Starting phenix.real_space_refine on Mon Feb 19 08:48:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smr_40601/02_2024/8smr_40601_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smr_40601/02_2024/8smr_40601.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smr_40601/02_2024/8smr_40601_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smr_40601/02_2024/8smr_40601_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smr_40601/02_2024/8smr_40601_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smr_40601/02_2024/8smr_40601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smr_40601/02_2024/8smr_40601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smr_40601/02_2024/8smr_40601_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smr_40601/02_2024/8smr_40601_updated.pdb" } resolution = 2.7 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= 0.002 sd= 0.182 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 19 7.16 5 Cu 1 5.60 5 S 141 5.16 5 C 15890 2.51 5 N 3934 2.21 5 O 4167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 58": "OD1" <-> "OD2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C GLU 136": "OE1" <-> "OE2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "I GLU 19": "OE1" <-> "OE2" Residue "I GLU 64": "OE1" <-> "OE2" Residue "I PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 165": "OD1" <-> "OD2" Residue "I ASP 244": "OD1" <-> "OD2" Residue "I PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 264": "OE1" <-> "OE2" Residue "I TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 399": "OE1" <-> "OE2" Residue "J GLU 78": "OE1" <-> "OE2" Residue "J GLU 132": "OE1" <-> "OE2" Residue "J PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 202": "OE1" <-> "OE2" Residue "J GLU 205": "OE1" <-> "OE2" Residue "J GLU 210": "OE1" <-> "OE2" Residue "J GLU 231": "OE1" <-> "OE2" Residue "J TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 41": "OD1" <-> "OD2" Residue "K ASP 69": "OD1" <-> "OD2" Residue "K GLU 125": "OE1" <-> "OE2" Residue "K ASP 163": "OD1" <-> "OD2" Residue "Z ASP 83": "OD1" <-> "OD2" Residue "Z ASP 96": "OD1" <-> "OD2" Residue "Z GLU 101": "OE1" <-> "OE2" Residue "Z GLU 104": "OE1" <-> "OE2" Residue "Z GLU 136": "OE1" <-> "OE2" Residue "Z ASP 141": "OD1" <-> "OD2" Residue "Z ASP 145": "OD1" <-> "OD2" Residue "Z ASP 193": "OD1" <-> "OD2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D ASP 20": "OD1" <-> "OD2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D ASP 225": "OD1" <-> "OD2" Residue "D PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 271": "OE1" <-> "OE2" Residue "D GLU 276": "OE1" <-> "OE2" Residue "D TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 305": "OD1" <-> "OD2" Residue "D TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "M ASP 31": "OD1" <-> "OD2" Residue "M TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 74": "OD1" <-> "OD2" Residue "M GLU 78": "OE1" <-> "OE2" Residue "M GLU 231": "OE1" <-> "OE2" Residue "M TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 166": "OE1" <-> "OE2" Residue "N ASP 174": "OD1" <-> "OD2" Residue "E PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 417": "OD1" <-> "OD2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "F PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 44": "OE1" <-> "OE2" Residue "F ASP 95": "OD1" <-> "OD2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F ASP 171": "OD1" <-> "OD2" Residue "F ASP 186": "OD1" <-> "OD2" Residue "G ASP 37": "OD1" <-> "OD2" Residue "G ASP 45": "OD1" <-> "OD2" Residue "G ASP 51": "OD1" <-> "OD2" Residue "G PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 116": "OD1" <-> "OD2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G ASP 171": "OD1" <-> "OD2" Residue "G GLU 232": "OE1" <-> "OE2" Residue "G TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 293": "OE1" <-> "OE2" Residue "G TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24154 Number of models: 1 Model: "" Number of chains: 24 Chain: "C" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1420 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 20, 'TRANS': 169} Chain: "I" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3267 Classifications: {'peptide': 403} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 379} Chain: "J" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1842 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 13, 'TRANS': 218} Chain: "K" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1306 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain: "L" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 115 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "Z" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1449 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 20, 'TRANS': 173} Chain: "D" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3267 Classifications: {'peptide': 403} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 379} Chain: "M" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1631 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 11, 'TRANS': 192} Chain breaks: 1 Chain: "N" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1306 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain: "O" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 115 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "E" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3719 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 452} Chain: "F" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1499 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 188} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "G" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2345 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 16, 'TRANS': 295} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'HEM': 2, 'I7Y': 1, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 11 Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'FES': 1, 'I7Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 149 Unusual residues: {'HEM': 2, 'U10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 89 Unusual residues: {' CA': 2, ' CU': 1, 'HEM': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 878 SG CYS C 124 85.827 89.782 77.166 1.00 85.05 S ATOM 913 SG CYS C 129 82.197 90.933 76.398 1.00 88.42 S ATOM 1090 SG CYS C 152 83.421 92.466 78.335 1.00 90.53 S ATOM 8848 SG CYS Z 124 43.111 59.333 39.809 1.00 50.08 S ATOM 9060 SG CYS Z 152 46.380 59.925 38.108 1.00 53.09 S Time building chain proxies: 12.70, per 1000 atoms: 0.53 Number of scatterers: 24154 At special positions: 0 Unit cell: (114.33, 140.08, 159.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cu 1 28.99 Fe 19 26.01 Ca 2 19.99 S 141 16.00 O 4167 8.00 N 3934 7.00 C 15890 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS J 165 " - pdb=" SG CYS J 191 " distance=2.03 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=33, symmetry=0 Number of additional bonds: simple=33, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.74 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES C 201 " pdb="FE2 FES C 201 " - pdb=" ND1 HIS C 155 " pdb="FE2 FES C 201 " - pdb=" ND1 HIS C 126 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 152 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 124 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 129 " pdb=" FES Z 201 " pdb="FE2 FES Z 201 " - pdb=" ND1 HIS Z 155 " pdb="FE2 FES Z 201 " - pdb=" ND1 HIS Z 126 " pdb="FE1 FES Z 201 " - pdb=" SG CYS Z 152 " pdb="FE1 FES Z 201 " - pdb=" SG CYS Z 124 " Number of angles added : 9 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5452 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 126 helices and 13 sheets defined 54.1% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'C' and resid 8 through 37 Proline residue: C 32 - end of helix removed outlier: 3.944A pdb=" N TRP C 37 " --> pdb=" O PHE C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 79 through 87 Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'I' and resid 2 through 11 removed outlier: 3.587A pdb=" N ARG I 11 " --> pdb=" O TRP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 21 Processing helix chain 'I' and resid 33 through 35 No H-bonds generated for 'chain 'I' and resid 33 through 35' Processing helix chain 'I' and resid 37 through 56 Processing helix chain 'I' and resid 66 through 75 Processing helix chain 'I' and resid 80 through 107 Processing helix chain 'I' and resid 116 through 139 removed outlier: 3.520A pdb=" N LEU I 138 " --> pdb=" O PHE I 134 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU I 139 " --> pdb=" O MET I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 158 removed outlier: 3.992A pdb=" N PHE I 156 " --> pdb=" O ILE I 152 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY I 157 " --> pdb=" O ILE I 153 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA I 158 " --> pdb=" O SER I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 171 Processing helix chain 'I' and resid 178 through 189 Processing helix chain 'I' and resid 191 through 210 Processing helix chain 'I' and resid 220 through 222 No H-bonds generated for 'chain 'I' and resid 220 through 222' Processing helix chain 'I' and resid 236 through 261 removed outlier: 6.667A pdb=" N THR I 241 " --> pdb=" O HIS I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 272 through 275 Processing helix chain 'I' and resid 291 through 302 Proline residue: I 295 - end of helix Processing helix chain 'I' and resid 306 through 326 removed outlier: 3.663A pdb=" N ILE I 317 " --> pdb=" O MET I 313 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU I 320 " --> pdb=" O ALA I 316 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE I 321 " --> pdb=" O ILE I 317 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 322 " --> pdb=" O ALA I 318 " (cutoff:3.500A) Proline residue: I 324 - end of helix Processing helix chain 'I' and resid 339 through 359 Processing helix chain 'I' and resid 365 through 383 removed outlier: 3.918A pdb=" N PHE I 382 " --> pdb=" O TYR I 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 385 through 391 removed outlier: 4.255A pdb=" N ARG I 390 " --> pdb=" O PRO I 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 50 Processing helix chain 'J' and resid 62 through 69 Processing helix chain 'J' and resid 73 through 79 Processing helix chain 'J' and resid 97 through 104 Processing helix chain 'J' and resid 114 through 118 Processing helix chain 'J' and resid 120 through 127 Processing helix chain 'J' and resid 155 through 158 No H-bonds generated for 'chain 'J' and resid 155 through 158' Processing helix chain 'J' and resid 205 through 223 Processing helix chain 'J' and resid 227 through 253 Processing helix chain 'K' and resid 24 through 30 removed outlier: 3.956A pdb=" N ALA K 29 " --> pdb=" O ALA K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 38 removed outlier: 3.962A pdb=" N HIS K 38 " --> pdb=" O GLY K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 69 Processing helix chain 'K' and resid 75 through 77 No H-bonds generated for 'chain 'K' and resid 75 through 77' Processing helix chain 'K' and resid 86 through 97 Processing helix chain 'K' and resid 108 through 120 removed outlier: 4.569A pdb=" N ALA K 112 " --> pdb=" O PRO K 108 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLN K 113 " --> pdb=" O ASN K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 166 Processing helix chain 'K' and resid 177 through 184 removed outlier: 3.878A pdb=" N LYS K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 199 removed outlier: 3.547A pdb=" N GLY K 199 " --> pdb=" O SER K 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 28 No H-bonds generated for 'chain 'L' and resid 25 through 28' Processing helix chain 'Z' and resid 10 through 37 Proline residue: Z 32 - end of helix removed outlier: 3.872A pdb=" N TRP Z 37 " --> pdb=" O PHE Z 33 " (cutoff:3.500A) Processing helix chain 'Z' and resid 43 through 45 No H-bonds generated for 'chain 'Z' and resid 43 through 45' Processing helix chain 'Z' and resid 79 through 91 Proline residue: Z 86 - end of helix removed outlier: 4.008A pdb=" N GLU Z 89 " --> pdb=" O LEU Z 85 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLY Z 90 " --> pdb=" O PRO Z 86 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLN Z 91 " --> pdb=" O SER Z 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 33 through 35 No H-bonds generated for 'chain 'D' and resid 33 through 35' Processing helix chain 'D' and resid 37 through 56 Processing helix chain 'D' and resid 66 through 75 Processing helix chain 'D' and resid 80 through 108 Processing helix chain 'D' and resid 116 through 139 removed outlier: 3.576A pdb=" N LEU D 139 " --> pdb=" O MET D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 158 removed outlier: 4.063A pdb=" N PHE D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY D 157 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 171 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 191 through 210 Processing helix chain 'D' and resid 220 through 222 No H-bonds generated for 'chain 'D' and resid 220 through 222' Processing helix chain 'D' and resid 236 through 261 removed outlier: 6.719A pdb=" N THR D 241 " --> pdb=" O HIS D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 275 Processing helix chain 'D' and resid 291 through 302 Proline residue: D 295 - end of helix Processing helix chain 'D' and resid 306 through 326 removed outlier: 4.103A pdb=" N LEU D 320 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE D 321 " --> pdb=" O ILE D 317 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Proline residue: D 324 - end of helix Processing helix chain 'D' and resid 339 through 358 Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.879A pdb=" N PHE D 382 " --> pdb=" O TYR D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 391 removed outlier: 4.342A pdb=" N ARG D 390 " --> pdb=" O PRO D 386 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 50 Processing helix chain 'M' and resid 62 through 69 Processing helix chain 'M' and resid 73 through 79 Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 114 through 117 No H-bonds generated for 'chain 'M' and resid 114 through 117' Processing helix chain 'M' and resid 120 through 127 Processing helix chain 'M' and resid 155 through 158 No H-bonds generated for 'chain 'M' and resid 155 through 158' Processing helix chain 'M' and resid 205 through 223 Processing helix chain 'M' and resid 227 through 255 removed outlier: 3.610A pdb=" N TYR M 236 " --> pdb=" O ARG M 232 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE M 247 " --> pdb=" O PHE M 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 30 removed outlier: 3.866A pdb=" N ALA N 29 " --> pdb=" O ALA N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 38 removed outlier: 3.946A pdb=" N HIS N 38 " --> pdb=" O GLY N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 69 Processing helix chain 'N' and resid 75 through 77 No H-bonds generated for 'chain 'N' and resid 75 through 77' Processing helix chain 'N' and resid 86 through 97 Processing helix chain 'N' and resid 108 through 120 removed outlier: 4.662A pdb=" N ALA N 112 " --> pdb=" O PRO N 108 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N GLN N 113 " --> pdb=" O ASN N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 154 through 166 Processing helix chain 'N' and resid 177 through 184 removed outlier: 3.985A pdb=" N LYS N 184 " --> pdb=" O SER N 180 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 199 Processing helix chain 'O' and resid 25 through 28 No H-bonds generated for 'chain 'O' and resid 25 through 28' Processing helix chain 'E' and resid 12 through 41 Processing helix chain 'E' and resid 43 through 46 Processing helix chain 'E' and resid 50 through 52 No H-bonds generated for 'chain 'E' and resid 50 through 52' Processing helix chain 'E' and resid 54 through 67 Proline residue: E 59 - end of helix removed outlier: 3.778A pdb=" N ILE E 66 " --> pdb=" O THR E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 86 removed outlier: 4.165A pdb=" N GLN E 83 " --> pdb=" O TYR E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 114 Processing helix chain 'E' and resid 132 through 151 removed outlier: 3.586A pdb=" N ALA E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 179 removed outlier: 5.108A pdb=" N HIS E 176 " --> pdb=" O THR E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 210 removed outlier: 4.083A pdb=" N ASN E 209 " --> pdb=" O TRP E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 231 Proline residue: E 228 - end of helix Processing helix chain 'E' and resid 238 through 252 Processing helix chain 'E' and resid 254 through 260 Proline residue: E 257 - end of helix Processing helix chain 'E' and resid 267 through 295 removed outlier: 4.386A pdb=" N ALA E 282 " --> pdb=" O LEU E 278 " (cutoff:3.500A) Proline residue: E 283 - end of helix removed outlier: 4.104A pdb=" N LEU E 295 " --> pdb=" O GLY E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 303 Processing helix chain 'E' and resid 306 through 329 Proline residue: E 326 - end of helix Processing helix chain 'E' and resid 331 through 336 removed outlier: 3.919A pdb=" N LEU E 336 " --> pdb=" O THR E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 351 Processing helix chain 'E' and resid 355 through 370 Proline residue: E 368 - end of helix Processing helix chain 'E' and resid 379 through 412 removed outlier: 3.861A pdb=" N GLY E 392 " --> pdb=" O LEU E 388 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU E 395 " --> pdb=" O ILE E 391 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR E 396 " --> pdb=" O GLY E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 460 Proline residue: E 433 - end of helix Processing helix chain 'E' and resid 465 through 472 removed outlier: 3.871A pdb=" N ALA E 472 " --> pdb=" O ILE E 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 9 Processing helix chain 'F' and resid 11 through 29 removed outlier: 4.066A pdb=" N GLY F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY F 26 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR F 28 " --> pdb=" O ILE F 24 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN F 29 " --> pdb=" O GLY F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 62 Processing helix chain 'F' and resid 65 through 67 No H-bonds generated for 'chain 'F' and resid 65 through 67' Processing helix chain 'F' and resid 77 through 83 Processing helix chain 'F' and resid 89 through 92 Processing helix chain 'F' and resid 118 through 124 removed outlier: 4.461A pdb=" N ALA F 123 " --> pdb=" O ASP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 131 No H-bonds generated for 'chain 'F' and resid 128 through 131' Processing helix chain 'F' and resid 153 through 162 Processing helix chain 'F' and resid 169 through 179 removed outlier: 4.555A pdb=" N ARG F 176 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 193 Processing helix chain 'G' and resid 3 through 27 Processing helix chain 'G' and resid 56 through 75 Processing helix chain 'G' and resid 104 through 126 Proline residue: G 121 - end of helix Processing helix chain 'G' and resid 131 through 136 removed outlier: 3.740A pdb=" N LYS G 136 " --> pdb=" O GLU G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 151 Processing helix chain 'G' and resid 153 through 156 No H-bonds generated for 'chain 'G' and resid 153 through 156' Processing helix chain 'G' and resid 180 through 189 Processing helix chain 'G' and resid 203 through 216 Processing helix chain 'G' and resid 231 through 241 removed outlier: 3.571A pdb=" N THR G 240 " --> pdb=" O GLN G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 282 Processing helix chain 'G' and resid 292 through 311 removed outlier: 7.317A pdb=" N ASN G 297 " --> pdb=" O GLU G 293 " (cutoff:3.500A) removed outlier: 9.984A pdb=" N ASP G 298 " --> pdb=" O HIS G 294 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS G 299 " --> pdb=" O LEU G 295 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 50 through 53 Processing sheet with id= B, first strand: chain 'C' and resid 62 through 67 Processing sheet with id= C, first strand: chain 'C' and resid 132 through 134 Processing sheet with id= D, first strand: chain 'I' and resid 26 through 28 Processing sheet with id= E, first strand: chain 'J' and resid 130 through 132 Processing sheet with id= F, first strand: chain 'J' and resid 161 through 164 Processing sheet with id= G, first strand: chain 'J' and resid 166 through 169 Processing sheet with id= H, first strand: chain 'Z' and resid 50 through 53 removed outlier: 6.695A pdb=" N THR Z 189 " --> pdb=" O PHE Z 182 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N PHE Z 182 " --> pdb=" O THR Z 189 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'Z' and resid 61 through 67 removed outlier: 3.856A pdb=" N GLN Z 61 " --> pdb=" O HIS Z 76 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'Z' and resid 132 through 134 Processing sheet with id= K, first strand: chain 'D' and resid 26 through 28 Processing sheet with id= L, first strand: chain 'M' and resid 130 through 132 Processing sheet with id= M, first strand: chain 'E' and resid 182 through 186 removed outlier: 6.828A pdb=" N LYS E 189 " --> pdb=" O VAL E 185 " (cutoff:3.500A) 1087 hydrogen bonds defined for protein. 3186 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.64 Time building geometry restraints manager: 11.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.36: 7519 1.36 - 1.57: 17094 1.57 - 1.78: 29 1.78 - 1.99: 232 1.99 - 2.21: 68 Bond restraints: 24942 Sorted by residual: bond pdb=" C03 I7Y I 504 " pdb=" C04 I7Y I 504 " ideal model delta sigma weight residual 1.357 1.668 -0.311 2.00e-02 2.50e+03 2.42e+02 bond pdb=" C03 I7Y Z 202 " pdb=" C04 I7Y Z 202 " ideal model delta sigma weight residual 1.357 1.668 -0.311 2.00e-02 2.50e+03 2.42e+02 bond pdb=" C04 I7Y I 504 " pdb=" O72 I7Y I 504 " ideal model delta sigma weight residual 1.515 1.218 0.297 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C04 I7Y Z 202 " pdb=" O72 I7Y Z 202 " ideal model delta sigma weight residual 1.515 1.218 0.297 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C73 I7Y Z 202 " pdb=" O72 I7Y Z 202 " ideal model delta sigma weight residual 1.310 1.582 -0.272 2.00e-02 2.50e+03 1.86e+02 ... (remaining 24937 not shown) Histogram of bond angle deviations from ideal: 75.13 - 95.85: 66 95.85 - 116.57: 16509 116.57 - 137.29: 17544 137.29 - 158.02: 2 158.02 - 178.74: 30 Bond angle restraints: 34151 Sorted by residual: angle pdb=" C74 I7Y I 504 " pdb=" C73 I7Y I 504 " pdb=" C76 I7Y I 504 " ideal model delta sigma weight residual 109.68 148.17 -38.49 3.00e+00 1.11e-01 1.65e+02 angle pdb=" C74 I7Y Z 202 " pdb=" C73 I7Y Z 202 " pdb=" C76 I7Y Z 202 " ideal model delta sigma weight residual 109.68 148.16 -38.48 3.00e+00 1.11e-01 1.65e+02 angle pdb=" C74 I7Y I 504 " pdb=" C73 I7Y I 504 " pdb=" O80 I7Y I 504 " ideal model delta sigma weight residual 109.99 79.89 30.10 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C74 I7Y Z 202 " pdb=" C73 I7Y Z 202 " pdb=" O80 I7Y Z 202 " ideal model delta sigma weight residual 109.99 79.90 30.09 3.00e+00 1.11e-01 1.01e+02 angle pdb=" CB GLN Z 169 " pdb=" CG GLN Z 169 " pdb=" CD GLN Z 169 " ideal model delta sigma weight residual 112.60 98.34 14.26 1.70e+00 3.46e-01 7.04e+01 ... (remaining 34146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.24: 12922 23.24 - 46.48: 979 46.48 - 69.72: 177 69.72 - 92.96: 66 92.96 - 116.19: 11 Dihedral angle restraints: 14155 sinusoidal: 5594 harmonic: 8561 Sorted by residual: dihedral pdb=" C2B HEC J 500 " pdb=" C3B HEC J 500 " pdb=" CAB HEC J 500 " pdb=" CBB HEC J 500 " ideal model delta sinusoidal sigma weight residual 60.00 132.70 -72.70 2 1.00e+01 1.00e-02 4.38e+01 dihedral pdb=" C2C HEC N 501 " pdb=" C3C HEC N 501 " pdb=" CAC HEC N 501 " pdb=" CBC HEC N 501 " ideal model delta sinusoidal sigma weight residual 60.00 116.70 -56.70 2 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" C6 U10 D 503 " pdb=" C7 U10 D 503 " pdb=" C8 U10 D 503 " pdb=" C9 U10 D 503 " ideal model delta sinusoidal sigma weight residual 101.51 -147.21 -111.27 1 2.00e+01 2.50e-03 3.27e+01 ... (remaining 14152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.316: 3585 0.316 - 0.632: 5 0.632 - 0.948: 0 0.948 - 1.264: 0 1.264 - 1.580: 2 Chirality restraints: 3592 Sorted by residual: chirality pdb=" C74 I7Y I 504 " pdb=" C03 I7Y I 504 " pdb=" C73 I7Y I 504 " pdb=" C75 I7Y I 504 " both_signs ideal model delta sigma weight residual False -2.72 -1.14 -1.58 2.00e-01 2.50e+01 6.24e+01 chirality pdb=" C74 I7Y Z 202 " pdb=" C03 I7Y Z 202 " pdb=" C73 I7Y Z 202 " pdb=" C75 I7Y Z 202 " both_signs ideal model delta sigma weight residual False -2.72 -1.14 -1.58 2.00e-01 2.50e+01 6.23e+01 chirality pdb=" C73 I7Y Z 202 " pdb=" C74 I7Y Z 202 " pdb=" O72 I7Y Z 202 " pdb=" O80 I7Y Z 202 " both_signs ideal model delta sigma weight residual False -2.35 -2.92 0.57 2.00e-01 2.50e+01 8.13e+00 ... (remaining 3589 not shown) Planarity restraints: 4244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC N 501 " -0.025 2.00e-02 2.50e+03 6.32e-02 8.99e+01 pdb=" C2C HEC N 501 " 0.173 2.00e-02 2.50e+03 pdb=" C3C HEC N 501 " -0.016 2.00e-02 2.50e+03 pdb=" C4C HEC N 501 " -0.007 2.00e-02 2.50e+03 pdb=" CAC HEC N 501 " -0.040 2.00e-02 2.50e+03 pdb=" CHC HEC N 501 " -0.031 2.00e-02 2.50e+03 pdb=" CHD HEC N 501 " 0.006 2.00e-02 2.50e+03 pdb=" CMC HEC N 501 " -0.048 2.00e-02 2.50e+03 pdb=" NC HEC N 501 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC K 501 " -0.018 2.00e-02 2.50e+03 5.68e-02 7.26e+01 pdb=" C2C HEC K 501 " 0.155 2.00e-02 2.50e+03 pdb=" C3C HEC K 501 " -0.037 2.00e-02 2.50e+03 pdb=" C4C HEC K 501 " -0.004 2.00e-02 2.50e+03 pdb=" CAC HEC K 501 " -0.021 2.00e-02 2.50e+03 pdb=" CHC HEC K 501 " -0.027 2.00e-02 2.50e+03 pdb=" CHD HEC K 501 " 0.002 2.00e-02 2.50e+03 pdb=" CMC HEC K 501 " -0.046 2.00e-02 2.50e+03 pdb=" NC HEC K 501 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC G 401 " -0.010 2.00e-02 2.50e+03 5.11e-02 5.87e+01 pdb=" C2C HEC G 401 " 0.137 2.00e-02 2.50e+03 pdb=" C3C HEC G 401 " -0.045 2.00e-02 2.50e+03 pdb=" C4C HEC G 401 " -0.006 2.00e-02 2.50e+03 pdb=" CAC HEC G 401 " -0.011 2.00e-02 2.50e+03 pdb=" CHC HEC G 401 " -0.025 2.00e-02 2.50e+03 pdb=" CHD HEC G 401 " 0.004 2.00e-02 2.50e+03 pdb=" CMC HEC G 401 " -0.042 2.00e-02 2.50e+03 pdb=" NC HEC G 401 " -0.001 2.00e-02 2.50e+03 ... (remaining 4241 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 266 2.56 - 3.14: 20223 3.14 - 3.73: 42699 3.73 - 4.31: 60357 4.31 - 4.90: 97804 Nonbonded interactions: 221349 Sorted by model distance: nonbonded pdb=" OG SER F 135 " pdb=" O1D HEC F 301 " model vdw 1.975 2.440 nonbonded pdb=" OG SER N 85 " pdb=" OD1 ASP N 88 " model vdw 2.024 2.440 nonbonded pdb=" OG1 THR C 181 " pdb=" OE1 GLN C 194 " model vdw 2.054 2.440 nonbonded pdb=" O LEU N 75 " pdb=" OG1 THR N 78 " model vdw 2.096 2.440 nonbonded pdb=" OH TYR E 238 " pdb=" OE2 GLU F 8 " model vdw 2.097 2.440 ... (remaining 221344 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 'C' and resid 6 through 195) selection = (chain 'Z' and resid 6 through 195) } ncs_group { reference = chain 'D' selection = (chain 'I' and (resid 1 through 403 or resid 501 through 503)) } ncs_group { reference = (chain 'J' and (resid 26 through 163 or resid 193 through 257 or resid 500)) selection = (chain 'M' and (resid 26 through 257 or resid 500)) } ncs_group { reference = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'L' selection = chain 'O' } 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.240 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 70.250 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 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 : 0.007 0.311 24942 Z= 0.498 Angle : 0.848 38.487 34151 Z= 0.391 Chirality : 0.059 1.580 3592 Planarity : 0.005 0.063 4244 Dihedral : 17.724 116.194 8700 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.66 % Favored : 97.31 % Rotamer: Outliers : 0.92 % Allowed : 19.42 % Favored : 79.66 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.98 % 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: 0.77 (0.15), residues: 2972 helix: 1.10 (0.13), residues: 1628 sheet: -2.47 (0.63), residues: 46 loop : -0.01 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 54 HIS 0.013 0.001 HIS Z 158 PHE 0.024 0.001 PHE I 255 TYR 0.014 0.001 TYR I 388 ARG 0.014 0.000 ARG J 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 456 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 52 MET cc_start: 0.8975 (mtp) cc_final: 0.8678 (mtm) REVERT: K 23 ASP cc_start: 0.7961 (t0) cc_final: 0.7717 (t70) REVERT: Z 76 HIS cc_start: 0.8477 (t-90) cc_final: 0.8212 (t-90) REVERT: D 3 LYS cc_start: 0.7442 (mptt) cc_final: 0.6407 (mppt) REVERT: E 229 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8578 (mmmt) REVERT: E 261 HIS cc_start: 0.7906 (OUTLIER) cc_final: 0.7421 (t-90) REVERT: E 410 MET cc_start: 0.8123 (mmm) cc_final: 0.7703 (mtm) REVERT: F 24 ILE cc_start: 0.7745 (mm) cc_final: 0.7469 (mp) REVERT: F 197 THR cc_start: 0.8972 (m) cc_final: 0.8746 (m) REVERT: G 45 ASP cc_start: 0.7812 (t70) cc_final: 0.7326 (t70) REVERT: G 195 MET cc_start: 0.8324 (tpt) cc_final: 0.7882 (tpt) outliers start: 22 outliers final: 15 residues processed: 469 average time/residue: 1.3702 time to fit residues: 739.8032 Evaluate side-chains 426 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 410 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain I residue 212 SER Chi-restraints excluded: chain I residue 361 GLN Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 473 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 192 HIS Chi-restraints excluded: chain G residue 241 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 8.9990 chunk 224 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 76 optimal weight: 0.1980 chunk 151 optimal weight: 0.9980 chunk 119 optimal weight: 0.3980 chunk 232 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 172 optimal weight: 0.3980 chunk 268 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 280 GLN K 113 GLN Z 3 ASN Z 51 GLN Z 158 HIS D 150 GLN D 361 GLN ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS E 407 GLN F 127 ASN G 31 GLN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 HIS ** G 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24942 Z= 0.229 Angle : 0.685 15.479 34151 Z= 0.299 Chirality : 0.043 0.225 3592 Planarity : 0.004 0.051 4244 Dihedral : 12.100 104.071 3522 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.72 % Allowed : 18.38 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.15), residues: 2972 helix: 1.24 (0.13), residues: 1625 sheet: -2.26 (0.56), residues: 62 loop : 0.09 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 147 HIS 0.007 0.001 HIS C 76 PHE 0.027 0.002 PHE I 255 TYR 0.025 0.002 TYR C 105 ARG 0.008 0.000 ARG C 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 447 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 150 GLN cc_start: 0.8381 (tm-30) cc_final: 0.8053 (tp40) REVERT: J 52 MET cc_start: 0.8914 (mtp) cc_final: 0.8704 (mtm) REVERT: Z 75 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8740 (m) REVERT: Z 76 HIS cc_start: 0.8476 (t-90) cc_final: 0.8203 (t-90) REVERT: Z 164 ARG cc_start: 0.8563 (mtm180) cc_final: 0.8183 (mtm180) REVERT: D 3 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6423 (mppt) REVERT: D 308 MET cc_start: 0.8266 (tpt) cc_final: 0.8040 (tpp) REVERT: D 328 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8020 (mmm160) REVERT: D 392 GLU cc_start: 0.8224 (pt0) cc_final: 0.7926 (pt0) REVERT: E 238 TYR cc_start: 0.6413 (t80) cc_final: 0.6192 (t80) REVERT: E 239 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7370 (mmm-85) REVERT: E 252 TYR cc_start: 0.5732 (OUTLIER) cc_final: 0.5471 (m-10) REVERT: E 261 HIS cc_start: 0.7987 (OUTLIER) cc_final: 0.7646 (t-90) REVERT: F 24 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7462 (mp) REVERT: F 127 ASN cc_start: 0.8761 (t0) cc_final: 0.8484 (t0) REVERT: F 171 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7430 (m-30) REVERT: F 184 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7616 (mt-10) REVERT: G 45 ASP cc_start: 0.7804 (t70) cc_final: 0.7019 (t0) REVERT: G 192 HIS cc_start: 0.7951 (OUTLIER) cc_final: 0.7735 (t-90) REVERT: G 195 MET cc_start: 0.8353 (tpt) cc_final: 0.7885 (tpt) REVERT: G 256 MET cc_start: 0.7299 (mtm) cc_final: 0.7097 (mtt) outliers start: 65 outliers final: 17 residues processed: 482 average time/residue: 1.3116 time to fit residues: 728.9472 Evaluate side-chains 451 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 424 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 192 HIS Chi-restraints excluded: chain G residue 288 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 223 optimal weight: 0.1980 chunk 183 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 269 optimal weight: 2.9990 chunk 290 optimal weight: 20.0000 chunk 239 optimal weight: 3.9990 chunk 267 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 216 optimal weight: 7.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 ASN I 280 GLN Z 3 ASN Z 51 GLN Z 169 GLN D 361 GLN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS E 407 GLN E 432 HIS G 31 GLN ** G 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 24942 Z= 0.392 Angle : 0.763 18.038 34151 Z= 0.332 Chirality : 0.046 0.290 3592 Planarity : 0.005 0.055 4244 Dihedral : 12.221 107.858 3503 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.85 % Allowed : 17.75 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 0.78 (0.15), residues: 2972 helix: 1.12 (0.13), residues: 1616 sheet: -2.30 (0.55), residues: 56 loop : 0.00 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 54 HIS 0.011 0.002 HIS I 87 PHE 0.023 0.002 PHE I 255 TYR 0.021 0.003 TYR J 221 ARG 0.008 0.001 ARG C 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 449 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 150 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8274 (tp-100) REVERT: J 255 TYR cc_start: 0.7564 (OUTLIER) cc_final: 0.7116 (t80) REVERT: Z 75 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8812 (m) REVERT: Z 76 HIS cc_start: 0.8580 (t-90) cc_final: 0.8280 (t-90) REVERT: Z 147 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8032 (mtpp) REVERT: D 308 MET cc_start: 0.8327 (tpt) cc_final: 0.8079 (tpp) REVERT: D 328 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7992 (mmm160) REVERT: D 392 GLU cc_start: 0.8456 (pt0) cc_final: 0.8236 (pt0) REVERT: E 38 SER cc_start: 0.8571 (m) cc_final: 0.8365 (p) REVERT: E 238 TYR cc_start: 0.6956 (t80) cc_final: 0.6663 (t80) REVERT: E 239 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7629 (mmm-85) REVERT: E 412 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.7519 (ttm170) REVERT: F 24 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7554 (mp) REVERT: F 127 ASN cc_start: 0.8772 (t0) cc_final: 0.8522 (t0) REVERT: F 171 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7441 (m-30) REVERT: G 45 ASP cc_start: 0.8040 (t70) cc_final: 0.7188 (t0) REVERT: G 83 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8370 (ptpp) REVERT: G 175 ARG cc_start: 0.8037 (mtp85) cc_final: 0.7776 (mtp85) REVERT: G 195 MET cc_start: 0.8407 (tpt) cc_final: 0.7906 (tpt) outliers start: 92 outliers final: 35 residues processed: 496 average time/residue: 1.3553 time to fit residues: 773.3416 Evaluate side-chains 469 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 426 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 110 LEU Chi-restraints excluded: chain Z residue 147 LYS Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 279 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 0.7980 chunk 202 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 180 optimal weight: 9.9990 chunk 270 optimal weight: 0.3980 chunk 286 optimal weight: 2.9990 chunk 141 optimal weight: 0.2980 chunk 256 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 280 GLN K 113 GLN Z 3 ASN Z 51 GLN Z 62 GLN Z 169 GLN D 361 GLN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS E 407 GLN ** G 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 24942 Z= 0.224 Angle : 0.663 15.071 34151 Z= 0.288 Chirality : 0.042 0.248 3592 Planarity : 0.004 0.056 4244 Dihedral : 11.665 105.005 3501 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.22 % Allowed : 18.71 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 0.94 (0.15), residues: 2972 helix: 1.26 (0.13), residues: 1620 sheet: -2.11 (0.58), residues: 54 loop : 0.05 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 54 HIS 0.010 0.001 HIS C 76 PHE 0.022 0.001 PHE I 255 TYR 0.021 0.002 TYR M 240 ARG 0.010 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 443 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 150 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8147 (tp40) REVERT: J 255 TYR cc_start: 0.7123 (OUTLIER) cc_final: 0.6546 (t80) REVERT: K 28 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8322 (tt0) REVERT: L 34 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7501 (mmtm) REVERT: Z 75 VAL cc_start: 0.9055 (OUTLIER) cc_final: 0.8840 (m) REVERT: Z 76 HIS cc_start: 0.8567 (t-90) cc_final: 0.8234 (t-90) REVERT: Z 169 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8101 (mm-40) REVERT: D 3 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6278 (mppt) REVERT: D 308 MET cc_start: 0.8314 (tpt) cc_final: 0.8057 (tpp) REVERT: D 328 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7950 (mmm160) REVERT: D 392 GLU cc_start: 0.8457 (pt0) cc_final: 0.8200 (pt0) REVERT: E 238 TYR cc_start: 0.6892 (t80) cc_final: 0.6596 (t80) REVERT: E 239 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7496 (mmm-85) REVERT: E 412 ARG cc_start: 0.7809 (ttm-80) cc_final: 0.7483 (ttm170) REVERT: E 452 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8314 (ttp) REVERT: F 24 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7560 (mp) REVERT: F 127 ASN cc_start: 0.8715 (t0) cc_final: 0.8456 (t0) REVERT: F 151 LYS cc_start: 0.6777 (mmmt) cc_final: 0.6493 (mmtt) REVERT: F 171 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7501 (m-30) REVERT: G 45 ASP cc_start: 0.8015 (t70) cc_final: 0.7232 (t0) REVERT: G 83 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8353 (ptpp) REVERT: G 175 ARG cc_start: 0.7980 (mtp85) cc_final: 0.7702 (mtp85) REVERT: G 195 MET cc_start: 0.8307 (tpt) cc_final: 0.7765 (tpt) REVERT: G 208 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8399 (mtpt) outliers start: 77 outliers final: 27 residues processed: 486 average time/residue: 1.3944 time to fit residues: 776.2915 Evaluate side-chains 459 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 420 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 28 GLN Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 169 GLN Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 279 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 118 optimal weight: 0.0050 chunk 244 optimal weight: 0.0070 chunk 197 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 256 optimal weight: 9.9990 chunk 72 optimal weight: 0.4980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 ASN I 280 GLN K 113 GLN Z 3 ASN Z 51 GLN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS E 407 GLN ** G 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24942 Z= 0.215 Angle : 0.649 14.753 34151 Z= 0.281 Chirality : 0.042 0.307 3592 Planarity : 0.004 0.054 4244 Dihedral : 11.456 105.824 3501 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.26 % Allowed : 19.25 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 1.01 (0.15), residues: 2972 helix: 1.33 (0.13), residues: 1618 sheet: -2.10 (0.59), residues: 54 loop : 0.07 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 147 HIS 0.011 0.001 HIS C 76 PHE 0.021 0.001 PHE I 255 TYR 0.019 0.002 TYR C 105 ARG 0.008 0.000 ARG C 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 437 time to evaluate : 2.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 5 MET cc_start: 0.8602 (mmm) cc_final: 0.8385 (mmp) REVERT: I 150 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8073 (tp40) REVERT: J 255 TYR cc_start: 0.7088 (OUTLIER) cc_final: 0.6563 (t80) REVERT: Z 75 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8848 (m) REVERT: Z 76 HIS cc_start: 0.8564 (t-90) cc_final: 0.8211 (t-90) REVERT: D 3 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6271 (mppt) REVERT: D 308 MET cc_start: 0.8314 (tpt) cc_final: 0.8053 (tpp) REVERT: D 328 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7968 (mmm160) REVERT: D 392 GLU cc_start: 0.8443 (pt0) cc_final: 0.8214 (pt0) REVERT: E 238 TYR cc_start: 0.6908 (t80) cc_final: 0.6606 (t80) REVERT: E 239 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7516 (mmm-85) REVERT: E 412 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7491 (ttm170) REVERT: E 452 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8323 (ttp) REVERT: E 469 LEU cc_start: 0.8609 (pp) cc_final: 0.8206 (mp) REVERT: F 24 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7722 (mp) REVERT: F 127 ASN cc_start: 0.8683 (t0) cc_final: 0.8437 (t0) REVERT: F 151 LYS cc_start: 0.6833 (mmmt) cc_final: 0.6567 (mmtt) REVERT: G 31 GLN cc_start: 0.8385 (mt0) cc_final: 0.8174 (mt0) REVERT: G 32 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.7113 (mtt-85) REVERT: G 45 ASP cc_start: 0.8120 (t70) cc_final: 0.7390 (t0) REVERT: G 83 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8333 (ptpp) REVERT: G 175 ARG cc_start: 0.7957 (mtp85) cc_final: 0.7682 (mtp85) REVERT: G 188 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.6380 (mtm) REVERT: G 195 MET cc_start: 0.8275 (tpt) cc_final: 0.7627 (tpt) REVERT: G 208 LYS cc_start: 0.8606 (ttmm) cc_final: 0.8322 (mtpt) outliers start: 78 outliers final: 31 residues processed: 482 average time/residue: 1.4145 time to fit residues: 781.4041 Evaluate side-chains 466 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 425 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 32 ARG Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 188 MET Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 279 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 286 optimal weight: 3.9990 chunk 237 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 94 optimal weight: 0.3980 chunk 150 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 280 GLN K 113 GLN Z 3 ASN Z 51 GLN Z 62 GLN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 GLN ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 GLN ** G 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24942 Z= 0.231 Angle : 0.656 16.116 34151 Z= 0.283 Chirality : 0.042 0.311 3592 Planarity : 0.004 0.054 4244 Dihedral : 11.393 106.315 3501 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.89 % Allowed : 19.80 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 1.05 (0.15), residues: 2972 helix: 1.36 (0.13), residues: 1617 sheet: -2.14 (0.57), residues: 57 loop : 0.11 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 54 HIS 0.012 0.001 HIS C 76 PHE 0.019 0.001 PHE I 255 TYR 0.023 0.002 TYR M 240 ARG 0.009 0.000 ARG C 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 436 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 150 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8103 (tp40) REVERT: J 255 TYR cc_start: 0.7090 (OUTLIER) cc_final: 0.6562 (t80) REVERT: Z 75 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8860 (m) REVERT: Z 76 HIS cc_start: 0.8566 (t-90) cc_final: 0.8208 (t-90) REVERT: Z 164 ARG cc_start: 0.8468 (mtm180) cc_final: 0.8140 (mtm180) REVERT: D 3 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6254 (mppt) REVERT: D 308 MET cc_start: 0.8320 (tpt) cc_final: 0.8056 (tpp) REVERT: M 231 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: E 238 TYR cc_start: 0.6985 (t80) cc_final: 0.6721 (t80) REVERT: E 239 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7780 (mtp85) REVERT: E 412 ARG cc_start: 0.7793 (ttm-80) cc_final: 0.7522 (ttm170) REVERT: E 462 GLN cc_start: 0.6890 (OUTLIER) cc_final: 0.6675 (pp30) REVERT: F 24 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7719 (mp) REVERT: F 171 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7516 (m-30) REVERT: G 31 GLN cc_start: 0.8396 (mt0) cc_final: 0.8169 (mt0) REVERT: G 51 ASP cc_start: 0.8526 (t0) cc_final: 0.8322 (t0) REVERT: G 83 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8328 (ptpp) REVERT: G 175 ARG cc_start: 0.7975 (mtp85) cc_final: 0.7642 (mtp85) REVERT: G 195 MET cc_start: 0.8256 (tpt) cc_final: 0.7598 (tpt) REVERT: G 208 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8325 (mtpt) outliers start: 69 outliers final: 38 residues processed: 475 average time/residue: 1.4248 time to fit residues: 777.6170 Evaluate side-chains 466 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 419 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 279 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 9.9990 chunk 32 optimal weight: 0.5980 chunk 163 optimal weight: 3.9990 chunk 209 optimal weight: 7.9990 chunk 162 optimal weight: 0.1980 chunk 241 optimal weight: 0.9980 chunk 159 optimal weight: 0.0040 chunk 285 optimal weight: 5.9990 chunk 178 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 ASN ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN K 113 GLN L 38 GLN Z 3 ASN Z 51 GLN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 GLN G 294 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24942 Z= 0.214 Angle : 0.649 15.660 34151 Z= 0.281 Chirality : 0.042 0.318 3592 Planarity : 0.004 0.056 4244 Dihedral : 11.157 107.057 3499 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.60 % Allowed : 19.97 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 1.11 (0.15), residues: 2972 helix: 1.44 (0.13), residues: 1606 sheet: -2.02 (0.57), residues: 57 loop : 0.10 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 147 HIS 0.008 0.001 HIS C 76 PHE 0.019 0.001 PHE I 255 TYR 0.022 0.002 TYR M 240 ARG 0.009 0.000 ARG C 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 424 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 150 GLN cc_start: 0.8383 (tm-30) cc_final: 0.8080 (tp40) REVERT: J 255 TYR cc_start: 0.7013 (OUTLIER) cc_final: 0.6466 (t80) REVERT: Z 76 HIS cc_start: 0.8566 (t-90) cc_final: 0.8195 (t-90) REVERT: Z 164 ARG cc_start: 0.8458 (mtm180) cc_final: 0.8095 (mtm180) REVERT: D 3 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6252 (mppt) REVERT: D 308 MET cc_start: 0.8319 (tpt) cc_final: 0.8067 (tpp) REVERT: N 105 MET cc_start: 0.8419 (mtp) cc_final: 0.8208 (mmp) REVERT: E 238 TYR cc_start: 0.6960 (t80) cc_final: 0.6707 (t80) REVERT: E 239 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7529 (mmm-85) REVERT: E 412 ARG cc_start: 0.7785 (ttm-80) cc_final: 0.7509 (ttm170) REVERT: E 462 GLN cc_start: 0.6890 (OUTLIER) cc_final: 0.6585 (pp30) REVERT: E 469 LEU cc_start: 0.8564 (pp) cc_final: 0.8159 (mp) REVERT: F 24 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7721 (mp) REVERT: F 171 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7549 (m-30) REVERT: G 45 ASP cc_start: 0.8312 (t70) cc_final: 0.7498 (t70) REVERT: G 83 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8332 (ptpp) REVERT: G 86 MET cc_start: 0.7425 (tpp) cc_final: 0.7173 (tpp) REVERT: G 175 ARG cc_start: 0.7976 (mtp85) cc_final: 0.7662 (mtp85) REVERT: G 195 MET cc_start: 0.8245 (tpt) cc_final: 0.7535 (tpt) REVERT: G 208 LYS cc_start: 0.8587 (ttmm) cc_final: 0.8224 (ttpp) outliers start: 62 outliers final: 33 residues processed: 458 average time/residue: 1.4447 time to fit residues: 754.0075 Evaluate side-chains 454 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 414 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 241 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 181 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 224 optimal weight: 0.5980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 ASN ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN K 113 GLN Z 3 ASN Z 51 GLN Z 62 GLN D 361 GLN ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 GLN G 209 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 24942 Z= 0.294 Angle : 0.703 17.460 34151 Z= 0.305 Chirality : 0.044 0.355 3592 Planarity : 0.004 0.058 4244 Dihedral : 11.240 111.057 3499 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.64 % Allowed : 20.59 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 0.95 (0.15), residues: 2972 helix: 1.27 (0.13), residues: 1631 sheet: -1.87 (0.59), residues: 57 loop : 0.03 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 54 HIS 0.008 0.001 HIS I 87 PHE 0.018 0.002 PHE I 95 TYR 0.030 0.002 TYR G 72 ARG 0.009 0.001 ARG C 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 426 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 150 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8103 (tp40) REVERT: J 255 TYR cc_start: 0.7349 (OUTLIER) cc_final: 0.6836 (t80) REVERT: Z 76 HIS cc_start: 0.8601 (t-90) cc_final: 0.8282 (t-90) REVERT: Z 164 ARG cc_start: 0.8490 (mtm180) cc_final: 0.8063 (mtm180) REVERT: D 308 MET cc_start: 0.8334 (tpt) cc_final: 0.8080 (tpp) REVERT: E 223 MET cc_start: 0.8120 (tmm) cc_final: 0.7875 (ttp) REVERT: E 238 TYR cc_start: 0.7090 (t80) cc_final: 0.6806 (t80) REVERT: E 412 ARG cc_start: 0.7819 (ttm-80) cc_final: 0.7542 (ttm170) REVERT: E 462 GLN cc_start: 0.6929 (OUTLIER) cc_final: 0.6558 (pp30) REVERT: F 24 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7879 (mp) REVERT: F 171 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7563 (m-30) REVERT: G 83 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8366 (ptpp) REVERT: G 86 MET cc_start: 0.7423 (tpp) cc_final: 0.7194 (tpp) REVERT: G 175 ARG cc_start: 0.8118 (mtp85) cc_final: 0.7765 (mtp85) REVERT: G 195 MET cc_start: 0.8274 (tpt) cc_final: 0.7613 (tpt) REVERT: G 208 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8276 (ttpp) outliers start: 63 outliers final: 36 residues processed: 462 average time/residue: 1.4075 time to fit residues: 748.0988 Evaluate side-chains 460 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 419 time to evaluate : 2.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 168 PHE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 241 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 0.9990 chunk 273 optimal weight: 0.5980 chunk 249 optimal weight: 9.9990 chunk 265 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 208 optimal weight: 0.7980 chunk 81 optimal weight: 0.0970 chunk 240 optimal weight: 7.9990 chunk 251 optimal weight: 9.9990 chunk 264 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN K 113 GLN Z 3 ASN Z 51 GLN D 280 GLN D 361 GLN N 113 GLN ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 GLN ** G 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24942 Z= 0.232 Angle : 0.678 17.115 34151 Z= 0.293 Chirality : 0.043 0.314 3592 Planarity : 0.004 0.059 4244 Dihedral : 10.993 103.273 3499 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.47 % Allowed : 20.64 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 1.00 (0.15), residues: 2972 helix: 1.30 (0.13), residues: 1639 sheet: -1.93 (0.59), residues: 57 loop : 0.08 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 147 HIS 0.006 0.001 HIS C 76 PHE 0.018 0.001 PHE I 255 TYR 0.029 0.002 TYR G 72 ARG 0.009 0.000 ARG C 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 421 time to evaluate : 2.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 GLU cc_start: 0.7726 (tp30) cc_final: 0.7241 (tp30) REVERT: I 150 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8137 (tp40) REVERT: J 255 TYR cc_start: 0.7136 (OUTLIER) cc_final: 0.6605 (t80) REVERT: Z 76 HIS cc_start: 0.8546 (t-90) cc_final: 0.8343 (t-90) REVERT: Z 164 ARG cc_start: 0.8483 (mtm180) cc_final: 0.8037 (mtm180) REVERT: D 3 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6248 (mptt) REVERT: D 308 MET cc_start: 0.8317 (tpt) cc_final: 0.8066 (tpp) REVERT: E 152 LYS cc_start: 0.8576 (mttm) cc_final: 0.8328 (mttt) REVERT: E 223 MET cc_start: 0.8089 (tmm) cc_final: 0.7825 (ttp) REVERT: E 238 TYR cc_start: 0.7062 (t80) cc_final: 0.6773 (t80) REVERT: E 412 ARG cc_start: 0.7748 (ttm-80) cc_final: 0.7475 (ttm170) REVERT: E 462 GLN cc_start: 0.6856 (OUTLIER) cc_final: 0.6501 (pp30) REVERT: F 171 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7580 (m-30) REVERT: G 83 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8385 (ptpp) REVERT: G 175 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7733 (mtp85) REVERT: G 195 MET cc_start: 0.8221 (tpt) cc_final: 0.7598 (tpt) REVERT: G 204 GLU cc_start: 0.6273 (tt0) cc_final: 0.5726 (tp30) REVERT: G 208 LYS cc_start: 0.8457 (ttmm) cc_final: 0.8178 (ttpp) outliers start: 59 outliers final: 34 residues processed: 454 average time/residue: 1.4332 time to fit residues: 744.8128 Evaluate side-chains 452 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 413 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 278 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 5.9990 chunk 281 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 133 optimal weight: 0.5980 chunk 195 optimal weight: 0.7980 chunk 294 optimal weight: 0.7980 chunk 271 optimal weight: 0.9980 chunk 234 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 181 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 ASN ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN K 113 GLN Z 3 ASN Z 51 GLN D 280 GLN ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24942 Z= 0.243 Angle : 0.690 17.331 34151 Z= 0.299 Chirality : 0.043 0.393 3592 Planarity : 0.004 0.059 4244 Dihedral : 10.969 103.223 3499 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.01 % Allowed : 21.26 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 1.01 (0.15), residues: 2972 helix: 1.30 (0.13), residues: 1638 sheet: -1.64 (0.61), residues: 57 loop : 0.07 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 54 HIS 0.006 0.001 HIS I 87 PHE 0.017 0.001 PHE I 95 TYR 0.026 0.002 TYR M 240 ARG 0.009 0.000 ARG C 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 427 time to evaluate : 2.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 GLU cc_start: 0.7695 (tp30) cc_final: 0.7171 (tp30) REVERT: I 150 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8142 (tp40) REVERT: J 255 TYR cc_start: 0.7235 (OUTLIER) cc_final: 0.6721 (t80) REVERT: Z 76 HIS cc_start: 0.8545 (t-90) cc_final: 0.8334 (t-90) REVERT: Z 164 ARG cc_start: 0.8495 (mtm180) cc_final: 0.8035 (mtm180) REVERT: D 3 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6245 (mptt) REVERT: D 308 MET cc_start: 0.8317 (tpt) cc_final: 0.8092 (tpp) REVERT: D 328 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7994 (mmm160) REVERT: E 152 LYS cc_start: 0.8560 (mttm) cc_final: 0.8278 (mttt) REVERT: E 223 MET cc_start: 0.8088 (tmm) cc_final: 0.7830 (ttp) REVERT: E 238 TYR cc_start: 0.7108 (t80) cc_final: 0.6830 (t80) REVERT: E 412 ARG cc_start: 0.7736 (ttm-80) cc_final: 0.7379 (ttm170) REVERT: E 462 GLN cc_start: 0.6767 (OUTLIER) cc_final: 0.6409 (pp30) REVERT: F 171 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7611 (m-30) REVERT: G 83 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8343 (ptpp) REVERT: G 175 ARG cc_start: 0.8042 (mtp85) cc_final: 0.7717 (mtp85) REVERT: G 188 MET cc_start: 0.7110 (mmm) cc_final: 0.6653 (mmm) REVERT: G 195 MET cc_start: 0.8222 (tpt) cc_final: 0.7588 (tpt) REVERT: G 204 GLU cc_start: 0.6221 (tt0) cc_final: 0.5316 (tp30) REVERT: G 208 LYS cc_start: 0.8461 (ttmm) cc_final: 0.8211 (ttpp) outliers start: 48 outliers final: 34 residues processed: 456 average time/residue: 1.4296 time to fit residues: 750.6903 Evaluate side-chains 458 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 418 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 130 CYS Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 168 PHE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 89 TYR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 278 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 71 optimal weight: 0.0060 chunk 216 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 241 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN K 113 GLN Z 3 ASN Z 51 GLN Z 61 GLN D 361 GLN ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 GLN ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.100685 restraints weight = 27610.396| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.09 r_work: 0.2591 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2449 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 24942 Z= 0.288 Angle : 0.714 18.306 34151 Z= 0.309 Chirality : 0.044 0.373 3592 Planarity : 0.004 0.059 4244 Dihedral : 11.105 104.118 3499 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.84 % Allowed : 21.31 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.98 % 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: 0.95 (0.15), residues: 2972 helix: 1.26 (0.13), residues: 1633 sheet: -1.64 (0.62), residues: 57 loop : 0.03 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 54 HIS 0.008 0.001 HIS I 87 PHE 0.033 0.002 PHE G 68 TYR 0.029 0.002 TYR M 240 ARG 0.009 0.001 ARG C 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11026.29 seconds wall clock time: 196 minutes 27.84 seconds (11787.84 seconds total)