Starting phenix.real_space_refine on Wed Feb 21 09:14:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0x_32928/02_2024/7x0x_32928_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0x_32928/02_2024/7x0x_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_32928/02_2024/7x0x_32928.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0x_32928/02_2024/7x0x_32928.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0x_32928/02_2024/7x0x_32928_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0x_32928/02_2024/7x0x_32928_updated.pdb" } resolution = 2.56 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= -0.001 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-dev-5238/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: 12.24, per 1000 atoms: 0.78 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: 6.08 Conformation dependent library (CDL) restraints added in 3.0 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: 3.04 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: 4.32 Time building geometry restraints manager: 6.63 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: 8695 20.75 - 41.50: 697 41.50 - 62.24: 159 62.24 - 82.99: 41 82.99 - 103.74: 8 Dihedral angle restraints: 9600 sinusoidal: 4052 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 9597 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.020 Extract box with map and model: 3.820 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 48.160 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 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:15.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.410 ------------------------------------------------------------------------------- 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 : 16.659 103.739 6008 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 % Allowed : 7.79 % Favored : 91.06 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 321 HIS 0.007 0.002 HIS A 62 PHE 0.012 0.002 PHE A 100 TYR 0.019 0.003 TYR C 47 ARG 0.016 0.001 ARG D 412 *********************** 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 : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 TRP cc_start: 0.9133 (p90) cc_final: 0.8770 (p90) REVERT: B 335 ARG cc_start: 0.7754 (mtp85) cc_final: 0.7427 (mtm110) REVERT: C 81 ASN cc_start: 0.8461 (t0) cc_final: 0.8220 (t0) REVERT: C 113 HIS cc_start: 0.7450 (t-90) cc_final: 0.7175 (t70) REVERT: C 141 TYR cc_start: 0.7176 (m-10) cc_final: 0.6840 (m-80) REVERT: A 81 ASN cc_start: 0.8373 (t0) cc_final: 0.8137 (t0) REVERT: A 87 LEU cc_start: 0.8517 (tt) cc_final: 0.8225 (tt) REVERT: A 141 TYR cc_start: 0.7061 (m-10) cc_final: 0.6800 (m-80) outliers start: 19 outliers final: 4 residues processed: 440 average time/residue: 1.0991 time to fit residues: 540.8532 Evaluate side-chains 351 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 347 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 285 ASP 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... Flipped N/Q/H residues before XYZ refinement: ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 HIS D 356 ASN D 415 ASN B 260 HIS B 356 ASN C 356 ASN C 415 ASN A 260 HIS A 356 ASN A 415 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16140 Z= 0.190 Angle : 0.617 8.957 21956 Z= 0.315 Chirality : 0.044 0.139 2328 Planarity : 0.005 0.086 2736 Dihedral : 11.258 129.198 2263 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.93 % Allowed : 14.92 % Favored : 81.16 % 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: -2.74 (0.17), residues: 1880 helix: -2.14 (0.13), residues: 1008 sheet: -0.19 (0.42), residues: 144 loop : -1.39 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 172 HIS 0.004 0.001 HIS B 260 PHE 0.009 0.001 PHE B 304 TYR 0.014 0.001 TYR B 154 ARG 0.014 0.001 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 2 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 415 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 350 time to evaluate : 1.789 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: D 91 ARG cc_start: 0.7793 (mpt-90) cc_final: 0.7591 (mpt180) REVERT: D 127 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7636 (mt0) REVERT: B 127 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7510 (mt0) REVERT: B 335 ARG cc_start: 0.7784 (mtp85) cc_final: 0.7431 (mtm110) REVERT: C 37 ILE cc_start: 0.8609 (mt) cc_final: 0.8336 (mt) REVERT: C 80 HIS cc_start: 0.6288 (m-70) cc_final: 0.6021 (m-70) REVERT: C 141 TYR cc_start: 0.7176 (m-10) cc_final: 0.6786 (m-80) REVERT: A 113 HIS cc_start: 0.7184 (t-90) cc_final: 0.6942 (t70) REVERT: A 141 TYR cc_start: 0.7112 (m-10) cc_final: 0.6856 (m-80) outliers start: 65 outliers final: 18 residues processed: 370 average time/residue: 1.1210 time to fit residues: 467.2207 Evaluate side-chains 340 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 320 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 454 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 171 optimal weight: 0.0020 chunk 184 optimal weight: 0.0040 chunk 152 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN B 260 HIS A 415 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16140 Z= 0.203 Angle : 0.581 7.173 21956 Z= 0.292 Chirality : 0.045 0.140 2328 Planarity : 0.004 0.074 2736 Dihedral : 10.181 94.503 2256 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.02 % Allowed : 17.15 % Favored : 79.83 % 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: -1.34 (0.19), residues: 1880 helix: -0.85 (0.15), residues: 1008 sheet: 0.20 (0.44), residues: 144 loop : -0.95 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 172 HIS 0.004 0.001 HIS C 260 PHE 0.012 0.001 PHE D 304 TYR 0.012 0.001 TYR B 47 ARG 0.018 0.001 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 3 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 385 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 335 time to evaluate : 1.536 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: D 87 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8578 (tt) REVERT: B 43 GLU cc_start: 0.7871 (mp0) cc_final: 0.7566 (mp0) REVERT: B 335 ARG cc_start: 0.7912 (mtp85) cc_final: 0.7527 (mtm110) REVERT: C 37 ILE cc_start: 0.8661 (mt) cc_final: 0.8414 (mt) REVERT: C 113 HIS cc_start: 0.7363 (t-90) cc_final: 0.7116 (t-170) REVERT: C 141 TYR cc_start: 0.7222 (m-10) cc_final: 0.6718 (m-80) REVERT: C 422 LYS cc_start: 0.8435 (mtmt) cc_final: 0.8150 (mtpt) REVERT: A 113 HIS cc_start: 0.7146 (t-90) cc_final: 0.6899 (t70) REVERT: A 141 TYR cc_start: 0.7145 (m-10) cc_final: 0.6890 (m-80) outliers start: 50 outliers final: 17 residues processed: 348 average time/residue: 1.1362 time to fit residues: 441.8814 Evaluate side-chains 334 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 316 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 225 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 88 optimal weight: 0.0770 chunk 18 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN D 415 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16140 Z= 0.265 Angle : 0.604 7.214 21956 Z= 0.303 Chirality : 0.047 0.166 2328 Planarity : 0.004 0.078 2736 Dihedral : 10.308 95.299 2256 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.20 % Allowed : 18.48 % Favored : 78.32 % 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: -0.85 (0.19), residues: 1880 helix: -0.39 (0.16), residues: 1008 sheet: 0.15 (0.44), residues: 144 loop : -0.75 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 172 HIS 0.006 0.001 HIS C 260 PHE 0.015 0.001 PHE D 304 TYR 0.014 0.002 TYR B 47 ARG 0.013 0.001 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 4 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 375 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 322 time to evaluate : 1.753 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: D 43 GLU cc_start: 0.7886 (mp0) cc_final: 0.7564 (mp0) REVERT: D 87 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8622 (tt) REVERT: D 127 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7689 (mt0) REVERT: D 422 LYS cc_start: 0.8441 (mtmt) cc_final: 0.8196 (mtpt) REVERT: D 475 ASP cc_start: 0.8098 (m-30) cc_final: 0.7827 (m-30) REVERT: B 43 GLU cc_start: 0.8003 (mp0) cc_final: 0.7615 (mp0) REVERT: B 127 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7631 (mt0) REVERT: B 196 ASN cc_start: 0.8013 (m110) cc_final: 0.7809 (m-40) REVERT: B 335 ARG cc_start: 0.7936 (mtp85) cc_final: 0.7663 (mtp85) REVERT: B 475 ASP cc_start: 0.8137 (m-30) cc_final: 0.7852 (m-30) REVERT: C 37 ILE cc_start: 0.8791 (mt) cc_final: 0.8527 (mt) REVERT: C 43 GLU cc_start: 0.7788 (mp0) cc_final: 0.7486 (mp0) REVERT: C 196 ASN cc_start: 0.7980 (m110) cc_final: 0.7774 (m-40) REVERT: C 422 LYS cc_start: 0.8438 (mtmt) cc_final: 0.8158 (mtpt) REVERT: A 234 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7399 (mptt) REVERT: A 422 LYS cc_start: 0.8384 (mtmt) cc_final: 0.8131 (mtpt) outliers start: 53 outliers final: 21 residues processed: 337 average time/residue: 1.1121 time to fit residues: 419.0455 Evaluate side-chains 328 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 303 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 322 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 0.9990 chunk 103 optimal weight: 0.0270 chunk 2 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 155 optimal weight: 0.0870 chunk 125 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 45 optimal weight: 0.3980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN A 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16140 Z= 0.141 Angle : 0.528 8.192 21956 Z= 0.263 Chirality : 0.042 0.133 2328 Planarity : 0.004 0.066 2736 Dihedral : 8.986 88.701 2256 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.90 % Allowed : 19.32 % Favored : 77.78 % 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: -0.31 (0.20), residues: 1880 helix: 0.18 (0.16), residues: 1020 sheet: 0.24 (0.44), residues: 144 loop : -0.69 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 172 HIS 0.002 0.001 HIS A 447 PHE 0.007 0.001 PHE D 33 TYR 0.011 0.001 TYR C 154 ARG 0.011 0.000 ARG C 274 *********************** REFINEMENT MACRO_CYCLE 5 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 368 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 320 time to evaluate : 1.768 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: D 43 GLU cc_start: 0.7901 (mp0) cc_final: 0.7517 (mp0) REVERT: D 475 ASP cc_start: 0.8083 (m-30) cc_final: 0.7807 (m-30) REVERT: B 43 GLU cc_start: 0.7945 (mp0) cc_final: 0.7499 (mp0) REVERT: B 65 GLN cc_start: 0.6754 (tp-100) cc_final: 0.6314 (tp-100) REVERT: B 76 LEU cc_start: 0.8786 (mt) cc_final: 0.8405 (mm) REVERT: B 335 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7480 (mtm110) REVERT: B 475 ASP cc_start: 0.8101 (m-30) cc_final: 0.7829 (m-30) REVERT: C 37 ILE cc_start: 0.8717 (mt) cc_final: 0.8455 (mt) REVERT: C 43 GLU cc_start: 0.7693 (mp0) cc_final: 0.7294 (mp0) REVERT: C 76 LEU cc_start: 0.8754 (mt) cc_final: 0.8445 (mm) REVERT: C 113 HIS cc_start: 0.7225 (t-90) cc_final: 0.6975 (t-170) REVERT: C 422 LYS cc_start: 0.8431 (mtmt) cc_final: 0.8171 (mtpt) REVERT: A 234 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7300 (mptt) REVERT: A 422 LYS cc_start: 0.8426 (mtmt) cc_final: 0.8176 (mtpt) outliers start: 48 outliers final: 24 residues processed: 332 average time/residue: 1.1667 time to fit residues: 432.9369 Evaluate side-chains 322 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 297 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 1.9990 chunk 163 optimal weight: 0.0970 chunk 35 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 60 optimal weight: 0.0050 chunk 95 optimal weight: 3.9990 overall best weight: 1.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN D 113 HIS ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN A 113 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16140 Z= 0.251 Angle : 0.595 8.542 21956 Z= 0.295 Chirality : 0.046 0.172 2328 Planarity : 0.004 0.061 2736 Dihedral : 9.491 94.902 2256 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.53 % Allowed : 18.66 % Favored : 76.81 % 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: -0.27 (0.20), residues: 1880 helix: 0.14 (0.16), residues: 1044 sheet: 0.27 (0.44), residues: 144 loop : -0.59 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 172 HIS 0.006 0.001 HIS C 260 PHE 0.009 0.001 PHE C 151 TYR 0.014 0.002 TYR D 47 ARG 0.010 0.001 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 6 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 371 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 296 time to evaluate : 1.685 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: D 475 ASP cc_start: 0.8078 (m-30) cc_final: 0.7788 (m-30) REVERT: B 43 GLU cc_start: 0.8001 (mp0) cc_final: 0.7489 (mp0) REVERT: B 335 ARG cc_start: 0.7896 (mtp85) cc_final: 0.7615 (mtp85) REVERT: B 475 ASP cc_start: 0.8107 (m-30) cc_final: 0.7827 (m-30) REVERT: C 37 ILE cc_start: 0.8831 (mt) cc_final: 0.8590 (mt) REVERT: C 43 GLU cc_start: 0.7802 (mp0) cc_final: 0.7342 (mp0) REVERT: C 76 LEU cc_start: 0.8777 (mt) cc_final: 0.8458 (mm) REVERT: C 113 HIS cc_start: 0.7270 (t-90) cc_final: 0.7026 (t-170) REVERT: C 127 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7656 (mt0) REVERT: A 196 ASN cc_start: 0.7785 (m110) cc_final: 0.7548 (m110) REVERT: A 234 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7329 (mptt) REVERT: A 422 LYS cc_start: 0.8463 (mtmt) cc_final: 0.8226 (mtpt) outliers start: 75 outliers final: 31 residues processed: 320 average time/residue: 1.1086 time to fit residues: 397.0046 Evaluate side-chains 326 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 293 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 454 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 181 optimal weight: 0.4980 chunk 113 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16140 Z= 0.261 Angle : 0.606 9.216 21956 Z= 0.300 Chirality : 0.047 0.173 2328 Planarity : 0.004 0.058 2736 Dihedral : 9.713 95.245 2256 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.05 % Allowed : 19.32 % Favored : 76.63 % 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: -0.24 (0.19), residues: 1880 helix: 0.18 (0.16), residues: 1044 sheet: 0.27 (0.44), residues: 144 loop : -0.59 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 172 HIS 0.005 0.001 HIS C 260 PHE 0.023 0.001 PHE B 304 TYR 0.014 0.002 TYR D 47 ARG 0.011 0.001 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 7 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 368 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 301 time to evaluate : 1.809 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: D 475 ASP cc_start: 0.8009 (m-30) cc_final: 0.7702 (m-30) REVERT: B 43 GLU cc_start: 0.8014 (mp0) cc_final: 0.7496 (mp0) REVERT: B 65 GLN cc_start: 0.6731 (tp-100) cc_final: 0.6183 (tp-100) REVERT: B 127 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7646 (mt0) REVERT: B 335 ARG cc_start: 0.7896 (mtp85) cc_final: 0.7624 (mtp85) REVERT: B 475 ASP cc_start: 0.8064 (m-30) cc_final: 0.7787 (m-30) REVERT: C 37 ILE cc_start: 0.8852 (mt) cc_final: 0.8617 (mt) REVERT: C 43 GLU cc_start: 0.7825 (mp0) cc_final: 0.7376 (mp0) REVERT: C 76 LEU cc_start: 0.8785 (mt) cc_final: 0.8457 (mm) REVERT: C 113 HIS cc_start: 0.7259 (t-90) cc_final: 0.7014 (t70) REVERT: C 127 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7655 (mt0) REVERT: A 196 ASN cc_start: 0.7911 (m110) cc_final: 0.7690 (m110) REVERT: A 234 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7307 (mptt) REVERT: A 422 LYS cc_start: 0.8468 (mtmt) cc_final: 0.8243 (mtpt) outliers start: 67 outliers final: 32 residues processed: 321 average time/residue: 1.1122 time to fit residues: 398.7759 Evaluate side-chains 326 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 291 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 454 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 54 optimal weight: 0.0470 chunk 35 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 16 optimal weight: 0.0010 chunk 142 optimal weight: 0.6980 chunk 164 optimal weight: 0.5980 overall best weight: 0.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16140 Z= 0.149 Angle : 0.546 9.604 21956 Z= 0.270 Chirality : 0.042 0.133 2328 Planarity : 0.004 0.055 2736 Dihedral : 8.613 89.024 2256 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.29 % Allowed : 21.20 % Favored : 76.51 % 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: 0.24 (0.20), residues: 1880 helix: 0.66 (0.16), residues: 1028 sheet: 0.31 (0.44), residues: 144 loop : -0.47 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 172 HIS 0.003 0.001 HIS D 62 PHE 0.007 0.001 PHE B 33 TYR 0.009 0.001 TYR D 154 ARG 0.009 0.000 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 8 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 345 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 307 time to evaluate : 2.024 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: D 76 LEU cc_start: 0.8663 (mt) cc_final: 0.8321 (mm) REVERT: D 196 ASN cc_start: 0.7733 (m110) cc_final: 0.7491 (m110) REVERT: D 475 ASP cc_start: 0.7889 (m-30) cc_final: 0.7598 (m-30) REVERT: B 43 GLU cc_start: 0.7974 (mp0) cc_final: 0.7460 (mp0) REVERT: B 65 GLN cc_start: 0.6753 (tp-100) cc_final: 0.6258 (tp-100) REVERT: B 76 LEU cc_start: 0.8679 (mt) cc_final: 0.8272 (mm) REVERT: B 335 ARG cc_start: 0.7862 (mtp85) cc_final: 0.7601 (mtp85) REVERT: B 475 ASP cc_start: 0.7977 (m-30) cc_final: 0.7686 (m-30) REVERT: C 37 ILE cc_start: 0.8780 (mt) cc_final: 0.8525 (mt) REVERT: C 43 GLU cc_start: 0.7792 (mp0) cc_final: 0.7331 (mp0) REVERT: C 76 LEU cc_start: 0.8742 (mt) cc_final: 0.8335 (mm) REVERT: C 113 HIS cc_start: 0.7223 (t-90) cc_final: 0.7002 (t-170) REVERT: A 76 LEU cc_start: 0.8670 (mt) cc_final: 0.8332 (mm) REVERT: A 196 ASN cc_start: 0.7757 (m110) cc_final: 0.7537 (m110) REVERT: A 234 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7217 (mptt) REVERT: A 422 LYS cc_start: 0.8446 (mtmt) cc_final: 0.8236 (mtpt) outliers start: 38 outliers final: 21 residues processed: 319 average time/residue: 1.1435 time to fit residues: 410.4314 Evaluate side-chains 310 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 288 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 chunk 159 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 58 GLN D 65 GLN D 113 HIS D 419 GLN B 58 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 GLN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS A 419 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 16140 Z= 0.388 Angle : 0.692 9.472 21956 Z= 0.343 Chirality : 0.051 0.215 2328 Planarity : 0.004 0.060 2736 Dihedral : 10.265 95.006 2256 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.78 % Allowed : 21.38 % Favored : 75.85 % 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: -0.25 (0.19), residues: 1880 helix: 0.21 (0.16), residues: 1044 sheet: 0.22 (0.44), residues: 144 loop : -0.65 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 172 HIS 0.009 0.002 HIS C 260 PHE 0.008 0.002 PHE B 151 TYR 0.019 0.002 TYR D 47 ARG 0.014 0.001 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 9 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 348 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 302 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 76 LEU cc_start: 0.8764 (mt) cc_final: 0.8427 (mm) REVERT: D 196 ASN cc_start: 0.7981 (m110) cc_final: 0.7777 (m-40) REVERT: D 475 ASP cc_start: 0.7963 (m-30) cc_final: 0.7648 (m-30) REVERT: B 127 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7720 (mt0) REVERT: B 196 ASN cc_start: 0.7963 (m110) cc_final: 0.7712 (m-40) REVERT: B 335 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7624 (mtp85) REVERT: B 475 ASP cc_start: 0.8027 (m-30) cc_final: 0.7706 (m-30) REVERT: C 37 ILE cc_start: 0.8901 (mt) cc_final: 0.8667 (mt) REVERT: C 43 GLU cc_start: 0.8001 (mp0) cc_final: 0.7487 (mp0) REVERT: C 76 LEU cc_start: 0.8854 (mt) cc_final: 0.8518 (mm) REVERT: C 113 HIS cc_start: 0.7254 (t-90) cc_final: 0.7008 (t70) REVERT: C 225 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8051 (mm) REVERT: A 91 ARG cc_start: 0.7985 (mpt180) cc_final: 0.7765 (mpt-90) outliers start: 46 outliers final: 17 residues processed: 312 average time/residue: 1.0844 time to fit residues: 379.6643 Evaluate side-chains 312 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 293 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 113 HIS D 419 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 GLN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16140 Z= 0.221 Angle : 0.610 9.845 21956 Z= 0.303 Chirality : 0.045 0.160 2328 Planarity : 0.004 0.060 2736 Dihedral : 9.866 95.067 2256 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.57 % Allowed : 22.46 % Favored : 75.97 % 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: 0.01 (0.20), residues: 1880 helix: 0.48 (0.16), residues: 1040 sheet: 0.19 (0.44), residues: 144 loop : -0.60 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 172 HIS 0.005 0.001 HIS B 446 PHE 0.007 0.001 PHE C 328 TYR 0.012 0.001 TYR B 47 ARG 0.013 0.001 ARG C 274 ********************** REFINEMENT MACRO_CYCLE 10 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 321 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 295 time to evaluate : 1.677 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: D 57 LYS cc_start: 0.8227 (pttt) cc_final: 0.7986 (pttt) REVERT: D 76 LEU cc_start: 0.8791 (mt) cc_final: 0.8438 (mm) REVERT: D 475 ASP cc_start: 0.7925 (m-30) cc_final: 0.7591 (m-30) REVERT: B 43 GLU cc_start: 0.8046 (mp0) cc_final: 0.7592 (mp0) REVERT: B 57 LYS cc_start: 0.7941 (pttt) cc_final: 0.7726 (ptpt) REVERT: B 65 GLN cc_start: 0.6731 (tp-100) cc_final: 0.6508 (tp-100) REVERT: B 475 ASP cc_start: 0.8007 (m-30) cc_final: 0.7695 (m-30) REVERT: C 37 ILE cc_start: 0.8852 (mt) cc_final: 0.8606 (mt) REVERT: C 43 GLU cc_start: 0.7939 (mp0) cc_final: 0.7456 (mp0) REVERT: C 76 LEU cc_start: 0.8793 (mt) cc_final: 0.8462 (mm) REVERT: C 113 HIS cc_start: 0.7227 (t-90) cc_final: 0.6999 (t70) REVERT: A 76 LEU cc_start: 0.8774 (mt) cc_final: 0.8442 (mm) outliers start: 26 outliers final: 18 residues processed: 297 average time/residue: 1.1544 time to fit residues: 383.2648 Evaluate side-chains 308 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 290 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 3.9990 chunk 137 optimal weight: 0.0670 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 18 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 113 HIS D 419 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 GLN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.151457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.113198 restraints weight = 16626.291| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.13 r_work: 0.3185 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16140 Z= 0.155 Angle : 0.561 9.750 21956 Z= 0.276 Chirality : 0.042 0.133 2328 Planarity : 0.004 0.052 2736 Dihedral : 8.640 88.664 2256 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.21 % Allowed : 22.83 % Favored : 75.97 % 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: 0.51 (0.20), residues: 1880 helix: 0.92 (0.16), residues: 1028 sheet: 0.29 (0.43), residues: 144 loop : -0.40 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 172 HIS 0.003 0.001 HIS C 447 PHE 0.006 0.001 PHE A 224 TYR 0.020 0.001 TYR B 423 ARG 0.012 0.000 ARG B 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6695.94 seconds wall clock time: 119 minutes 34.14 seconds (7174.14 seconds total)