Starting phenix.real_space_refine on Wed Apr 17 12:29:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snh_40625/04_2024/8snh_40625_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snh_40625/04_2024/8snh_40625.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snh_40625/04_2024/8snh_40625_trim_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/8snh_40625/04_2024/8snh_40625_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snh_40625/04_2024/8snh_40625_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snh_40625/04_2024/8snh_40625.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snh_40625/04_2024/8snh_40625.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snh_40625/04_2024/8snh_40625_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snh_40625/04_2024/8snh_40625_trim_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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 19 7.16 5 Cu 1 5.60 5 S 140 5.16 5 C 15892 2.51 5 N 3937 2.21 5 O 4174 1.98 5 H 19392 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 "C ASP 58": "OD1" <-> "OD2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C GLU 136": "OE1" <-> "OE2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C ASP 193": "OD1" <-> "OD2" Residue "I PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 244": "OD1" <-> "OD2" Residue "J TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 189": "OE1" <-> "OE2" Residue "J GLU 205": "OE1" <-> "OE2" Residue "J PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 76": "OE1" <-> "OE2" Residue "K ASP 86": "OD1" <-> "OD2" Residue "K ASP 91": "OD1" <-> "OD2" Residue "L GLU 30": "OE1" <-> "OE2" Residue "Z ASP 83": "OD1" <-> "OD2" Residue "Z GLU 101": "OE1" <-> "OE2" Residue "Z ASP 145": "OD1" <-> "OD2" Residue "Z TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z ASP 185": "OD1" <-> "OD2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D ASP 20": "OD1" <-> "OD2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D ASP 244": "OD1" <-> "OD2" Residue "M GLU 78": "OE1" <-> "OE2" Residue "M ASP 133": "OD1" <-> "OD2" Residue "M GLU 210": "OE1" <-> "OE2" Residue "M GLU 231": "OE1" <-> "OE2" Residue "M TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 254": "OE1" <-> "OE2" Residue "N GLU 57": "OE1" <-> "OE2" Residue "N PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 174": "OD1" <-> "OD2" Residue "O GLU 30": "OE1" <-> "OE2" Residue "F PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 58": "OD1" <-> "OD2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F ASP 169": "OD1" <-> "OD2" Residue "F ASP 171": "OD1" <-> "OD2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G GLU 49": "OE1" <-> "OE2" Residue "G PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "G TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "G TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 150": "OD1" <-> "OD2" Residue "G ASP 162": "OD1" <-> "OD2" Residue "G ASP 170": "OD1" <-> "OD2" Residue "G GLU 216": "OE1" <-> "OE2" Residue "G TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 283": "OE1" <-> "OE2" Residue "G TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 43557 Number of models: 1 Model: "" Number of chains: 24 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: "C" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2827 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 20, 'TRANS': 169} Chain: "I" Number of atoms: 6556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 6556 Classifications: {'peptide': 403} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 379} Chain: "J" Number of atoms: 3663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3663 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 13, 'TRANS': 218} Chain: "K" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2585 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain: "L" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 244 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "Z" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2883 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 20, 'TRANS': 173} Chain: "D" Number of atoms: 6556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 6556 Classifications: {'peptide': 403} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 379} Chain: "M" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 3250 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 11, 'TRANS': 192} Chain breaks: 1 Chain: "N" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2585 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain: "O" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 244 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "F" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 2917 Classifications: {'peptide': 200} Modifications used: {'NH3': 1} 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: 4655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4655 Classifications: {'peptide': 304} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 289} 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: "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: "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 5498 SG CYS C 124 85.925 89.842 78.269 1.00 73.85 S ATOM 5565 SG CYS C 129 82.145 90.282 77.754 1.00 84.77 S ATOM 5902 SG CYS C 152 83.432 92.560 79.326 1.00 77.21 S ATOM 21406 SG CYS Z 124 43.257 59.253 40.939 1.00 43.68 S ATOM 21811 SG CYS Z 152 46.202 59.766 39.023 1.00 46.64 S Time building chain proxies: 19.11, per 1000 atoms: 0.44 Number of scatterers: 43557 At special positions: 0 Unit cell: (115.36, 141.11, 161.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cu 1 28.99 Fe 19 26.01 Ca 2 19.99 S 140 16.00 O 4174 8.00 N 3937 7.00 C 15892 6.00 H 19392 1.00 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: 36.50 Conformation dependent library (CDL) restraints added in 4.4 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 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5434 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 127 helices and 13 sheets defined 52.5% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.82 Creating SS restraints... 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 'C' and resid 8 through 37 Proline residue: C 32 - end of helix removed outlier: 3.982A 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 9 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 137 Processing helix chain 'I' and resid 143 through 158 removed outlier: 4.007A pdb=" N PHE I 156 " --> pdb=" O ILE I 152 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY I 157 " --> pdb=" O ILE I 153 " (cutoff:3.500A) removed outlier: 3.567A 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: 6.681A 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: 3.633A pdb=" N ILE I 317 " --> pdb=" O MET I 313 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU I 320 " --> pdb=" O ALA I 316 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE I 321 " --> pdb=" O ILE I 317 " (cutoff:3.500A) removed outlier: 3.645A 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: 3.925A pdb=" N PHE I 382 " --> pdb=" O TYR I 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 385 through 391 removed outlier: 4.289A 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 126 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: 3.977A pdb=" N ALA K 29 " --> pdb=" O ALA K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 38 removed outlier: 3.943A 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 111 through 120 Processing helix chain 'K' and resid 154 through 166 Processing helix chain 'K' and resid 177 through 184 removed outlier: 3.879A pdb=" N LYS K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 198 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: 3.876A 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: 3.973A pdb=" N GLU Z 89 " --> pdb=" O LEU Z 85 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLY Z 90 " --> pdb=" O PRO Z 86 " (cutoff:3.500A) removed outlier: 5.982A 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 137 Processing helix chain 'D' and resid 143 through 158 removed outlier: 4.033A pdb=" N PHE D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY D 157 " --> pdb=" O ILE D 153 " (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 236 through 261 removed outlier: 6.734A 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 removed outlier: 3.622A pdb=" N ALA D 298 " --> pdb=" O PRO D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 326 removed outlier: 4.527A pdb=" N LEU D 320 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE D 321 " --> pdb=" O ILE D 317 " (cutoff:3.500A) removed outlier: 3.721A 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: 3.885A pdb=" N PHE D 382 " --> pdb=" O TYR D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 391 removed outlier: 4.388A 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: 3.606A pdb=" N TYR M 236 " --> pdb=" O ARG M 232 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 30 removed outlier: 3.837A pdb=" N ALA N 29 " --> pdb=" O ALA N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 38 removed outlier: 3.939A 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 111 through 120 Processing helix chain 'N' and resid 154 through 166 Processing helix chain 'N' and resid 177 through 184 removed outlier: 4.012A 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 'F' and resid 3 through 9 Processing helix chain 'F' and resid 11 through 29 removed outlier: 4.056A pdb=" N GLY F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY F 26 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR F 28 " --> pdb=" O ILE F 24 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN F 29 " --> pdb=" O GLY F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' 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: 4.442A 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 178 removed outlier: 4.727A pdb=" N ARG F 176 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 4.796A 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 removed outlier: 4.151A pdb=" N THR G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 72 through 75 No H-bonds generated for 'chain 'G' and resid 72 through 75' Processing helix chain 'G' and resid 95 through 109 Processing helix chain 'G' and resid 111 through 119 removed outlier: 3.625A pdb=" N ALA G 115 " --> pdb=" O GLY G 111 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR G 117 " --> pdb=" O ILE G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 142 Processing helix chain 'G' and resid 173 through 180 removed outlier: 4.561A pdb=" N ILE G 178 " --> pdb=" O ILE G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 199 No H-bonds generated for 'chain 'G' and resid 197 through 199' Processing helix chain 'G' and resid 202 through 205 No H-bonds generated for 'chain 'G' and resid 202 through 205' Processing helix chain 'G' and resid 222 through 232 removed outlier: 3.754A pdb=" N VAL G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 272 Processing helix chain 'G' and resid 290 through 301 removed outlier: 3.579A pdb=" N LEU G 294 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA G 296 " --> pdb=" O HIS G 292 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE G 298 " --> pdb=" O LEU G 294 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR G 299 " --> pdb=" O ALA G 295 " (cutoff:3.500A) Processing sheet with id= A, 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) Processing sheet with id= B, first strand: chain 'C' and resid 50 through 53 Processing sheet with id= C, first strand: chain 'C' and resid 62 through 67 Processing sheet with id= D, first strand: chain 'C' and resid 132 through 134 Processing sheet with id= E, first strand: chain 'I' and resid 26 through 28 Processing sheet with id= F, first strand: chain 'J' and resid 130 through 132 Processing sheet with id= G, first strand: chain 'J' and resid 161 through 164 Processing sheet with id= H, first strand: chain 'J' and resid 166 through 169 Processing sheet with id= I, first strand: chain 'Z' and resid 50 through 53 Processing sheet with id= J, first strand: chain 'Z' and resid 62 through 67 Processing sheet with id= K, first strand: chain 'Z' and resid 132 through 134 Processing sheet with id= L, first strand: chain 'D' and resid 26 through 28 Processing sheet with id= M, first strand: chain 'M' and resid 130 through 132 1037 hydrogen bonds defined for protein. 3009 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: 16.23 Time building geometry restraints manager: 37.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.11: 19379 1.11 - 1.38: 9774 1.38 - 1.66: 14878 1.66 - 1.93: 242 1.93 - 2.21: 68 Bond restraints: 44341 Sorted by residual: bond pdb=" C03 I7Y I 501 " pdb=" C04 I7Y I 501 " 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 501 " pdb=" O72 I7Y I 501 " 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 44336 not shown) Histogram of bond angle deviations from ideal: 75.17 - 96.04: 70 96.04 - 116.92: 54202 116.92 - 137.80: 24033 137.80 - 158.67: 2 158.67 - 179.55: 30 Bond angle restraints: 78337 Sorted by residual: angle pdb=" C74 I7Y I 501 " pdb=" C73 I7Y I 501 " pdb=" C76 I7Y I 501 " 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 501 " pdb=" C73 I7Y I 501 " pdb=" O80 I7Y I 501 " 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=" CD ARG F 77 " pdb=" CG ARG F 77 " pdb=" HG3 ARG F 77 " ideal model delta sigma weight residual 108.00 78.09 29.91 3.00e+00 1.11e-01 9.94e+01 ... (remaining 78332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.24: 19271 23.24 - 46.48: 1379 46.48 - 69.72: 372 69.72 - 92.96: 59 92.96 - 116.19: 11 Dihedral angle restraints: 21092 sinusoidal: 10972 harmonic: 10120 Sorted by residual: dihedral pdb=" C2B HEC G 401 " pdb=" C3B HEC G 401 " pdb=" CAB HEC G 401 " pdb=" CBB HEC G 401 " ideal model delta sinusoidal sigma weight residual 60.00 133.66 -73.66 2 1.00e+01 1.00e-02 4.42e+01 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 60.00 129.52 -69.52 2 1.00e+01 1.00e-02 4.21e+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 60.00 117.18 -57.18 2 1.00e+01 1.00e-02 3.39e+01 ... (remaining 21089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.316: 3578 0.316 - 0.632: 5 0.632 - 0.948: 0 0.948 - 1.264: 0 1.264 - 1.580: 2 Chirality restraints: 3585 Sorted by residual: chirality pdb=" C74 I7Y I 501 " pdb=" C03 I7Y I 501 " pdb=" C73 I7Y I 501 " pdb=" C75 I7Y I 501 " 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 3582 not shown) Planarity restraints: 6605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC N 501 " -0.025 2.00e-02 2.50e+03 6.25e-02 8.80e+01 pdb=" C2C HEC N 501 " 0.171 2.00e-02 2.50e+03 pdb=" C3C HEC N 501 " -0.015 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 " -0.030 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 5.67e-02 7.23e+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 F 301 " -0.013 2.00e-02 2.50e+03 3.10e-02 2.16e+01 pdb=" C2C HEC F 301 " 0.083 2.00e-02 2.50e+03 pdb=" C3C HEC F 301 " 0.005 2.00e-02 2.50e+03 pdb=" C4C HEC F 301 " -0.004 2.00e-02 2.50e+03 pdb=" CAC HEC F 301 " -0.027 2.00e-02 2.50e+03 pdb=" CHC HEC F 301 " -0.017 2.00e-02 2.50e+03 pdb=" CHD HEC F 301 " 0.002 2.00e-02 2.50e+03 pdb=" CMC HEC F 301 " -0.024 2.00e-02 2.50e+03 pdb=" NC HEC F 301 " -0.006 2.00e-02 2.50e+03 ... (remaining 6602 not shown) Histogram of nonbonded interaction distances: 1.33 - 1.98: 477 1.98 - 2.64: 52126 2.64 - 3.29: 130654 3.29 - 3.95: 173736 3.95 - 4.60: 267558 Nonbonded interactions: 624551 Sorted by model distance: nonbonded pdb=" OD2 ASP E 417 " pdb="HH21 ARG G 137 " model vdw 1.331 1.850 nonbonded pdb=" OE1 GLU Z 104 " pdb=" H GLU Z 104 " model vdw 1.400 1.850 nonbonded pdb=" H CYS Z 124 " pdb=" O CYS Z 129 " model vdw 1.490 1.850 nonbonded pdb=" HH TYR J 240 " pdb=" O VAL Z 21 " model vdw 1.519 1.850 nonbonded pdb=" O TRP D 291 " pdb=" HG1 THR D 294 " model vdw 1.535 1.850 ... (remaining 624546 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 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name H \ G13 or name HG21 or name HG22 or name HG23)) or resid 7 through 128 or (resid 12 \ 9 and (name N or name CA or name C or name O or name CB or name SG or name H or \ name HA or name HB2 or name HB3)) or resid 130 through 195)) } ncs_group { reference = (chain 'D' and (resid 1 through 403 or resid 502)) selection = (chain 'I' and (resid 1 through 403 or resid 502)) } ncs_group { reference = (chain 'J' and (resid 26 through 163 or (resid 193 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name H \ A or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or \ resid 194 through 257 or resid 500)) selection = (chain 'M' and ((resid 26 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 27 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: 1.840 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: 0.690 Extract box with map and model: 10.060 Check model and map are aligned: 0.680 Set scattering table: 0.410 Process input model: 150.000 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.290 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:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 177.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 24949 Z= 0.441 Angle : 0.830 38.487 34152 Z= 0.377 Chirality : 0.059 1.580 3585 Planarity : 0.004 0.063 4245 Dihedral : 17.823 116.194 8734 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.90 % Favored : 97.00 % Rotamer: Outliers : 1.04 % Allowed : 19.96 % Favored : 79.00 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.01 % 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: 0.51 (0.16), residues: 2964 helix: 0.80 (0.13), residues: 1624 sheet: -2.00 (0.63), residues: 56 loop : -0.00 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 54 HIS 0.006 0.001 HIS I 188 PHE 0.025 0.001 PHE G 68 TYR 0.044 0.002 TYR G 264 ARG 0.013 0.000 ARG J 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 439 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 414 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 261 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.7411 (t-90) REVERT: E 410 MET cc_start: 0.8113 (mmm) cc_final: 0.7715 (mtm) REVERT: D 3 LYS cc_start: 0.8143 (mmtp) cc_final: 0.7809 (mppt) outliers start: 25 outliers final: 15 residues processed: 434 average time/residue: 2.5707 time to fit residues: 1293.7378 Evaluate side-chains 403 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 387 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 130 SER Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 212 SER Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 0.5980 chunk 223 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 172 optimal weight: 0.2980 chunk 267 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS E 407 GLN Z 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.0473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24949 Z= 0.206 Angle : 0.612 13.958 34152 Z= 0.274 Chirality : 0.040 0.169 3585 Planarity : 0.004 0.054 4245 Dihedral : 11.331 109.662 3516 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.90 % Favored : 97.03 % Rotamer: Outliers : 2.04 % Allowed : 18.17 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 0.75 (0.16), residues: 2964 helix: 0.99 (0.13), residues: 1626 sheet: -2.01 (0.57), residues: 70 loop : 0.15 (0.18), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 204 HIS 0.006 0.001 HIS E 300 PHE 0.022 0.001 PHE M 243 TYR 0.014 0.001 TYR I 388 ARG 0.005 0.000 ARG J 253 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 454 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 405 time to evaluate : 3.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 238 TYR cc_start: 0.6399 (t80) cc_final: 0.6139 (t80) REVERT: E 410 MET cc_start: 0.8209 (mmm) cc_final: 0.7831 (mtt) REVERT: D 3 LYS cc_start: 0.8133 (mmtp) cc_final: 0.7795 (mppt) REVERT: D 308 MET cc_start: 0.8252 (tpp) cc_final: 0.8028 (tpt) REVERT: M 231 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: F 158 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.7034 (mt-10) REVERT: F 171 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7359 (m-30) REVERT: G 28 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7415 (ppp-140) outliers start: 49 outliers final: 20 residues processed: 434 average time/residue: 2.6160 time to fit residues: 1321.6912 Evaluate side-chains 412 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 388 time to evaluate : 3.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 28 ARG Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 279 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 chunk 289 optimal weight: 6.9990 chunk 239 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 chunk 91 optimal weight: 0.4980 chunk 215 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS E 407 GLN Z 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 24949 Z= 0.329 Angle : 0.678 16.035 34152 Z= 0.302 Chirality : 0.042 0.169 3585 Planarity : 0.004 0.057 4245 Dihedral : 11.336 110.310 3501 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.50 % Favored : 97.44 % Rotamer: Outliers : 2.21 % Allowed : 18.21 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 0.65 (0.15), residues: 2964 helix: 0.91 (0.13), residues: 1627 sheet: -2.04 (0.53), residues: 76 loop : 0.13 (0.18), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 204 HIS 0.009 0.001 HIS I 87 PHE 0.019 0.002 PHE I 95 TYR 0.024 0.002 TYR G 264 ARG 0.008 0.001 ARG G 166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 453 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 400 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 238 TYR cc_start: 0.6999 (t80) cc_final: 0.6707 (t80) REVERT: E 279 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.8001 (mp) REVERT: E 410 MET cc_start: 0.8546 (mmm) cc_final: 0.8235 (mtt) REVERT: E 412 ARG cc_start: 0.7951 (ttm-80) cc_final: 0.7658 (ttm170) REVERT: E 462 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6805 (pt0) REVERT: I 361 GLN cc_start: 0.8078 (mt0) cc_final: 0.7813 (mt0) REVERT: J 255 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.6958 (t80) REVERT: Z 12 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7821 (ttm-80) REVERT: D 3 LYS cc_start: 0.8138 (mmtp) cc_final: 0.7803 (mppt) REVERT: D 308 MET cc_start: 0.8276 (tpp) cc_final: 0.8062 (tpt) REVERT: M 231 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: N 57 GLU cc_start: 0.8470 (tt0) cc_final: 0.8239 (tt0) REVERT: F 171 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7481 (m-30) REVERT: G 8 TYR cc_start: 0.6952 (t80) cc_final: 0.6746 (t80) REVERT: G 28 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7409 (ppp-140) outliers start: 53 outliers final: 29 residues processed: 433 average time/residue: 2.6774 time to fit residues: 1344.6067 Evaluate side-chains 422 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 386 time to evaluate : 3.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain Z residue 12 ARG Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 231 GLU 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 G residue 28 ARG Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 134 MET Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 265 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 269 optimal weight: 6.9990 chunk 285 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 255 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS Z 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24949 Z= 0.246 Angle : 0.615 14.874 34152 Z= 0.276 Chirality : 0.040 0.239 3585 Planarity : 0.004 0.056 4245 Dihedral : 10.762 108.570 3499 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.80 % Favored : 97.13 % Rotamer: Outliers : 2.38 % Allowed : 18.21 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 2964 helix: 1.02 (0.13), residues: 1625 sheet: -2.04 (0.53), residues: 76 loop : 0.18 (0.18), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 54 HIS 0.009 0.001 HIS E 244 PHE 0.017 0.001 PHE M 243 TYR 0.023 0.002 TYR G 264 ARG 0.007 0.000 ARG G 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 464 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 407 time to evaluate : 3.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 238 TYR cc_start: 0.7040 (t80) cc_final: 0.6817 (t80) REVERT: E 410 MET cc_start: 0.8614 (mmm) cc_final: 0.8408 (mtt) REVERT: E 412 ARG cc_start: 0.7962 (ttm-80) cc_final: 0.7706 (ttm170) REVERT: E 462 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6753 (pt0) REVERT: J 255 TYR cc_start: 0.7310 (OUTLIER) cc_final: 0.6827 (t80) REVERT: Z 12 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7813 (ttm-80) REVERT: D 3 LYS cc_start: 0.8132 (mmtp) cc_final: 0.7802 (mppt) REVERT: D 308 MET cc_start: 0.8263 (tpp) cc_final: 0.8043 (tpt) REVERT: M 231 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: F 158 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7096 (mt-10) REVERT: F 171 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7514 (m-30) REVERT: G 28 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7475 (ppp-140) REVERT: G 192 ILE cc_start: 0.7691 (mm) cc_final: 0.7377 (mm) outliers start: 57 outliers final: 28 residues processed: 439 average time/residue: 2.6573 time to fit residues: 1355.0248 Evaluate side-chains 428 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 393 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 167 SER Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain Z residue 12 ARG Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 28 ARG Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 134 MET Chi-restraints excluded: chain G residue 137 ARG Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 237 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 212 optimal weight: 0.2980 chunk 117 optimal weight: 0.1980 chunk 243 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 255 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 3 ASN G 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24949 Z= 0.199 Angle : 0.590 14.423 34152 Z= 0.264 Chirality : 0.039 0.141 3585 Planarity : 0.004 0.055 4245 Dihedral : 10.350 107.114 3497 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.67 % Favored : 97.30 % Rotamer: Outliers : 1.67 % Allowed : 19.38 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 0.96 (0.16), residues: 2964 helix: 1.22 (0.13), residues: 1618 sheet: -2.07 (0.53), residues: 76 loop : 0.21 (0.18), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 147 HIS 0.008 0.001 HIS E 244 PHE 0.016 0.001 PHE M 243 TYR 0.024 0.001 TYR G 264 ARG 0.007 0.000 ARG G 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 441 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 401 time to evaluate : 3.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 238 TYR cc_start: 0.6992 (t80) cc_final: 0.6726 (t80) REVERT: E 412 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7708 (ttm170) REVERT: E 462 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6745 (pt0) REVERT: I 361 GLN cc_start: 0.7933 (mt0) cc_final: 0.7573 (mt0) REVERT: J 255 TYR cc_start: 0.7262 (OUTLIER) cc_final: 0.6802 (t80) REVERT: Z 12 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7818 (ttm-80) REVERT: D 3 LYS cc_start: 0.8127 (mmtp) cc_final: 0.7801 (mppt) REVERT: D 308 MET cc_start: 0.8255 (tpp) cc_final: 0.8055 (tpt) REVERT: M 231 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: F 171 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7534 (m-30) REVERT: F 185 MET cc_start: 0.8682 (tpp) cc_final: 0.8359 (tpp) REVERT: G 28 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7396 (ppp-140) REVERT: G 175 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7936 (tm-30) REVERT: G 192 ILE cc_start: 0.7702 (mm) cc_final: 0.7405 (mm) REVERT: G 288 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8075 (tmmm) outliers start: 40 outliers final: 21 residues processed: 426 average time/residue: 2.6322 time to fit residues: 1297.7013 Evaluate side-chains 422 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 393 time to evaluate : 3.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain Z residue 12 ARG Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain M residue 231 GLU 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 G residue 28 ARG Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 137 ARG Chi-restraints excluded: chain G residue 175 GLU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 288 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 95 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 285 optimal weight: 4.9990 chunk 236 optimal weight: 0.1980 chunk 132 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 157 HIS ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 ASN I 280 GLN Z 3 ASN G 172 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24949 Z= 0.206 Angle : 0.586 13.867 34152 Z= 0.262 Chirality : 0.039 0.141 3585 Planarity : 0.004 0.055 4245 Dihedral : 10.219 105.574 3497 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.70 % Favored : 97.27 % Rotamer: Outliers : 1.67 % Allowed : 19.17 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.16), residues: 2964 helix: 1.34 (0.13), residues: 1615 sheet: -2.02 (0.48), residues: 86 loop : 0.22 (0.18), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 147 HIS 0.009 0.001 HIS E 244 PHE 0.016 0.001 PHE J 247 TYR 0.029 0.001 TYR G 264 ARG 0.008 0.000 ARG G 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 445 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 405 time to evaluate : 3.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 238 TYR cc_start: 0.7057 (t80) cc_final: 0.6791 (t80) REVERT: E 357 MET cc_start: 0.8757 (tpp) cc_final: 0.8505 (mmp) REVERT: E 412 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7720 (ttm170) REVERT: E 436 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8290 (mt) REVERT: E 462 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6841 (pt0) REVERT: I 3 LYS cc_start: 0.7079 (mppt) cc_final: 0.6510 (mttm) REVERT: I 361 GLN cc_start: 0.7966 (mt0) cc_final: 0.7559 (mt0) REVERT: J 255 TYR cc_start: 0.7230 (OUTLIER) cc_final: 0.6767 (t80) REVERT: Z 12 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7832 (ttm-80) REVERT: D 3 LYS cc_start: 0.8128 (mmtp) cc_final: 0.7805 (mppt) REVERT: M 231 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: F 158 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7099 (mt-10) REVERT: F 185 MET cc_start: 0.8698 (tpp) cc_final: 0.8380 (tpp) REVERT: G 28 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7442 (ppp-140) REVERT: G 192 ILE cc_start: 0.7696 (mm) cc_final: 0.7400 (mm) REVERT: G 288 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8221 (tmmm) outliers start: 40 outliers final: 24 residues processed: 428 average time/residue: 2.3971 time to fit residues: 1188.0267 Evaluate side-chains 427 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotame------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 284 optimal weight: 9.9990 chunk 177 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24949 Z= 0.239 Angle : 0.603 14.484 34152 Z= 0.270 Chirality : 0.040 0.140 3585 Planarity : 0.004 0.055 4245 Dihedral : 10.238 104.790 3494 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.73 % Favored : 97.23 % Rotamer: Outliers : 1.79 % Allowed : 19.21 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.16), residues: 2964 helix: 1.32 (0.13), residues: 1620 sheet: -2.02 (0.48), residues: 86 loop : 0.23 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 54 HIS 0.008 0.001 HIS E 244 PHE 0.017 0.001 PHE I 95 TYR 0.032 0.002 TYR G 264 ARG 0.009 0.000 ARG G 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 451 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 408 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 238 TYR cc_start: 0.7219 (t80) cc_final: 0.6943 (t80) REVERT: E 357 MET cc_start: 0.8836 (tpp) cc_final: 0.8627 (mmt) REVERT: E 412 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7680 (ttm170) REVERT: E 436 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8318 (mt) REVERT: E 462 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6839 (pt0) REVERT: I 361 GLN cc_start: 0.7940 (mt0) cc_final: 0.7505 (mt0) REVERT: J 255 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6928 (t80) REVERT: Z 12 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7823 (ttm-80) REVERT: D 3 LYS cc_start: 0.8127 (mmtp) cc_final: 0.7798 (mppt) REVERT: M 231 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: F 158 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7108 (mt-10) REVERT: F 171 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: F 185 MET cc_start: 0.8698 (tpp) cc_final: 0.8435 (tpp) REVERT: G 28 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7662 (ppp-140) outliers start: 43 outliers final: 23 residues processed: 433 average time/residue: 2.4895 time to fit residues: 1247.0956 Evaluate side-chains 428 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 397 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 168 PHE Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain Z residue 12 ARG Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain G residue 28 ARG Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 137 ARG Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 288 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 175 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 223 optimal weight: 0.6980 chunk 258 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: