Starting phenix.real_space_refine on Mon Apr 15 16:45:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gae_29895/04_2024/8gae_29895_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gae_29895/04_2024/8gae_29895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gae_29895/04_2024/8gae_29895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gae_29895/04_2024/8gae_29895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gae_29895/04_2024/8gae_29895_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gae_29895/04_2024/8gae_29895_trim_updated.pdb" } resolution = 3.3 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians K 2 8.98 5 Mn 2 7.51 5 P 6 5.49 5 Mg 2 5.21 5 S 93 5.16 5 C 11222 2.51 5 N 3003 2.21 5 O 3418 1.98 5 H 17630 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 20": "OE1" <-> "OE2" Residue "A ASP 49": "OD1" <-> "OD2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 122": "OD1" <-> "OD2" Residue "A PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 188": "OD1" <-> "OD2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A ASP 278": "OD1" <-> "OD2" Residue "A TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A ASP 382": "OD1" <-> "OD2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 545": "OE1" <-> "OE2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A GLU 569": "OE1" <-> "OE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A ASP 631": "OD1" <-> "OD2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "A GLU 643": "OE1" <-> "OE2" Residue "A ASP 653": "OD1" <-> "OD2" Residue "A GLU 671": "OE1" <-> "OE2" Residue "B PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B ASP 278": "OD1" <-> "OD2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B GLU 300": "OE1" <-> "OE2" Residue "B TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 314": "OD1" <-> "OD2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 342": "OD1" <-> "OD2" Residue "B PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B ASP 367": "OD1" <-> "OD2" Residue "B TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 384": "OE1" <-> "OE2" Residue "B ARG 392": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 422": "OD1" <-> "OD2" Residue "B TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 443": "OE1" <-> "OE2" Residue "B ASP 464": "OD1" <-> "OD2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B GLU 489": "OE1" <-> "OE2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "B ASP 572": "OD1" <-> "OD2" Residue "B GLU 576": "OE1" <-> "OE2" Residue "B GLU 603": "OE1" <-> "OE2" Residue "B ASP 631": "OD1" <-> "OD2" Residue "B ASP 672": "OD1" <-> "OD2" Residue "C GLU 11": "OE1" <-> "OE2" Residue "C ASP 14": "OD1" <-> "OD2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C ASP 24": "OD1" <-> "OD2" Residue "C ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 38": "OE1" <-> "OE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C ARG 167": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 200": "OE1" <-> "OE2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 245": "OD1" <-> "OD2" Residue "C ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "D ASP 415": "OD1" <-> "OD2" Residue "D TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 450": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 467": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 478": "OE1" <-> "OE2" Residue "D ASP 486": "OD1" <-> "OD2" Residue "D GLU 515": "OE1" <-> "OE2" Residue "D ASP 530": "OD1" <-> "OD2" Residue "D GLU 545": "OE1" <-> "OE2" Residue "D ASP 555": "OD1" <-> "OD2" Residue "D PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 594": "OE1" <-> "OE2" Residue "D PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 607": "OE1" <-> "OE2" Residue "E TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E GLU 175": "OE1" <-> "OE2" Residue "E TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 182": "OE1" <-> "OE2" Residue "E ASP 183": "OD1" <-> "OD2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 228": "OE1" <-> "OE2" Residue "E GLU 233": "OE1" <-> "OE2" Residue "E ASP 242": "OD1" <-> "OD2" Residue "E PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "E GLU 262": "OE1" <-> "OE2" Residue "E TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 275": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 281": "OE1" <-> "OE2" Residue "E ASP 295": "OD1" <-> "OD2" Residue "E PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 307": "OD1" <-> "OD2" Residue "E TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "E TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 359": "OD1" <-> "OD2" Residue "E ARG 373": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 395": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 409": "OD1" <-> "OD2" Residue "E GLU 416": "OE1" <-> "OE2" Residue "E GLU 417": "OE1" <-> "OE2" Residue "E GLU 432": "OE1" <-> "OE2" Residue "E GLU 435": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 35378 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 10338 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 17, 'TRANS': 617} Chain breaks: 1 Chain: "B" Number of atoms: 10284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 10284 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 17, 'TRANS': 615} Chain breaks: 1 Chain: "C" Number of atoms: 4303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 4303 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 4, 'TRANS': 254} Chain: "D" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 3072 Classifications: {'peptide': 189} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "E" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 7317 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 16, 'TRANS': 442} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.12, per 1000 atoms: 0.43 Number of scatterers: 35378 At special positions: 0 Unit cell: (148.63, 151.135, 153.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Mn 2 24.99 K 2 19.00 S 93 16.00 P 6 15.00 Mg 2 11.99 O 3418 8.00 N 3003 7.00 C 11222 6.00 H 17630 1.00 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: 29.23 Conformation dependent library (CDL) restraints added in 3.8 seconds 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4138 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 13 sheets defined 47.0% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.42 Creating SS restraints... Processing helix chain 'A' and resid 21 through 30 Processing helix chain 'A' and resid 36 through 58 removed outlier: 3.714A pdb=" N GLU A 42 " --> pdb=" O PHE A 39 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 43 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A 44 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A 53 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG A 55 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU A 57 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 109 through 116 removed outlier: 3.804A pdb=" N MET A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 195 through 205 removed outlier: 3.771A pdb=" N LYS A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 298 through 309 removed outlier: 3.527A pdb=" N GLU A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 369 No H-bonds generated for 'chain 'A' and resid 366 through 369' Processing helix chain 'A' and resid 372 through 376 removed outlier: 3.714A pdb=" N ASN A 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE A 376 " --> pdb=" O TYR A 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 376' Processing helix chain 'A' and resid 398 through 421 removed outlier: 3.598A pdb=" N ARG A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 443 removed outlier: 4.679A pdb=" N LYS A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 454 removed outlier: 4.581A pdb=" N GLU A 453 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 475 removed outlier: 3.569A pdb=" N ARG A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 498 through 505 removed outlier: 3.524A pdb=" N GLU A 501 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ARG A 502 " --> pdb=" O PHE A 499 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG A 504 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 524 removed outlier: 3.851A pdb=" N VAL A 522 " --> pdb=" O GLU A 519 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN A 523 " --> pdb=" O TYR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 561 through 570 removed outlier: 3.681A pdb=" N LYS A 568 " --> pdb=" O CYS A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 608 Processing helix chain 'A' and resid 614 through 620 Processing helix chain 'A' and resid 633 through 644 Processing helix chain 'A' and resid 649 through 666 removed outlier: 3.569A pdb=" N VAL A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 657 " --> pdb=" O ASP A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 687 removed outlier: 3.852A pdb=" N LEU A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 31 Processing helix chain 'B' and resid 36 through 60 removed outlier: 3.502A pdb=" N PHE B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 44 " --> pdb=" O ARG B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 95 through 103 removed outlier: 3.571A pdb=" N LEU B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 removed outlier: 3.726A pdb=" N ALA B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 187 through 193 removed outlier: 5.604A pdb=" N GLU B 191 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 298 through 309 removed outlier: 3.828A pdb=" N SER B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 398 through 421 removed outlier: 3.776A pdb=" N LYS B 406 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL B 409 " --> pdb=" O LYS B 406 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS B 412 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 413 " --> pdb=" O LYS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 443 removed outlier: 3.845A pdb=" N LYS B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 437 " --> pdb=" O PHE B 433 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 443 " --> pdb=" O LEU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 454 removed outlier: 3.835A pdb=" N GLU B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 475 removed outlier: 3.617A pdb=" N VAL B 473 " --> pdb=" O LEU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 495 Processing helix chain 'B' and resid 501 through 505 Processing helix chain 'B' and resid 516 through 522 removed outlier: 3.588A pdb=" N GLU B 519 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 522 " --> pdb=" O GLU B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 571 removed outlier: 4.087A pdb=" N LYS B 552 " --> pdb=" O GLU B 548 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 561 " --> pdb=" O LYS B 557 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 608 Processing helix chain 'B' and resid 614 through 619 removed outlier: 4.494A pdb=" N GLY B 618 " --> pdb=" O SER B 615 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR B 619 " --> pdb=" O THR B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 644 removed outlier: 3.788A pdb=" N ALA B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 666 removed outlier: 3.517A pdb=" N PHE B 659 " --> pdb=" O VAL B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 687 Processing helix chain 'C' and resid 5 through 7 No H-bonds generated for 'chain 'C' and resid 5 through 7' Processing helix chain 'C' and resid 16 through 18 No H-bonds generated for 'chain 'C' and resid 16 through 18' Processing helix chain 'C' and resid 25 through 72 removed outlier: 3.936A pdb=" N ARG C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 111 removed outlier: 3.513A pdb=" N GLN C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 161 removed outlier: 5.577A pdb=" N GLU C 153 " --> pdb=" O LYS C 149 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS C 154 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU C 156 " --> pdb=" O VAL C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 183 removed outlier: 4.774A pdb=" N LEU C 175 " --> pdb=" O GLN C 172 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER C 176 " --> pdb=" O LYS C 173 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS C 183 " --> pdb=" O HIS C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 194 removed outlier: 5.026A pdb=" N LEU C 190 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 225 Processing helix chain 'C' and resid 235 through 239 removed outlier: 3.501A pdb=" N THR C 239 " --> pdb=" O GLN C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 258 removed outlier: 4.092A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 433 Processing helix chain 'D' and resid 442 through 462 removed outlier: 4.496A pdb=" N LYS D 462 " --> pdb=" O TYR D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 517 No H-bonds generated for 'chain 'D' and resid 514 through 517' Processing helix chain 'D' and resid 527 through 543 Processing helix chain 'D' and resid 554 through 562 removed outlier: 3.714A pdb=" N VAL D 561 " --> pdb=" O ILE D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 593 removed outlier: 4.670A pdb=" N VAL D 592 " --> pdb=" O CYS D 588 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS D 593 " --> pdb=" O VAL D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 609 Processing helix chain 'E' and resid 24 through 40 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.813A pdb=" N LEU E 57 " --> pdb=" O GLN E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 74 Processing helix chain 'E' and resid 78 through 91 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 112 through 125 Processing helix chain 'E' and resid 130 through 152 removed outlier: 3.591A pdb=" N GLN E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS E 146 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 170 removed outlier: 3.730A pdb=" N ILE E 167 " --> pdb=" O SER E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 199 Processing helix chain 'E' and resid 206 through 222 Processing helix chain 'E' and resid 247 through 256 Processing helix chain 'E' and resid 279 through 292 removed outlier: 3.835A pdb=" N ILE E 283 " --> pdb=" O SER E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 296 No H-bonds generated for 'chain 'E' and resid 294 through 296' Processing helix chain 'E' and resid 307 through 312 removed outlier: 3.870A pdb=" N GLN E 311 " --> pdb=" O ASP E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 322 Processing helix chain 'E' and resid 325 through 337 Processing helix chain 'E' and resid 363 through 368 removed outlier: 4.348A pdb=" N LYS E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 386 Processing helix chain 'E' and resid 408 through 417 Processing helix chain 'E' and resid 438 through 440 No H-bonds generated for 'chain 'E' and resid 438 through 440' Processing sheet with id= A, first strand: chain 'A' and resid 212 through 215 removed outlier: 3.899A pdb=" N LYS A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 317 through 322 removed outlier: 3.786A pdb=" N ALA A 317 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 321 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL A 357 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N PHE A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 456 through 458 Processing sheet with id= D, first strand: chain 'A' and resid 532 through 535 removed outlier: 6.005A pdb=" N VAL A 511 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 577 through 580 removed outlier: 4.360A pdb=" N LYS A 577 " --> pdb=" O LYS A 624 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 166 through 169 removed outlier: 7.009A pdb=" N HIS B 184 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL B 143 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE B 182 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL B 145 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS B 180 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR B 147 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLY B 178 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE B 75 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR B 214 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR B 216 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 217 " --> pdb=" O ILE B 277 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 317 through 323 removed outlier: 3.960A pdb=" N ALA B 317 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE B 321 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET B 363 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL B 357 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N PHE B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 532 through 535 Processing sheet with id= I, first strand: chain 'B' and resid 577 through 580 removed outlier: 4.006A pdb=" N LYS B 577 " --> pdb=" O LYS B 624 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 474 through 477 removed outlier: 4.351A pdb=" N THR D 481 " --> pdb=" O HIS D 477 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 227 through 229 removed outlier: 3.742A pdb=" N CYS E 343 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N TYR E 422 " --> pdb=" O LEU E 349 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N CYS E 442 " --> pdb=" O ALA E 437 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA E 437 " --> pdb=" O CYS E 442 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 297 through 301 removed outlier: 6.508A pdb=" N TYR E 266 " --> pdb=" O HIS E 298 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU E 300 " --> pdb=" O TYR E 266 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE E 268 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE E 267 " --> pdb=" O LYS E 236 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR E 238 " --> pdb=" O ILE E 267 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASN E 269 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N CYS E 240 " --> pdb=" O ASN E 269 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU E 464 " --> pdb=" O ILE E 237 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL E 239 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE E 462 " --> pdb=" O VAL E 239 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN E 472 " --> pdb=" O HIS E 463 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 388 through 390 735 hydrogen bonds defined for protein. 1881 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: 13.57 Time building geometry restraints manager: 30.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.55 - 0.81: 3 0.81 - 1.06: 4086 1.06 - 1.32: 17171 1.32 - 1.57: 14273 1.57 - 1.82: 163 Bond restraints: 35696 Sorted by residual: bond pdb=" N PHE A 39 " pdb=" H PHE A 39 " ideal model delta sigma weight residual 0.860 0.553 0.307 2.00e-02 2.50e+03 2.35e+02 bond pdb=" CB SER E 378 " pdb=" OG SER E 378 " ideal model delta sigma weight residual 1.417 1.160 0.257 2.00e-02 2.50e+03 1.66e+02 bond pdb=" CZ ARG B 291 " pdb=" NH2 ARG B 291 " ideal model delta sigma weight residual 1.330 1.176 0.154 1.30e-02 5.92e+03 1.40e+02 bond pdb=" CZ ARG A 177 " pdb=" NH2 ARG A 177 " ideal model delta sigma weight residual 1.330 1.189 0.141 1.30e-02 5.92e+03 1.18e+02 bond pdb=" CA PHE A 39 " pdb=" HA PHE A 39 " ideal model delta sigma weight residual 0.970 0.756 0.214 2.00e-02 2.50e+03 1.15e+02 ... (remaining 35691 not shown) Histogram of bond angle deviations from ideal: 79.10 - 91.20: 2 91.20 - 103.30: 361 103.30 - 115.39: 43633 115.39 - 127.49: 20277 127.49 - 139.59: 320 Bond angle restraints: 64593 Sorted by residual: angle pdb=" PB ATP B 803 " pdb=" O3B ATP B 803 " pdb=" PG ATP B 803 " ideal model delta sigma weight residual 139.87 122.61 17.26 1.00e+00 1.00e+00 2.98e+02 angle pdb=" PA ATP B 803 " pdb=" O3A ATP B 803 " pdb=" PB ATP B 803 " ideal model delta sigma weight residual 136.83 121.28 15.55 1.00e+00 1.00e+00 2.42e+02 angle pdb=" C THR A 190 " pdb=" N GLU A 191 " pdb=" CA GLU A 191 " ideal model delta sigma weight residual 120.38 139.59 -19.21 1.37e+00 5.33e-01 1.97e+02 angle pdb=" C THR A 60 " pdb=" N ASP A 61 " pdb=" CA ASP A 61 " ideal model delta sigma weight residual 122.28 131.81 -9.53 8.80e-01 1.29e+00 1.17e+02 angle pdb=" C LEU B 388 " pdb=" N ASN B 389 " pdb=" CA ASN B 389 " ideal model delta sigma weight residual 120.75 136.32 -15.57 1.51e+00 4.39e-01 1.06e+02 ... (remaining 64588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.09: 15988 31.09 - 62.18: 552 62.18 - 93.28: 109 93.28 - 124.37: 2 124.37 - 155.46: 1 Dihedral angle restraints: 16652 sinusoidal: 9180 harmonic: 7472 Sorted by residual: dihedral pdb=" N ASP B 151 " pdb=" C ASP B 151 " pdb=" CA ASP B 151 " pdb=" CB ASP B 151 " ideal model delta harmonic sigma weight residual 122.80 146.13 -23.33 0 2.50e+00 1.60e-01 8.71e+01 dihedral pdb=" C ASP B 151 " pdb=" N ASP B 151 " pdb=" CA ASP B 151 " pdb=" CB ASP B 151 " ideal model delta harmonic sigma weight residual -122.60 -145.38 22.78 0 2.50e+00 1.60e-01 8.31e+01 dihedral pdb=" N TRP A 312 " pdb=" C TRP A 312 " pdb=" CA TRP A 312 " pdb=" CB TRP A 312 " ideal model delta harmonic sigma weight residual 122.80 143.28 -20.48 0 2.50e+00 1.60e-01 6.71e+01 ... (remaining 16649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.204: 2450 0.204 - 0.408: 170 0.408 - 0.612: 20 0.612 - 0.816: 2 0.816 - 1.020: 2 Chirality restraints: 2644 Sorted by residual: chirality pdb=" CA ASP B 151 " pdb=" N ASP B 151 " pdb=" C ASP B 151 " pdb=" CB ASP B 151 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" CA TRP A 312 " pdb=" N TRP A 312 " pdb=" C TRP A 312 " pdb=" CB TRP A 312 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" CA LYS C 160 " pdb=" N LYS C 160 " pdb=" C LYS C 160 " pdb=" CB LYS C 160 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 2641 not shown) Planarity restraints: 5225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 612 " 0.202 9.50e-02 1.11e+02 1.81e-01 6.42e+02 pdb=" NE ARG B 612 " 0.111 2.00e-02 2.50e+03 pdb=" CZ ARG B 612 " 0.095 2.00e-02 2.50e+03 pdb=" NH1 ARG B 612 " 0.054 2.00e-02 2.50e+03 pdb=" NH2 ARG B 612 " 0.144 2.00e-02 2.50e+03 pdb="HH11 ARG B 612 " -0.155 2.00e-02 2.50e+03 pdb="HH12 ARG B 612 " -0.094 2.00e-02 2.50e+03 pdb="HH21 ARG B 612 " -0.368 2.00e-02 2.50e+03 pdb="HH22 ARG B 612 " 0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 539 " 0.296 2.00e-02 2.50e+03 1.26e-01 4.75e+02 pdb=" CG TYR D 539 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR D 539 " -0.081 2.00e-02 2.50e+03 pdb=" CD2 TYR D 539 " -0.074 2.00e-02 2.50e+03 pdb=" CE1 TYR D 539 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 TYR D 539 " -0.046 2.00e-02 2.50e+03 pdb=" CZ TYR D 539 " 0.043 2.00e-02 2.50e+03 pdb=" OH TYR D 539 " 0.248 2.00e-02 2.50e+03 pdb=" HD1 TYR D 539 " -0.061 2.00e-02 2.50e+03 pdb=" HD2 TYR D 539 " -0.080 2.00e-02 2.50e+03 pdb=" HE1 TYR D 539 " -0.065 2.00e-02 2.50e+03 pdb=" HE2 TYR D 539 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 425 " -0.195 9.50e-02 1.11e+02 1.43e-01 3.67e+02 pdb=" NE ARG E 425 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG E 425 " -0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG E 425 " -0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG E 425 " -0.042 2.00e-02 2.50e+03 pdb="HH11 ARG E 425 " -0.236 2.00e-02 2.50e+03 pdb="HH12 ARG E 425 " 0.232 2.00e-02 2.50e+03 pdb="HH21 ARG E 425 " 0.023 2.00e-02 2.50e+03 pdb="HH22 ARG E 425 " 0.164 2.00e-02 2.50e+03 ... (remaining 5222 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.26: 3692 2.26 - 2.98: 90594 2.98 - 3.70: 127118 3.70 - 4.42: 189115 4.42 - 5.14: 297546 Nonbonded interactions: 708065 Sorted by model distance: nonbonded pdb=" HA LEU B 333 " pdb="HD22 LEU B 333 " model vdw 1.540 2.440 nonbonded pdb=" OE1 GLU A 70 " pdb=" H GLU A 70 " model vdw 1.565 1.850 nonbonded pdb=" H THR A 297 " pdb=" HG1 THR A 297 " model vdw 1.596 2.100 nonbonded pdb=" OE1 GLN A 326 " pdb=" H GLN A 326 " model vdw 1.631 1.850 nonbonded pdb=" OE1 GLU A 11 " pdb=" H GLU A 11 " model vdw 1.645 1.850 ... (remaining 708060 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' and (resid 10 through 220 or resid 273 through 319 or (resid 320 and \ (name N or name CA or name C or name O or name CB or name CG or name ND1 or name \ CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or nam \ e HD2 or name HE1 or name HE2)) or resid 321 through 691 or resid 801 through 80 \ 2)) selection = (chain 'B' and (resid 10 through 691 or resid 801 through 802)) } 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.400 Extract box with map and model: 8.690 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 114.810 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.110 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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 : 0.016 0.257 18066 Z= 1.031 Angle : 2.114 19.205 24304 Z= 1.431 Chirality : 0.122 1.020 2644 Planarity : 0.017 0.281 3120 Dihedral : 14.874 155.461 6975 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.99 % Favored : 97.96 % Rotamer: Outliers : 0.05 % Allowed : 0.56 % Favored : 99.38 % Cbeta Deviations : 1.30 % 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: -1.76 (0.16), residues: 2156 helix: -1.44 (0.14), residues: 968 sheet: 0.21 (0.32), residues: 249 loop : -1.08 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.139 0.026 TRP D 511 HIS 0.034 0.005 HIS A 632 PHE 0.117 0.014 PHE E 476 TYR 0.261 0.025 TYR D 539 ARG 0.026 0.001 ARG B 291 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 3.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 MET cc_start: 0.9380 (ttp) cc_final: 0.9143 (tmm) REVERT: A 602 MET cc_start: 0.9408 (tpt) cc_final: 0.9077 (tpt) REVERT: A 617 MET cc_start: 0.8923 (ptm) cc_final: 0.8711 (ptm) REVERT: A 620 MET cc_start: 0.8472 (tpt) cc_final: 0.8190 (tpp) REVERT: D 553 ASN cc_start: 0.9242 (t0) cc_final: 0.8869 (t0) outliers start: 1 outliers final: 1 residues processed: 146 average time/residue: 0.8770 time to fit residues: 182.5022 Evaluate side-chains 114 residues out of total 1951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 266 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN B 396 GLN B 632 HIS D 454 GLN E 211 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18066 Z= 0.290 Angle : 0.655 7.570 24304 Z= 0.365 Chirality : 0.040 0.153 2644 Planarity : 0.005 0.077 3120 Dihedral : 8.602 122.671 2412 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.51 % Allowed : 3.64 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.17), residues: 2156 helix: -0.39 (0.15), residues: 1009 sheet: -0.04 (0.33), residues: 247 loop : -1.03 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 197 HIS 0.014 0.002 HIS C 161 PHE 0.020 0.002 PHE E 278 TYR 0.037 0.002 TYR D 539 ARG 0.006 0.001 ARG E 275 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4312 Ramachandran restraints generated. 2156 Oldfield, 0 Emsley, 2156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 MET cc_start: 0.8422 (mtm) cc_final: 0.8203 (ttm) REVERT: A 553 MET cc_start: 0.9507 (ttp) cc_final: 0.9141 (tmm) REVERT: A 602 MET cc_start: 0.9235 (tpt) cc_final: 0.8992 (tpt) REVERT: A 621 MET cc_start: 0.8783 (ppp) cc_final: 0.8509 (ppp) REVERT: B 114 MET cc_start: 0.9054 (tpp) cc_final: 0.8741 (tmm) REVERT: D 581 MET cc_start: 0.9125 (mtp) cc_final: 0.8679 (mmm) REVERT: E 141 LYS cc_start: 0.9192 (tppt) cc_final: 0.8839 (tptt) REVERT: E 327 MET cc_start: 0.9340 (mmt) cc_final: 0.8820 (mmm) outliers start: 10 outliers final: 6 residues processed: 115 average time/residue: 0.9247 time to fit residues: 150.0183 Evaluate side-chains 107 residues out of total 1951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain E residue 266 TYR Chi-restraints excluded: chain E residue 351 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 161 optimal weight: 4.9990 chunk 132 optimal weight: 40.0000 chunk 53 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 210 optimal weight: 9.9990 chunk 173 optimal weight: 20.0000 chunk 193 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3109 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: