Starting phenix.real_space_refine (version: dev) on Fri Mar 17 14:26:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nho_12335/03_2023/7nho_12335_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nho_12335/03_2023/7nho_12335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nho_12335/03_2023/7nho_12335.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nho_12335/03_2023/7nho_12335.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nho_12335/03_2023/7nho_12335_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nho_12335/03_2023/7nho_12335_updated.pdb" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B ASP 125": "OD1" <-> "OD2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "B PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 95": "OD1" <-> "OD2" Residue "C PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 296": "OE1" <-> "OE2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C GLU 355": "OE1" <-> "OE2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C ASP 371": "OD1" <-> "OD2" Residue "C GLU 401": "OE1" <-> "OE2" Residue "C ARG 437": "NH1" <-> "NH2" Residue "C PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "D ASP 25": "OD1" <-> "OD2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D GLU 242": "OE1" <-> "OE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 297": "OD1" <-> "OD2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D ASP 308": "OD1" <-> "OD2" Residue "D TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 333": "OD1" <-> "OD2" Residue "D GLU 337": "OE1" <-> "OE2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "E PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ASP 68": "OD1" <-> "OD2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "H PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 34": "NH1" <-> "NH2" Residue "K TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 19": "OD1" <-> "OD2" Residue "L ARG 7": "NH1" <-> "NH2" Residue "L PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 30": "OE1" <-> "OE2" Residue "T GLU 2": "OE1" <-> "OE2" Residue "T PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 25": "OE1" <-> "OE2" Residue "y ARG 43": "NH1" <-> "NH2" Residue "Z PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 19800 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2627 Classifications: {'peptide': 335} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 319} Chain: "B" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3812 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 31, 'TRANS': 453} Chain: "C" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3465 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 24, 'TRANS': 423} Chain: "D" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2705 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 15, 'TRANS': 324} Chain: "E" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 635 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain: "F" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "H" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 511 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "I" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 286 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "K" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 293 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "L" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 304 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "M" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 267 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "T" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 256 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 2, 'TRANS': 27} Chain: "X" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 254 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "y" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 208 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "Z" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 479 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "A" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 469 Unusual residues: {' CL': 1, ' FE': 1, ' MN': 1, 'BCR': 1, 'BCT': 1, 'CLA': 4, 'LHG': 2, 'PHO': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 1215 Unusual residues: {'BCR': 3, 'CLA': 16, 'LMG': 1} Classifications: {'undetermined': 20} Link IDs: {None: 19} Chain: "C" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 980 Unusual residues: {'BCR': 2, 'CLA': 13, 'LMG': 1} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "D" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 414 Unusual residues: {'CLA': 2, 'LMG': 3, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.20, per 1000 atoms: 0.62 Number of scatterers: 19800 At special positions: 0 Unit cell: (111.18, 107.91, 136.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Fe 2 26.01 Mn 1 24.99 Cl 1 17.00 S 66 16.00 P 2 15.00 Mg 35 11.99 O 3097 8.00 N 2832 7.00 C 13764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=25, symmetry=0 Number of additional bonds: simple=25, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.34 Conformation dependent library (CDL) restraints added in 2.5 seconds 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3764 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 6 sheets defined 55.7% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 32 through 54 removed outlier: 4.106A pdb=" N ILE A 36 " --> pdb=" O TRP A 32 " (cutoff:3.500A) Proline residue: A 39 - end of helix removed outlier: 3.822A pdb=" N ILE A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 110 through 136 removed outlier: 3.505A pdb=" N LEU A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N HIS A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TRP A 131 " --> pdb=" O MET A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 158 removed outlier: 3.501A pdb=" N SER A 148 " --> pdb=" O CYS A 144 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 196 through 220 Processing helix chain 'A' and resid 233 through 236 removed outlier: 3.572A pdb=" N GLY A 236 " --> pdb=" O ALA A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 236' Processing helix chain 'A' and resid 248 through 258 removed outlier: 3.634A pdb=" N ARG A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 293 Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'B' and resid 16 through 43 Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 93 through 116 removed outlier: 3.671A pdb=" N ILE B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 156 Processing helix chain 'B' and resid 187 through 190 Processing helix chain 'B' and resid 195 through 218 removed outlier: 3.703A pdb=" N VAL B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS B 202 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B 206 " --> pdb=" O HIS B 202 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 234 through 257 Processing helix chain 'B' and resid 272 through 275 No H-bonds generated for 'chain 'B' and resid 272 through 275' Processing helix chain 'B' and resid 279 through 293 removed outlier: 3.604A pdb=" N GLU B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 307 through 311 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 331 through 334 No H-bonds generated for 'chain 'B' and resid 331 through 334' Processing helix chain 'B' and resid 392 through 395 No H-bonds generated for 'chain 'B' and resid 392 through 395' Processing helix chain 'B' and resid 414 through 426 removed outlier: 3.703A pdb=" N LYS B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N PHE B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 474 removed outlier: 3.867A pdb=" N PHE B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 30 removed outlier: 6.039A pdb=" N ASN C 27 " --> pdb=" O TRP C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 62 removed outlier: 3.846A pdb=" N GLY C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS C 62 " --> pdb=" O PHE C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 97 through 122 removed outlier: 4.060A pdb=" N ALA C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 168 removed outlier: 4.256A pdb=" N LEU C 163 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 201 removed outlier: 3.725A pdb=" N TYR C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' Processing helix chain 'C' and resid 218 through 240 Processing helix chain 'C' and resid 246 through 249 No H-bonds generated for 'chain 'C' and resid 246 through 249' Processing helix chain 'C' and resid 258 through 280 Processing helix chain 'C' and resid 294 through 312 removed outlier: 4.142A pdb=" N SER C 298 " --> pdb=" O GLY C 294 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 311 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 357 No H-bonds generated for 'chain 'C' and resid 355 through 357' Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.532A pdb=" N ASN C 370 " --> pdb=" O ASN C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 410 through 441 Processing helix chain 'C' and resid 454 through 456 No H-bonds generated for 'chain 'C' and resid 454 through 456' Processing helix chain 'D' and resid 15 through 22 Processing helix chain 'D' and resid 31 through 54 removed outlier: 4.019A pdb=" N ILE D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU D 36 " --> pdb=" O TRP D 32 " (cutoff:3.500A) Proline residue: D 39 - end of helix removed outlier: 3.669A pdb=" N THR D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 109 through 136 removed outlier: 3.562A pdb=" N ILE D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 156 removed outlier: 3.654A pdb=" N SER D 147 " --> pdb=" O ALA D 143 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 167 through 169 No H-bonds generated for 'chain 'D' and resid 167 through 169' Processing helix chain 'D' and resid 175 through 189 Processing helix chain 'D' and resid 191 through 193 No H-bonds generated for 'chain 'D' and resid 191 through 193' Processing helix chain 'D' and resid 195 through 219 removed outlier: 3.576A pdb=" N ALA D 212 " --> pdb=" O ALA D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 256 removed outlier: 3.620A pdb=" N GLN D 255 " --> pdb=" O ARG D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 289 Proline residue: D 275 - end of helix Processing helix chain 'D' and resid 299 through 307 Processing helix chain 'D' and resid 314 through 333 Proline residue: D 331 - end of helix Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'E' and resid 10 through 14 Processing helix chain 'E' and resid 17 through 39 removed outlier: 4.833A pdb=" N ILE E 25 " --> pdb=" O VAL E 21 " (cutoff:3.500A) Proline residue: E 28 - end of helix removed outlier: 3.947A pdb=" N VAL E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 46 No H-bonds generated for 'chain 'E' and resid 43 through 46' Processing helix chain 'E' and resid 72 through 81 Processing helix chain 'F' and resid 18 through 24 Processing helix chain 'F' and resid 28 through 42 removed outlier: 3.502A pdb=" N ALA F 38 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN F 41 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE F 42 " --> pdb=" O ALA F 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 10 Processing helix chain 'H' and resid 12 through 14 No H-bonds generated for 'chain 'H' and resid 12 through 14' Processing helix chain 'H' and resid 28 through 49 removed outlier: 4.236A pdb=" N VAL H 33 " --> pdb=" O PRO H 29 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE H 34 " --> pdb=" O LEU H 30 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY H 36 " --> pdb=" O ALA H 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 24 removed outlier: 3.630A pdb=" N ILE I 6 " --> pdb=" O GLU I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 29 No H-bonds generated for 'chain 'I' and resid 27 through 29' Processing helix chain 'K' and resid 15 through 24 Proline residue: K 20 - end of helix removed outlier: 3.518A pdb=" N VAL K 24 " --> pdb=" O LEU K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 42 removed outlier: 3.864A pdb=" N PHE K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU K 33 " --> pdb=" O PRO K 29 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE K 37 " --> pdb=" O LEU K 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 35 removed outlier: 4.583A pdb=" N SER L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR L 34 " --> pdb=" O LEU L 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 30 removed outlier: 3.677A pdb=" N ILE M 9 " --> pdb=" O GLN M 5 " (cutoff:3.500A) Proline residue: M 18 - end of helix removed outlier: 3.689A pdb=" N THR M 29 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU M 30 " --> pdb=" O TYR M 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 22 Processing helix chain 'X' and resid 5 through 34 Processing helix chain 'y' and resid 22 through 39 removed outlier: 4.154A pdb=" N GLY y 29 " --> pdb=" O ILE y 25 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE y 30 " --> pdb=" O ALA y 26 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLY y 32 " --> pdb=" O ILE y 28 " (cutoff:3.500A) Proline residue: y 33 - end of helix removed outlier: 3.924A pdb=" N ILE y 36 " --> pdb=" O GLY y 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2 through 28 Proline residue: Z 24 - end of helix Processing helix chain 'Z' and resid 37 through 56 Processing sheet with id= A, first strand: chain 'B' and resid 166 through 169 Processing sheet with id= B, first strand: chain 'B' and resid 343 through 347 Processing sheet with id= C, first strand: chain 'B' and resid 336 through 340 removed outlier: 7.118A pdb=" N GLU B 431 " --> pdb=" O GLN B 338 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 369 through 371 Processing sheet with id= E, first strand: chain 'C' and resid 173 through 175 Processing sheet with id= F, first strand: chain 'C' and resid 329 through 331 758 hydrogen bonds defined for protein. 2232 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.86 Time building geometry restraints manager: 8.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.36: 5641 1.36 - 1.56: 14363 1.56 - 1.76: 356 1.76 - 1.95: 118 1.95 - 2.15: 144 Bond restraints: 20622 Sorted by residual: bond pdb=" CAD CLA C 512 " pdb=" CBD CLA C 512 " ideal model delta sigma weight residual 1.563 1.687 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C3D CLA B 615 " pdb=" CAD CLA B 615 " ideal model delta sigma weight residual 1.454 1.577 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" CAD CLA B 603 " pdb=" CBD CLA B 603 " ideal model delta sigma weight residual 1.563 1.685 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C3D CLA B 610 " pdb=" CAD CLA B 610 " ideal model delta sigma weight residual 1.454 1.571 -0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" CAD CLA B 602 " pdb=" CBD CLA B 602 " ideal model delta sigma weight residual 1.563 1.676 -0.113 2.00e-02 2.50e+03 3.22e+01 ... (remaining 20617 not shown) Histogram of bond angle deviations from ideal: 84.40 - 103.32: 487 103.32 - 122.24: 22934 122.24 - 141.16: 4983 141.16 - 160.08: 15 160.08 - 179.00: 72 Bond angle restraints: 28491 Sorted by residual: angle pdb=" CA GLU C 401 " pdb=" CB GLU C 401 " pdb=" CG GLU C 401 " ideal model delta sigma weight residual 114.10 134.49 -20.39 2.00e+00 2.50e-01 1.04e+02 angle pdb=" N ASP C 348 " pdb=" CA ASP C 348 " pdb=" C ASP C 348 " ideal model delta sigma weight residual 113.17 103.93 9.24 1.26e+00 6.30e-01 5.38e+01 angle pdb=" C1A CLA C 506 " pdb=" C2A CLA C 506 " pdb=" CAA CLA C 506 " ideal model delta sigma weight residual 110.32 90.58 19.74 3.00e+00 1.11e-01 4.33e+01 angle pdb=" CB GLU C 401 " pdb=" CG GLU C 401 " pdb=" CD GLU C 401 " ideal model delta sigma weight residual 112.60 123.61 -11.01 1.70e+00 3.46e-01 4.20e+01 angle pdb=" N SER E 16 " pdb=" CA SER E 16 " pdb=" C SER E 16 " ideal model delta sigma weight residual 108.46 98.84 9.62 1.51e+00 4.39e-01 4.06e+01 ... (remaining 28486 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.44: 9798 24.44 - 48.88: 621 48.88 - 73.32: 147 73.32 - 97.76: 62 97.76 - 122.20: 11 Dihedral angle restraints: 10639 sinusoidal: 4742 harmonic: 5897 Sorted by residual: dihedral pdb=" CA MET H 35 " pdb=" C MET H 35 " pdb=" N GLY H 36 " pdb=" CA GLY H 36 " ideal model delta harmonic sigma weight residual 180.00 88.31 91.69 0 5.00e+00 4.00e-02 3.36e+02 dihedral pdb=" CA GLN M 32 " pdb=" C GLN M 32 " pdb=" N GLN M 33 " pdb=" CA GLN M 33 " ideal model delta harmonic sigma weight residual 180.00 -121.37 -58.63 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CA ARG y 42 " pdb=" C ARG y 42 " pdb=" N ARG y 43 " pdb=" CA ARG y 43 " ideal model delta harmonic sigma weight residual -180.00 -143.89 -36.11 0 5.00e+00 4.00e-02 5.22e+01 ... (remaining 10636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.807: 2705 0.807 - 1.614: 1 1.614 - 2.420: 0 2.420 - 3.227: 0 3.227 - 4.034: 37 Chirality restraints: 2743 Sorted by residual: chirality pdb=" C8 CLA B 616 " pdb=" C10 CLA B 616 " pdb=" C7 CLA B 616 " pdb=" C9 CLA B 616 " both_signs ideal model delta sigma weight residual False 2.59 -1.44 4.03 2.00e-01 2.50e+01 4.07e+02 chirality pdb=" C8 CLA B 605 " pdb=" C10 CLA B 605 " pdb=" C7 CLA B 605 " pdb=" C9 CLA B 605 " both_signs ideal model delta sigma weight residual False 2.59 -1.33 3.93 2.00e-01 2.50e+01 3.86e+02 chirality pdb=" C8 CLA A 408 " pdb=" C10 CLA A 408 " pdb=" C7 CLA A 408 " pdb=" C9 CLA A 408 " both_signs ideal model delta sigma weight residual False 2.59 -1.25 3.85 2.00e-01 2.50e+01 3.70e+02 ... (remaining 2740 not shown) Planarity restraints: 3571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A CLA C 506 " 0.174 2.00e-02 2.50e+03 1.42e-01 3.04e+02 pdb=" C2A CLA C 506 " -0.224 2.00e-02 2.50e+03 pdb=" C4A CLA C 506 " 0.048 2.00e-02 2.50e+03 pdb=" CHA CLA C 506 " 0.009 2.00e-02 2.50e+03 pdb=" NA CLA C 506 " 0.136 2.00e-02 2.50e+03 pdb="MG CLA C 506 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO D 405 " -0.073 2.00e-02 2.50e+03 9.73e-02 2.13e+02 pdb=" C1B PHO D 405 " -0.007 2.00e-02 2.50e+03 pdb=" C2B PHO D 405 " -0.040 2.00e-02 2.50e+03 pdb=" C3B PHO D 405 " -0.062 2.00e-02 2.50e+03 pdb=" C4B PHO D 405 " -0.071 2.00e-02 2.50e+03 pdb=" CAB PHO D 405 " 0.173 2.00e-02 2.50e+03 pdb=" CHB PHO D 405 " 0.167 2.00e-02 2.50e+03 pdb=" CHC PHO D 405 " 0.020 2.00e-02 2.50e+03 pdb=" CMB PHO D 405 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C PHO D 405 " -0.073 2.00e-02 2.50e+03 8.31e-02 1.55e+02 pdb=" C2C PHO D 405 " -0.056 2.00e-02 2.50e+03 pdb=" C3C PHO D 405 " -0.053 2.00e-02 2.50e+03 pdb=" C4C PHO D 405 " -0.072 2.00e-02 2.50e+03 pdb=" CAC PHO D 405 " 0.011 2.00e-02 2.50e+03 pdb=" CHC PHO D 405 " 0.108 2.00e-02 2.50e+03 pdb=" CHD PHO D 405 " 0.149 2.00e-02 2.50e+03 pdb=" CMC PHO D 405 " 0.070 2.00e-02 2.50e+03 pdb=" NC PHO D 405 " -0.084 2.00e-02 2.50e+03 ... (remaining 3568 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 41 2.56 - 3.14: 14000 3.14 - 3.73: 29300 3.73 - 4.31: 44245 4.31 - 4.90: 71819 Nonbonded interactions: 159405 Sorted by model distance: nonbonded pdb=" NE2 HIS D 214 " pdb="FE FE A 401 " model vdw 1.974 2.340 nonbonded pdb=" NE2 HIS A 215 " pdb="FE FE A 401 " model vdw 2.069 2.340 nonbonded pdb=" OG1 THR B 128 " pdb=" OE1 GLU B 130 " model vdw 2.213 2.440 nonbonded pdb=" N GLU D 343 " pdb=" OE1 GLU D 343 " model vdw 2.308 2.520 nonbonded pdb=" OE2 GLU C 129 " pdb=" O TYR C 137 " model vdw 2.440 3.040 ... (remaining 159400 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Mn 1 7.51 5 Fe 2 7.16 5 P 2 5.49 5 Mg 35 5.21 5 S 66 5.16 5 Cl 1 4.86 5 C 13764 2.51 5 N 2832 2.21 5 O 3097 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 5.640 Check model and map are aligned: 0.270 Process input model: 51.440 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.220 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:17.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 : 0.014 0.124 20622 Z= 0.823 Angle : 2.157 20.394 28491 Z= 1.023 Chirality : 0.436 4.034 2743 Planarity : 0.017 0.161 3571 Dihedral : 18.544 122.200 6875 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.45 % Favored : 94.41 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.16), residues: 2056 helix: -1.01 (0.13), residues: 1180 sheet: -0.83 (0.88), residues: 22 loop : -2.28 (0.18), residues: 854 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 640 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 12 residues processed: 652 average time/residue: 0.8495 time to fit residues: 636.3435 Evaluate side-chains 466 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 454 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 5 residues processed: 8 average time/residue: 0.3451 time to fit residues: 5.1518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 157 optimal weight: 0.0970 chunk 60 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 182 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 187 GLN A 296 ASN A 301 ASN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN B 179 GLN B 194 ASN B 274 GLN B 282 GLN B 285 ASN C 366 ASN C 373 GLN D 98 GLN ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN D 164 GLN D 186 GLN D 255 GLN ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN M 28 GLN X 33 GLN y 21 GLN Z 31 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2891 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: