : -0.05 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP c 77 HIS 0.002 0.001 HIS F 56 PHE 0.025 0.001 PHE c 80 TYR 0.011 0.001 TYR A 50 ARG 0.003 0.000 ARG F 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 17 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 233 is missing expected H atoms. Skipping. Residue THR 2 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 196 time to evaluate : 2.612 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: g 59 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7542 (mtt) REVERT: j 35 SER cc_start: 0.8763 (t) cc_final: 0.8548 (m) REVERT: m 5 CYS cc_start: 0.7661 (p) cc_final: 0.7410 (p) REVERT: n 129 MET cc_start: 0.7021 (ttp) cc_final: 0.6695 (ttp) outliers start: 13 outliers final: 8 residues processed: 203 average time/residue: 0.7163 time to fit residues: 223.5928 Evaluate side-chains 201 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 192 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain b residue 247 LEU Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain d residue 251 LEU Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 151 ASN Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain o residue 89 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 149 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 110 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17500 Z= 0.251 Angle : 0.479 5.118 23787 Z= 0.264 Chirality : 0.036 0.129 2900 Planarity : 0.003 0.056 2969 Dihedral : 4.020 50.089 2496 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.80 % Allowed : 6.39 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 2.02 (0.17), residues: 2313 helix: 1.85 (0.12), residues: 1732 sheet: -1.17 (0.87), residues: 30 loop : -0.04 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP c 77 HIS 0.002 0.001 HIS d 78 PHE 0.027 0.001 PHE c 80 TYR 0.010 0.001 TYR o 127 ARG 0.002 0.000 ARG m 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 17 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 233 is missing expected H atoms. Skipping. Residue THR 2 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 197 time to evaluate : 2.868 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: c 80 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8697 (p90) REVERT: d 128 HIS cc_start: 0.5868 (m170) cc_final: 0.5608 (m170) REVERT: d 179 ILE cc_start: 0.8246 (mm) cc_final: 0.7877 (mm) REVERT: d 223 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7606 (mp) REVERT: g 59 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7429 (mtt) REVERT: l 50 LEU cc_start: 0.8476 (tp) cc_final: 0.8201 (tt) REVERT: m 5 CYS cc_start: 0.7652 (p) cc_final: 0.7381 (p) REVERT: n 129 MET cc_start: 0.7029 (ttp) cc_final: 0.6694 (ttp) outliers start: 14 outliers final: 9 residues processed: 204 average time/residue: 0.6515 time to fit residues: 201.9647 Evaluate side-chains 202 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 190 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain b residue 247 LEU Chi-restraints excluded: chain c residue 80 PHE Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 251 LEU Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 151 ASN Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain o residue 89 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 0.7980 chunk 194 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 216 optimal weight: 0.9980 chunk 179 optimal weight: 0.1980 chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** n 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17500 Z= 0.173 Angle : 0.452 6.279 23787 Z= 0.247 Chirality : 0.036 0.128 2900 Planarity : 0.003 0.054 2969 Dihedral : 3.882 46.594 2496 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.86 % Allowed : 6.96 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 2.32 (0.17), residues: 2313 helix: 2.04 (0.12), residues: 1737 sheet: -1.24 (0.85), residues: 30 loop : 0.16 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 312 HIS 0.006 0.001 HIS o 98 PHE 0.020 0.001 PHE c 80 TYR 0.016 0.001 TYR d 289 ARG 0.002 0.000 ARG d 321 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 17 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 233 is missing expected H atoms. Skipping. Residue THR 2 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 202 time to evaluate : 2.993 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: B 1 MET cc_start: 0.7917 (tpt) cc_final: 0.7571 (tpp) REVERT: c 80 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8649 (p90) REVERT: d 128 HIS cc_start: 0.5856 (m170) cc_final: 0.5603 (m170) REVERT: d 179 ILE cc_start: 0.8225 (mm) cc_final: 0.7862 (mm) REVERT: d 223 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7583 (mp) REVERT: g 59 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7251 (mtt) REVERT: l 50 LEU cc_start: 0.8461 (tp) cc_final: 0.8227 (tt) REVERT: n 129 MET cc_start: 0.7050 (ttp) cc_final: 0.6728 (ttp) outliers start: 15 outliers final: 9 residues processed: 210 average time/residue: 0.6540 time to fit residues: 208.9720 Evaluate side-chains 206 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 194 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain c residue 80 PHE Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 251 LEU Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 151 ASN Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain j residue 45 LEU Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain o residue 89 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 182 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 215 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17500 Z= 0.227 Angle : 0.466 6.058 23787 Z= 0.256 Chirality : 0.036 0.126 2900 Planarity : 0.003 0.049 2969 Dihedral : 3.882 45.309 2496 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.86 % Allowed : 7.59 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 (0.17), residues: 2313 helix: 2.03 (0.12), residues: 1737 sheet: -1.29 (0.83), residues: 30 loop : 0.16 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP d 312 HIS 0.006 0.001 HIS F 56 PHE 0.024 0.001 PHE c 80 TYR 0.011 0.001 TYR d 289 ARG 0.002 0.000 ARG d 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 17 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 233 is missing expected H atoms. Skipping. Residue THR 2 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 193 time to evaluate : 3.006 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: B 1 MET cc_start: 0.7903 (tpt) cc_final: 0.7584 (tpp) REVERT: c 80 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8710 (p90) REVERT: d 128 HIS cc_start: 0.5953 (m170) cc_final: 0.5733 (m170) REVERT: d 179 ILE cc_start: 0.8228 (mm) cc_final: 0.7869 (mm) REVERT: d 223 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7599 (mp) REVERT: g 59 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7293 (mtt) REVERT: l 50 LEU cc_start: 0.8467 (tp) cc_final: 0.8251 (tt) REVERT: n 129 MET cc_start: 0.7078 (ttp) cc_final: 0.6749 (ttp) outliers start: 15 outliers final: 11 residues processed: 202 average time/residue: 0.6796 time to fit residues: 207.5353 Evaluate side-chains 205 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 191 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain c residue 80 PHE Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 251 LEU Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 151 ASN Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain j residue 2 THR Chi-restraints excluded: chain j residue 45 LEU Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain o residue 89 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 169 optimal weight: 0.3980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17500 Z= 0.190 Angle : 0.453 6.083 23787 Z= 0.248 Chirality : 0.036 0.125 2900 Planarity : 0.003 0.049 2969 Dihedral : 3.815 42.250 2496 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.91 % Allowed : 7.93 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 2.46 (0.17), residues: 2313 helix: 2.14 (0.12), residues: 1738 sheet: -1.20 (0.83), residues: 30 loop : 0.20 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 312 HIS 0.007 0.001 HIS F 56 PHE 0.024 0.001 PHE B 93 TYR 0.012 0.001 TYR d 289 ARG 0.003 0.000 ARG F 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 17 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 233 is missing expected H atoms. Skipping. Residue THR 2 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 198 time to evaluate : 2.769 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: B 1 MET cc_start: 0.7873 (tpt) cc_final: 0.7550 (tpp) REVERT: c 80 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.8687 (p90) REVERT: d 128 HIS cc_start: 0.5975 (m170) cc_final: 0.5761 (m170) REVERT: d 179 ILE cc_start: 0.8219 (mm) cc_final: 0.7862 (mm) REVERT: d 223 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7676 (mp) REVERT: m 5 CYS cc_start: 0.7418 (p) cc_final: 0.7159 (p) REVERT: n 129 MET cc_start: 0.7075 (ttp) cc_final: 0.6733 (ttp) REVERT: n 131 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7973 (mp) outliers start: 16 outliers final: 11 residues processed: 208 average time/residue: 0.6966 time to fit residues: 222.1411 Evaluate side-chains 208 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 194 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain c residue 80 PHE Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 251 LEU Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 151 ASN Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain j residue 2 THR Chi-restraints excluded: chain j residue 45 LEU Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 131 LEU Chi-restraints excluded: chain o residue 89 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 181 optimal weight: 0.5980 chunk 190 optimal weight: 3.9990 chunk 200 optimal weight: 0.5980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 156 GLN ** n 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17500 Z= 0.215 Angle : 0.462 5.908 23787 Z= 0.253 Chirality : 0.036 0.126 2900 Planarity : 0.003 0.045 2969 Dihedral : 3.810 40.323 2496 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.97 % Allowed : 7.87 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 2.43 (0.17), residues: 2313 helix: 2.13 (0.12), residues: 1738 sheet: -1.23 (0.84), residues: 30 loop : 0.15 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP d 312 HIS 0.005 0.001 HIS F 56 PHE 0.023 0.001 PHE c 80 TYR 0.012 0.001 TYR d 289 ARG 0.003 0.000 ARG F 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 17 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 233 is missing expected H atoms. Skipping. Residue THR 2 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 199 time to evaluate : 2.795 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: B 1 MET cc_start: 0.7838 (tpt) cc_final: 0.7490 (tpp) REVERT: c 80 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.8736 (p90) REVERT: d 128 HIS cc_start: 0.6017 (m170) cc_final: 0.5807 (m170) REVERT: d 179 ILE cc_start: 0.8194 (mm) cc_final: 0.7836 (mm) REVERT: d 223 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7685 (mp) REVERT: m 5 CYS cc_start: 0.7490 (p) cc_final: 0.7146 (p) REVERT: n 129 MET cc_start: 0.7069 (ttp) cc_final: 0.6752 (ttp) REVERT: n 131 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7977 (mp) outliers start: 17 outliers final: 13 residues processed: 211 average time/residue: 0.6770 time to fit residues: 216.5737 Evaluate side-chains 215 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 199 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain c residue 80 PHE Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 251 LEU Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 151 ASN Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain j residue 2 THR Chi-restraints excluded: chain j residue 45 LEU Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 131 LEU Chi-restraints excluded: chain o residue 89 ASP Chi-restraints excluded: chain o residue 159 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 223 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17500 Z= 0.217 Angle : 0.462 5.874 23787 Z= 0.253 Chirality : 0.036 0.136 2900 Planarity : 0.003 0.046 2969 Dihedral : 3.802 38.563 2496 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.91 % Allowed : 7.93 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 2.44 (0.17), residues: 2313 helix: 2.14 (0.12), residues: 1738 sheet: -1.19 (0.84), residues: 30 loop : 0.17 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP d 312 HIS 0.004 0.001 HIS F 56 PHE 0.025 0.001 PHE B 93 TYR 0.019 0.001 TYR c 113 ARG 0.003 0.000 ARG F 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 17 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue MET 74 is missing expected H atoms. Skipping. Residue VAL 89 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LYS 5 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Residue THR 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue SER 20 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue SER 23 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 44 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue TYR 52 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LEU 109 is missing expected H atoms. Skipping. Residue LYS 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LEU 139 is missing expected H atoms. Skipping. Residue SER 140 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue LYS 163 is missing expected H atoms. Skipping. Residue ILE 233 is missing expected H atoms. Skipping. Residue THR 2 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 195 time to evaluate : 2.805 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: B 1 MET cc_start: 0.7832 (tpt) cc_final: 0.7499 (tpp) REVERT: c 80 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8737 (p90) REVERT: d 128 HIS cc_start: 0.6033 (m170) cc_final: 0.5830 (m170) REVERT: d 179 ILE cc_start: 0.8195 (mm) cc_final: 0.7841 (mm) REVERT: d 223 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7674 (mp) REVERT: m 5 CYS cc_start: 0.7514 (p) cc_final: 0.7182 (p) REVERT: n 129 MET cc_start: 0.7077 (ttp) cc_final: 0.6752 (ttp) REVERT: n 131 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7972 (mp) outliers start: 16 outliers final: 12 residues processed: 207 average time/residue: 0.6653 time to fit residues: 209.5868 Evaluate side-chains 208 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 193 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain c residue 80 PHE Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 251 LEU Chi-restraints excluded: chain h residue 129 MET Chi-restraints excluded: chain h residue 151 ASN Chi-restraints excluded: chain i residue 100 SER Chi-restraints excluded: chain j residue 2 THR Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain n residue 26 LEU Chi-restraints excluded: chain n residue 131 LEU Chi-restraints excluded: chain o residue 89 ASP Chi-restraints excluded: chain o residue 159 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** n 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.146048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.101481 restraints weight = 50182.052| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.50 r_work: 0.3134 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17500 Z= 0.264 Angle : 0.478 5.774 23787 Z= 0.263 Chirality : 0.037 0.131 2900 Planarity : 0.003 0.045 2969 Dihedral : 3.867 38.913 2496 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.86 % Allowed : 8.21 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 2.33 (0.17), residues: 2313 helix: 2.07 (0.12), residues: 1735 sheet: -1.17 (0.85), residues: 30 loop : 0.05 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP d 312 HIS 0.005 0.001 HIS F 56 PHE 0.025 0.001 PHE c 80 TYR 0.014 0.001 TYR c 113 ARG 0.003 0.000 ARG F 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6842.64 seconds wall clock time: 121 minutes 28.62 seconds (7288.62 seconds total)