Starting phenix.real_space_refine (version: 1.21rc1) on Sat May 13 00:20:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0x_32928/05_2023/7x0x_32928_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0x_32928/05_2023/7x0x_32928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0x_32928/05_2023/7x0x_32928.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0x_32928/05_2023/7x0x_32928.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0x_32928/05_2023/7x0x_32928_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0x_32928/05_2023/7x0x_32928_updated.pdb" } resolution = 2.56 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= -0.001 sd= 0.186 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14652 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 64 5.16 5 C 10096 2.51 5 N 2680 2.21 5 O 2832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 16": "NH1" <-> "NH2" Residue "D GLU 18": "OE1" <-> "OE2" Residue "D ASP 19": "OD1" <-> "OD2" Residue "D GLU 41": "OE1" <-> "OE2" Residue "D TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 88": "OD1" <-> "OD2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 160": "OD1" <-> "OD2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D ARG 266": "NH1" <-> "NH2" Residue "D PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 335": "NH1" <-> "NH2" Residue "D GLU 347": "OE1" <-> "OE2" Residue "D GLU 391": "OE1" <-> "OE2" Residue "D GLU 428": "OE1" <-> "OE2" Residue "D ASP 450": "OD1" <-> "OD2" Residue "B ARG 16": "NH1" <-> "NH2" Residue "B GLU 18": "OE1" <-> "OE2" Residue "B ASP 19": "OD1" <-> "OD2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 160": "OD1" <-> "OD2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B GLU 391": "OE1" <-> "OE2" Residue "B GLU 428": "OE1" <-> "OE2" Residue "B ASP 450": "OD1" <-> "OD2" Residue "C ARG 16": "NH1" <-> "NH2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C ASP 19": "OD1" <-> "OD2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 160": "OD1" <-> "OD2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C ARG 266": "NH1" <-> "NH2" Residue "C PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 335": "NH1" <-> "NH2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "C GLU 391": "OE1" <-> "OE2" Residue "C GLU 428": "OE1" <-> "OE2" Residue "C ASP 450": "OD1" <-> "OD2" Residue "A ARG 16": "NH1" <-> "NH2" Residue "A GLU 18": "OE1" <-> "OE2" Residue "A ASP 19": "OD1" <-> "OD2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 160": "OD1" <-> "OD2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A GLU 428": "OE1" <-> "OE2" Residue "A ASP 450": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 15680 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3867 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 26, 'TRANS': 449} Chain breaks: 2 Chain: "B" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3867 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 26, 'TRANS': 449} Chain breaks: 2 Chain: "C" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3867 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 26, 'TRANS': 449} Chain breaks: 2 Chain: "A" Number of atoms: 3867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3867 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 26, 'TRANS': 449} Chain breaks: 2 Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.06, per 1000 atoms: 0.58 Number of scatterers: 15680 At special positions: 0 Unit cell: (125.005, 127.179, 77.177, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 8 15.00 O 2832 8.00 N 2680 7.00 C 10096 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=0, symmetry=0 Time building additional restraints: 6.38 Conformation dependent library (CDL) restraints added in 2.5 seconds 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3592 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 4 sheets defined 51.1% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'D' and resid 21 through 26 Processing helix chain 'D' and resid 44 through 46 No H-bonds generated for 'chain 'D' and resid 44 through 46' Processing helix chain 'D' and resid 50 through 69 removed outlier: 3.661A pdb=" N ALA D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER D 66 " --> pdb=" O HIS D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 93 removed outlier: 3.869A pdb=" N LEU D 87 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 119 removed outlier: 3.914A pdb=" N VAL D 110 " --> pdb=" O PRO D 106 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 116 " --> pdb=" O ASP D 112 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU D 117 " --> pdb=" O HIS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 160 removed outlier: 3.926A pdb=" N LYS D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 208 removed outlier: 3.916A pdb=" N LEU D 205 " --> pdb=" O PRO D 201 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU D 206 " --> pdb=" O SER D 202 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N THR D 207 " --> pdb=" O ASN D 203 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ARG D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 227 removed outlier: 3.568A pdb=" N LYS D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 235 No H-bonds generated for 'chain 'D' and resid 232 through 235' Processing helix chain 'D' and resid 248 through 252 Processing helix chain 'D' and resid 258 through 274 removed outlier: 3.753A pdb=" N ILE D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE D 271 " --> pdb=" O MET D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 303 removed outlier: 3.529A pdb=" N LEU D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG D 294 " --> pdb=" O GLY D 290 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG D 298 " --> pdb=" O ARG D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 333 Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'D' and resid 356 through 368 Processing helix chain 'D' and resid 374 through 384 removed outlier: 3.525A pdb=" N ASP D 383 " --> pdb=" O LYS D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 401 removed outlier: 3.608A pdb=" N SER D 401 " --> pdb=" O TRP D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 423 removed outlier: 3.600A pdb=" N TYR D 423 " --> pdb=" O GLN D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 433 removed outlier: 3.512A pdb=" N TRP D 433 " --> pdb=" O TYR D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 437 No H-bonds generated for 'chain 'D' and resid 435 through 437' Processing helix chain 'D' and resid 448 through 450 No H-bonds generated for 'chain 'D' and resid 448 through 450' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 474 through 493 removed outlier: 3.584A pdb=" N GLU D 479 " --> pdb=" O ASP D 475 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D 482 " --> pdb=" O ARG D 478 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU D 490 " --> pdb=" O SER D 486 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE D 493 " --> pdb=" O ARG D 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 44 through 46 No H-bonds generated for 'chain 'B' and resid 44 through 46' Processing helix chain 'B' and resid 50 through 69 removed outlier: 3.662A pdb=" N ALA B 61 " --> pdb=" O LYS B 57 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 66 " --> pdb=" O HIS B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.869A pdb=" N LEU B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 119 removed outlier: 3.913A pdb=" N VAL B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU B 117 " --> pdb=" O HIS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 160 removed outlier: 3.926A pdb=" N LYS B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 208 removed outlier: 3.916A pdb=" N LEU B 205 " --> pdb=" O PRO B 201 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU B 206 " --> pdb=" O SER B 202 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR B 207 " --> pdb=" O ASN B 203 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ARG B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 227 removed outlier: 3.568A pdb=" N LYS B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 235 No H-bonds generated for 'chain 'B' and resid 232 through 235' Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 258 through 274 removed outlier: 3.752A pdb=" N ILE B 270 " --> pdb=" O ARG B 266 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 271 " --> pdb=" O MET B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 303 removed outlier: 3.528A pdb=" N LEU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 333 Processing helix chain 'B' and resid 339 through 351 Processing helix chain 'B' and resid 356 through 368 Processing helix chain 'B' and resid 374 through 384 removed outlier: 3.524A pdb=" N ASP B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 401 removed outlier: 3.608A pdb=" N SER B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 removed outlier: 3.601A pdb=" N TYR B 423 " --> pdb=" O GLN B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 removed outlier: 3.512A pdb=" N TRP B 433 " --> pdb=" O TYR B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 448 through 450 No H-bonds generated for 'chain 'B' and resid 448 through 450' Processing helix chain 'B' and resid 453 through 458 Processing helix chain 'B' and resid 474 through 493 removed outlier: 3.585A pdb=" N GLU B 479 " --> pdb=" O ASP B 475 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 482 " --> pdb=" O ARG B 478 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B 483 " --> pdb=" O GLU B 479 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 493 " --> pdb=" O ARG B 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 44 through 46 No H-bonds generated for 'chain 'C' and resid 44 through 46' Processing helix chain 'C' and resid 50 through 69 removed outlier: 3.661A pdb=" N ALA C 61 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C 65 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 66 " --> pdb=" O HIS C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 93 removed outlier: 3.868A pdb=" N LEU C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 119 removed outlier: 3.914A pdb=" N VAL C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS C 116 " --> pdb=" O ASP C 112 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU C 117 " --> pdb=" O HIS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 160 removed outlier: 3.926A pdb=" N LYS C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP C 160 " --> pdb=" O LYS C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 208 removed outlier: 3.915A pdb=" N LEU C 205 " --> pdb=" O PRO C 201 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU C 206 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR C 207 " --> pdb=" O ASN C 203 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ARG C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 227 removed outlier: 3.567A pdb=" N LYS C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 235 No H-bonds generated for 'chain 'C' and resid 232 through 235' Processing helix chain 'C' and resid 248 through 252 Processing helix chain 'C' and resid 258 through 274 removed outlier: 3.752A pdb=" N ILE C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 271 " --> pdb=" O MET C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 303 removed outlier: 3.528A pdb=" N LEU C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG C 298 " --> pdb=" O ARG C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 333 Processing helix chain 'C' and resid 339 through 351 Processing helix chain 'C' and resid 356 through 368 Processing helix chain 'C' and resid 374 through 384 removed outlier: 3.524A pdb=" N ASP C 383 " --> pdb=" O LYS C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 401 removed outlier: 3.609A pdb=" N SER C 401 " --> pdb=" O TRP C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 423 removed outlier: 3.601A pdb=" N TYR C 423 " --> pdb=" O GLN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 433 removed outlier: 3.512A pdb=" N TRP C 433 " --> pdb=" O TYR C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 437 No H-bonds generated for 'chain 'C' and resid 435 through 437' Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 453 through 458 Processing helix chain 'C' and resid 474 through 493 removed outlier: 3.585A pdb=" N GLU C 479 " --> pdb=" O ASP C 475 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 482 " --> pdb=" O ARG C 478 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR C 488 " --> pdb=" O ALA C 484 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU C 490 " --> pdb=" O SER C 486 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE C 493 " --> pdb=" O ARG C 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 26 Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 50 through 69 removed outlier: 3.663A pdb=" N ALA A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 66 " --> pdb=" O HIS A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 93 removed outlier: 3.869A pdb=" N LEU A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 119 removed outlier: 3.914A pdb=" N VAL A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 116 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 117 " --> pdb=" O HIS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 160 removed outlier: 3.926A pdb=" N LYS A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 208 removed outlier: 3.916A pdb=" N LEU A 205 " --> pdb=" O PRO A 201 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR A 207 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ARG A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 227 removed outlier: 3.568A pdb=" N LYS A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 258 through 274 removed outlier: 3.753A pdb=" N ILE A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 271 " --> pdb=" O MET A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 303 removed outlier: 3.528A pdb=" N LEU A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG A 298 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 333 Processing helix chain 'A' and resid 339 through 351 Processing helix chain 'A' and resid 356 through 368 Processing helix chain 'A' and resid 374 through 384 removed outlier: 3.525A pdb=" N ASP A 383 " --> pdb=" O LYS A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 401 removed outlier: 3.609A pdb=" N SER A 401 " --> pdb=" O TRP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 423 removed outlier: 3.601A pdb=" N TYR A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 433 removed outlier: 3.512A pdb=" N TRP A 433 " --> pdb=" O TYR A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 474 through 493 removed outlier: 3.586A pdb=" N GLU A 479 " --> pdb=" O ASP A 475 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 482 " --> pdb=" O ARG A 478 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU A 490 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 125 through 129 removed outlier: 4.805A pdb=" N ASN D 101 " --> pdb=" O TRP D 10 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER D 31 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL D 9 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE D 33 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N PHE D 11 " --> pdb=" O PHE D 33 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL D 35 " --> pdb=" O PHE D 11 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N THR D 75 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N TRP D 38 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE D 77 " --> pdb=" O TRP D 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 125 through 129 removed outlier: 4.805A pdb=" N ASN B 101 " --> pdb=" O TRP B 10 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER B 31 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL B 9 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE B 33 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N PHE B 11 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL B 35 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N THR B 75 " --> pdb=" O PHE B 36 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N TRP B 38 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE B 77 " --> pdb=" O TRP B 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 125 through 129 removed outlier: 4.805A pdb=" N ASN C 101 " --> pdb=" O TRP C 10 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER C 31 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL C 9 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE C 33 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N PHE C 11 " --> pdb=" O PHE C 33 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL C 35 " --> pdb=" O PHE C 11 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N THR C 75 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N TRP C 38 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE C 77 " --> pdb=" O TRP C 38 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 125 through 129 removed outlier: 4.806A pdb=" N ASN A 101 " --> pdb=" O TRP A 10 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER A 31 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL A 9 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE A 33 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N PHE A 11 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL A 35 " --> pdb=" O PHE A 11 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N THR A 75 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N TRP A 38 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A 77 " --> pdb=" O TRP A 38 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1584 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: 4.36 Time building geometry restraints manager: 6.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4898 1.34 - 1.46: 3179 1.46 - 1.57: 7951 1.57 - 1.69: 12 1.69 - 1.81: 100 Bond restraints: 16140 Sorted by residual: bond pdb=" O5B FAD A 701 " pdb=" PA FAD A 701 " ideal model delta sigma weight residual 1.634 1.533 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" O5B FAD C 701 " pdb=" PA FAD C 701 " ideal model delta sigma weight residual 1.634 1.533 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" O5B FAD B 701 " pdb=" PA FAD B 701 " ideal model delta sigma weight residual 1.634 1.533 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" O5B FAD D 701 " pdb=" PA FAD D 701 " ideal model delta sigma weight residual 1.634 1.534 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" O2P FAD C 701 " pdb=" P FAD C 701 " ideal model delta sigma weight residual 1.495 1.401 0.094 2.00e-02 2.50e+03 2.21e+01 ... (remaining 16135 not shown) Histogram of bond angle deviations from ideal: 97.69 - 104.99: 333 104.99 - 112.30: 7594 112.30 - 119.61: 6326 119.61 - 126.92: 7313 126.92 - 134.23: 390 Bond angle restraints: 21956 Sorted by residual: angle pdb=" N LEU C 194 " pdb=" CA LEU C 194 " pdb=" C LEU C 194 " ideal model delta sigma weight residual 114.16 102.07 12.09 1.48e+00 4.57e-01 6.68e+01 angle pdb=" N LEU B 194 " pdb=" CA LEU B 194 " pdb=" C LEU B 194 " ideal model delta sigma weight residual 114.16 102.14 12.02 1.48e+00 4.57e-01 6.59e+01 angle pdb=" N LEU D 194 " pdb=" CA LEU D 194 " pdb=" C LEU D 194 " ideal model delta sigma weight residual 114.16 102.35 11.81 1.48e+00 4.57e-01 6.37e+01 angle pdb=" N LEU A 194 " pdb=" CA LEU A 194 " pdb=" C LEU A 194 " ideal model delta sigma weight residual 114.16 102.38 11.78 1.48e+00 4.57e-01 6.33e+01 angle pdb=" CA GLU B 197 " pdb=" CB GLU B 197 " pdb=" CG GLU B 197 " ideal model delta sigma weight residual 114.10 129.68 -15.58 2.00e+00 2.50e-01 6.07e+01 ... (remaining 21951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.75: 8639 20.75 - 41.50: 641 41.50 - 62.24: 123 62.24 - 82.99: 17 82.99 - 103.74: 8 Dihedral angle restraints: 9428 sinusoidal: 3880 harmonic: 5548 Sorted by residual: dihedral pdb=" CA MET D 175 " pdb=" C MET D 175 " pdb=" N PRO D 176 " pdb=" CA PRO D 176 " ideal model delta harmonic sigma weight residual 180.00 154.81 25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA MET C 175 " pdb=" C MET C 175 " pdb=" N PRO C 176 " pdb=" CA PRO C 176 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA MET A 175 " pdb=" C MET A 175 " pdb=" N PRO A 176 " pdb=" CA PRO A 176 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 9425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1536 0.054 - 0.109: 619 0.109 - 0.163: 143 0.163 - 0.218: 18 0.218 - 0.272: 12 Chirality restraints: 2328 Sorted by residual: chirality pdb=" CB ILE A 86 " pdb=" CA ILE A 86 " pdb=" CG1 ILE A 86 " pdb=" CG2 ILE A 86 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB ILE B 86 " pdb=" CA ILE B 86 " pdb=" CG1 ILE B 86 " pdb=" CG2 ILE B 86 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB ILE D 86 " pdb=" CA ILE D 86 " pdb=" CG1 ILE D 86 " pdb=" CG2 ILE D 86 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 2325 not shown) Planarity restraints: 2736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 338 " -0.041 5.00e-02 4.00e+02 6.22e-02 6.20e+00 pdb=" N PRO D 339 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 339 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 339 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 338 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.18e+00 pdb=" N PRO B 339 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 339 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 339 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 338 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.16e+00 pdb=" N PRO A 339 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " 0.034 5.00e-02 4.00e+02 ... (remaining 2733 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4264 2.80 - 3.33: 13116 3.33 - 3.85: 25983 3.85 - 4.38: 32564 4.38 - 4.90: 52898 Nonbonded interactions: 128825 Sorted by model distance: nonbonded pdb=" OE1 GLU A 347 " pdb=" OH TYR A 429 " model vdw 2.280 2.440 nonbonded pdb=" OE1 GLU D 347 " pdb=" OH TYR D 429 " model vdw 2.280 2.440 nonbonded pdb=" OE1 GLU B 347 " pdb=" OH TYR B 429 " model vdw 2.281 2.440 nonbonded pdb=" OE1 GLU C 347 " pdb=" OH TYR C 429 " model vdw 2.281 2.440 nonbonded pdb=" NZ LYS B 329 " pdb=" OE1 GLU A 462 " model vdw 2.363 2.520 ... (remaining 128820 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.030 Extract box with map and model: 4.130 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 41.690 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:15.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 : 0.008 0.101 16140 Z= 0.539 Angle : 0.999 15.578 21956 Z= 0.536 Chirality : 0.062 0.272 2328 Planarity : 0.007 0.062 2736 Dihedral : 15.310 103.739 5836 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.09 (0.14), residues: 1880 helix: -4.33 (0.06), residues: 1008 sheet: -0.78 (0.42), residues: 144 loop : -2.13 (0.20), residues: 728 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 435 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 4 residues processed: 440 average time/residue: 0.9856 time to fit residues: 486.0955 Evaluate side-chains 350 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 346 time to evaluate : 1.870 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 2.4630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 170 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: