Starting phenix.real_space_refine on Tue May 14 08:26:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5l_19739/05_2024/8s5l_19739_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5l_19739/05_2024/8s5l_19739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5l_19739/05_2024/8s5l_19739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5l_19739/05_2024/8s5l_19739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5l_19739/05_2024/8s5l_19739_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5l_19739/05_2024/8s5l_19739_trim_updated.pdb" } resolution = 3.8 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= 0.012 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 4 5.49 5 S 78 5.16 5 C 8650 2.51 5 N 2372 2.21 5 O 2578 1.98 5 H 13567 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 86": "OD1" <-> "OD2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 316": "OD1" <-> "OD2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 477": "OD1" <-> "OD2" Residue "B ASP 506": "OD1" <-> "OD2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 281": "OD1" <-> "OD2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C GLU 399": "OE1" <-> "OE2" Residue "C ASP 538": "OD1" <-> "OD2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D ASP 316": "OD1" <-> "OD2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D ASP 376": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 27253 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 5618 Classifications: {'peptide': 363} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 342} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 7904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7904 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Chain: "C" Number of atoms: 7909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7909 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Chain: "D" Number of atoms: 5618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 5618 Classifications: {'peptide': 363} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 342} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'HEM': 1, 'PLP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'HEM': 1, 'PLP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 177 SG CYS A 52 79.352 132.334 41.782 1.00 56.77 S ATOM 21608 SG CYS D 52 47.665 28.331 41.717 1.00 56.13 S Time building chain proxies: 11.84, per 1000 atoms: 0.43 Number of scatterers: 27253 At special positions: 0 Unit cell: (127.958, 159.714, 83.126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 78 16.00 P 4 15.00 O 2578 8.00 N 2372 7.00 C 8650 6.00 H 13567 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.64 Conformation dependent library (CDL) restraints added in 2.8 seconds 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3196 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 13 sheets defined 36.4% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.80 Creating SS restraints... Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 80 through 83 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 227 through 234 removed outlier: 3.910A pdb=" N HIS A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 242 Processing helix chain 'A' and resid 259 through 271 removed outlier: 3.813A pdb=" N ILE A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 294 Processing helix chain 'A' and resid 329 through 342 Processing helix chain 'A' and resid 348 through 363 removed outlier: 3.709A pdb=" N LYS A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLU A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 388 through 394 Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'B' and resid 60 through 62 No H-bonds generated for 'chain 'B' and resid 60 through 62' Processing helix chain 'B' and resid 95 through 98 No H-bonds generated for 'chain 'B' and resid 95 through 98' Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 149 through 161 Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 203 through 213 Processing helix chain 'B' and resid 227 through 234 removed outlier: 3.832A pdb=" N HIS B 232 " --> pdb=" O ASN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 262 through 271 Processing helix chain 'B' and resid 291 through 294 Processing helix chain 'B' and resid 328 through 342 Processing helix chain 'B' and resid 348 through 360 removed outlier: 4.268A pdb=" N LYS B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 381 Processing helix chain 'B' and resid 388 through 394 Processing helix chain 'B' and resid 399 through 403 Processing helix chain 'B' and resid 408 through 411 removed outlier: 4.076A pdb=" N HIS B 411 " --> pdb=" O TRP B 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 408 through 411' Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 431 through 440 removed outlier: 3.647A pdb=" N GLU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 470 Processing helix chain 'B' and resid 479 through 481 No H-bonds generated for 'chain 'B' and resid 479 through 481' Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 536 through 547 Processing helix chain 'C' and resid 60 through 62 No H-bonds generated for 'chain 'C' and resid 60 through 62' Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'C' and resid 94 through 98 Processing helix chain 'C' and resid 118 through 132 removed outlier: 3.569A pdb=" N ARG C 121 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER C 123 " --> pdb=" O ASP C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 161 Processing helix chain 'C' and resid 175 through 183 Processing helix chain 'C' and resid 203 through 213 Processing helix chain 'C' and resid 227 through 234 removed outlier: 3.826A pdb=" N HIS C 232 " --> pdb=" O ASN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'C' and resid 259 through 271 removed outlier: 3.542A pdb=" N LYS C 267 " --> pdb=" O GLY C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 294 Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 328 through 342 removed outlier: 3.666A pdb=" N ARG C 336 " --> pdb=" O PHE C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 360 removed outlier: 4.218A pdb=" N LYS C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 388 through 394 Processing helix chain 'C' and resid 399 through 403 Processing helix chain 'C' and resid 408 through 411 removed outlier: 4.025A pdb=" N HIS C 411 " --> pdb=" O TRP C 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 408 through 411' Processing helix chain 'C' and resid 414 through 416 No H-bonds generated for 'chain 'C' and resid 414 through 416' Processing helix chain 'C' and resid 431 through 441 removed outlier: 3.708A pdb=" N LYS C 441 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 470 Processing helix chain 'C' and resid 479 through 481 No H-bonds generated for 'chain 'C' and resid 479 through 481' Processing helix chain 'C' and resid 496 through 503 Processing helix chain 'C' and resid 536 through 547 Processing helix chain 'D' and resid 60 through 62 No H-bonds generated for 'chain 'D' and resid 60 through 62' Processing helix chain 'D' and resid 80 through 83 Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 121 through 132 Processing helix chain 'D' and resid 149 through 161 Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 203 through 213 Processing helix chain 'D' and resid 227 through 234 removed outlier: 3.901A pdb=" N HIS D 232 " --> pdb=" O ASN D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 244 Processing helix chain 'D' and resid 259 through 271 removed outlier: 3.856A pdb=" N LYS D 267 " --> pdb=" O GLY D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 294 Processing helix chain 'D' and resid 329 through 342 Processing helix chain 'D' and resid 348 through 363 removed outlier: 3.715A pdb=" N LYS D 359 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN D 362 " --> pdb=" O VAL D 358 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLU D 363 " --> pdb=" O LYS D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 381 No H-bonds generated for 'chain 'D' and resid 379 through 381' Processing helix chain 'D' and resid 388 through 394 Processing helix chain 'D' and resid 399 through 401 No H-bonds generated for 'chain 'D' and resid 399 through 401' Processing sheet with id= A, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.680A pdb=" N LEU A 374 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N MET A 250 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ILE A 373 " --> pdb=" O MET A 250 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL A 252 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE A 278 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS A 322 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N ASP A 281 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE A 324 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 217 through 219 removed outlier: 6.476A pdb=" N THR A 141 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG A 164 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLU A 144 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE A 166 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR A 146 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL A 168 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLU A 187 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N MET A 169 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL A 189 " --> pdb=" O MET A 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 89 through 91 Processing sheet with id= D, first strand: chain 'B' and resid 217 through 219 removed outlier: 6.801A pdb=" N THR B 141 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG B 164 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLU B 144 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE B 166 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU B 187 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N MET B 169 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL B 189 " --> pdb=" O MET B 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 250 through 254 removed outlier: 6.519A pdb=" N ARG B 276 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ALA B 253 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE B 278 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS B 322 " --> pdb=" O GLY B 279 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP B 281 " --> pdb=" O LYS B 322 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE B 324 " --> pdb=" O ASP B 281 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 488 through 490 removed outlier: 4.003A pdb=" N GLY B 532 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N HIS B 513 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL B 530 " --> pdb=" O HIS B 513 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLN B 515 " --> pdb=" O GLN B 528 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLN B 528 " --> pdb=" O GLN B 515 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLN B 517 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLN B 526 " --> pdb=" O GLN B 517 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 89 through 91 Processing sheet with id= H, first strand: chain 'C' and resid 217 through 219 removed outlier: 6.899A pdb=" N THR C 141 " --> pdb=" O HIS C 218 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ARG C 164 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N GLU C 144 " --> pdb=" O ARG C 164 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE C 166 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU C 187 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N MET C 169 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL C 189 " --> pdb=" O MET C 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 250 through 254 removed outlier: 6.539A pdb=" N ARG C 276 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ALA C 253 " --> pdb=" O ARG C 276 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE C 278 " --> pdb=" O ALA C 253 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 488 through 491 removed outlier: 3.841A pdb=" N VAL C 511 " --> pdb=" O GLY C 532 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY C 532 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N HIS C 513 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL C 530 " --> pdb=" O HIS C 513 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLN C 515 " --> pdb=" O GLN C 528 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLN C 528 " --> pdb=" O GLN C 515 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 445 through 449 removed outlier: 3.576A pdb=" N VAL C 459 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY C 457 " --> pdb=" O VAL C 448 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.754A pdb=" N LEU D 374 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N MET D 250 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ILE D 373 " --> pdb=" O MET D 250 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL D 252 " --> pdb=" O ILE D 373 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG D 276 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ALA D 253 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE D 278 " --> pdb=" O ALA D 253 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS D 322 " --> pdb=" O GLY D 279 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ASP D 281 " --> pdb=" O LYS D 322 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE D 324 " --> pdb=" O ASP D 281 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 217 through 219 removed outlier: 6.586A pdb=" N THR D 141 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG D 164 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLU D 144 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE D 166 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR D 146 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL D 168 " --> pdb=" O THR D 146 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU D 187 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N MET D 169 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL D 189 " --> pdb=" O MET D 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= M 363 hydrogen bonds defined for protein. 1029 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: 10.76 Time building geometry restraints manager: 22.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.08: 13529 1.08 - 1.32: 2427 1.32 - 1.56: 11441 1.56 - 1.81: 113 1.81 - 2.05: 25 Bond restraints: 27535 Sorted by residual: bond pdb=" OP4 LLP D 119 " pdb=" P LLP D 119 " ideal model delta sigma weight residual 1.726 1.643 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" OP4 LLP A 119 " pdb=" P LLP A 119 " ideal model delta sigma weight residual 1.726 1.644 0.082 2.00e-02 2.50e+03 1.66e+01 bond pdb=" C3 LLP D 119 " pdb=" O3 LLP D 119 " ideal model delta sigma weight residual 1.330 1.395 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C3 LLP A 119 " pdb=" O3 LLP A 119 " ideal model delta sigma weight residual 1.330 1.395 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C4 LLP D 119 " pdb=" C4' LLP D 119 " ideal model delta sigma weight residual 1.464 1.524 -0.060 2.00e-02 2.50e+03 9.12e+00 ... (remaining 27530 not shown) Histogram of bond angle deviations from ideal: 86.08 - 104.53: 279 104.53 - 122.97: 46600 122.97 - 141.42: 3051 141.42 - 159.87: 0 159.87 - 178.32: 8 Bond angle restraints: 49938 Sorted by residual: angle pdb=" O LLP A 119 " pdb=" C LLP A 119 " pdb=" N ASP A 120 " ideal model delta sigma weight residual 123.00 86.08 36.92 1.60e+00 3.91e-01 5.33e+02 angle pdb=" O LLP D 119 " pdb=" C LLP D 119 " pdb=" N ASP D 120 " ideal model delta sigma weight residual 123.00 87.69 35.31 1.60e+00 3.91e-01 4.87e+02 angle pdb=" OP1 LLP A 119 " pdb=" P LLP A 119 " pdb=" OP4 LLP A 119 " ideal model delta sigma weight residual 100.47 110.60 -10.13 3.00e+00 1.11e-01 1.14e+01 angle pdb=" OP1 LLP D 119 " pdb=" P LLP D 119 " pdb=" OP4 LLP D 119 " ideal model delta sigma weight residual 100.47 110.28 -9.81 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C LYS B 384 " pdb=" CA LYS B 384 " pdb=" CB LYS B 384 " ideal model delta sigma weight residual 110.42 115.84 -5.42 1.99e+00 2.53e-01 7.41e+00 ... (remaining 49933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.03: 12326 35.03 - 70.05: 406 70.05 - 105.08: 40 105.08 - 140.10: 2 140.10 - 175.13: 1 Dihedral angle restraints: 12775 sinusoidal: 7189 harmonic: 5586 Sorted by residual: dihedral pdb=" C5A PLP C 602 " pdb=" O4P PLP C 602 " pdb=" P PLP C 602 " pdb=" O1P PLP C 602 " ideal model delta sinusoidal sigma weight residual 76.43 -98.70 175.13 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5 PLP B 602 " pdb=" C4 PLP B 602 " pdb=" C4A PLP B 602 " pdb=" O4A PLP B 602 " ideal model delta sinusoidal sigma weight residual 0.00 -137.31 137.31 1 2.00e+01 2.50e-03 4.16e+01 dihedral pdb=" C5A PLP B 602 " pdb=" O4P PLP B 602 " pdb=" P PLP B 602 " pdb=" O1P PLP B 602 " ideal model delta sinusoidal sigma weight residual 76.43 -58.43 134.86 1 2.00e+01 2.50e-03 4.09e+01 ... (remaining 12772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1405 0.036 - 0.073: 519 0.073 - 0.109: 131 0.109 - 0.146: 53 0.146 - 0.182: 4 Chirality restraints: 2112 Sorted by residual: chirality pdb=" CA PRO A 375 " pdb=" N PRO A 375 " pdb=" C PRO A 375 " pdb=" CB PRO A 375 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.29e-01 chirality pdb=" CA PRO B 375 " pdb=" N PRO B 375 " pdb=" C PRO B 375 " pdb=" CB PRO B 375 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CA PRO C 375 " pdb=" N PRO C 375 " pdb=" C PRO C 375 " pdb=" CB PRO C 375 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.57e-01 ... (remaining 2109 not shown) Planarity restraints: 4075 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LLP A 119 " 0.137 2.00e-02 2.50e+03 2.22e-01 4.92e+02 pdb=" C LLP A 119 " -0.384 2.00e-02 2.50e+03 pdb=" O LLP A 119 " 0.135 2.00e-02 2.50e+03 pdb=" N ASP A 120 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LLP D 119 " -0.132 2.00e-02 2.50e+03 2.16e-01 4.66e+02 pdb=" C LLP D 119 " 0.374 2.00e-02 2.50e+03 pdb=" O LLP D 119 " -0.131 2.00e-02 2.50e+03 pdb=" N ASP D 120 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 374 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.12e+00 pdb=" N PRO A 375 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.025 5.00e-02 4.00e+02 ... (remaining 4072 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 993 2.14 - 2.75: 52169 2.75 - 3.37: 78081 3.37 - 3.98: 98272 3.98 - 4.60: 155978 Nonbonded interactions: 385493 Sorted by model distance: nonbonded pdb=" OD2 ASP C 249 " pdb=" H ARG C 369 " model vdw 1.525 1.850 nonbonded pdb=" OD2 ASP B 249 " pdb=" H ARG B 369 " model vdw 1.536 1.850 nonbonded pdb=" O LEU C 268 " pdb=" H CYS C 272 " model vdw 1.541 1.850 nonbonded pdb=" OE1 GLU D 201 " pdb=" H GLU D 201 " model vdw 1.546 1.850 nonbonded pdb=" OE1 GLU B 399 " pdb=" H GLU B 399 " model vdw 1.546 1.850 ... (remaining 385488 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 'D' } ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 42 through 118 or (resid 119 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE or name NZ )) or resid \ 120 through 548 or resid 601 through 602)) } 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 group one per residue 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: 7.040 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: 0.420 Extract box with map and model: 26.870 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 87.410 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.130 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 : 0.006 0.086 13968 Z= 0.375 Angle : 0.782 36.925 18972 Z= 0.430 Chirality : 0.043 0.182 2112 Planarity : 0.007 0.222 2432 Dihedral : 15.676 175.125 5214 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.56 % Favored : 94.21 % Rotamer: Outliers : 0.14 % Allowed : 12.70 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.18 (0.21), residues: 1726 helix: 0.05 (0.20), residues: 656 sheet: -1.07 (0.29), residues: 262 loop : 0.30 (0.24), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 323 HIS 0.005 0.001 HIS D 203 PHE 0.012 0.002 PHE A 324 TYR 0.015 0.002 TYR D 233 ARG 0.005 0.001 ARG D 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 2.263 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 outliers start: 2 outliers final: 2 residues processed: 119 average time/residue: 0.5474 time to fit residues: 99.1096 Evaluate side-chains 113 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 387 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 501 HIS ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.0477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 13968 Z= 0.319 Angle : 0.569 7.289 18972 Z= 0.283 Chirality : 0.042 0.154 2112 Planarity : 0.004 0.033 2432 Dihedral : 9.384 157.157 1916 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.35 % Favored : 95.42 % Rotamer: Outliers : 1.09 % Allowed : 13.46 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.19 (0.21), residues: 1726 helix: 0.11 (0.20), residues: 658 sheet: -1.13 (0.29), residues: 266 loop : 0.27 (0.24), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 323 HIS 0.004 0.001 HIS D 203 PHE 0.011 0.001 PHE A 324 TYR 0.012 0.002 TYR D 233 ARG 0.003 0.000 ARG D 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 2.234 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: C 531 PHE cc_start: 0.7597 (m-10) cc_final: 0.7207 (m-10) outliers start: 16 outliers final: 13 residues processed: 123 average time/residue: 0.5352 time to fit residues: 101.3490 Evaluate side-chains 123 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 187 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13968 Z= 0.275 Angle : 0.541 6.852 18972 Z= 0.268 Chirality : 0.041 0.153 2112 Planarity : 0.004 0.035 2432 Dihedral : 8.937 149.059 1915 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.75 % Favored : 95.02 % Rotamer: Outliers : 1.57 % Allowed : 13.80 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.14 (0.21), residues: 1726 helix: 0.19 (0.21), residues: 658 sheet: -1.07 (0.30), residues: 266 loop : 0.25 (0.24), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 323 HIS 0.004 0.001 HIS D 203 PHE 0.011 0.001 PHE C 443 TYR 0.010 0.001 TYR D 233 ARG 0.003 0.000 ARG D 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 2.206 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: B 387 SER cc_start: 0.9160 (OUTLIER) cc_final: 0.8856 (p) REVERT: D 173 MET cc_start: 0.8848 (mmm) cc_final: 0.8571 (mmm) outliers start: 23 outliers final: 17 residues processed: 133 average time/residue: 0.5327 time to fit residues: 109.7005 Evaluate side-chains 131 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 13968 Z= 0.271 Angle : 0.535 7.012 18972 Z= 0.263 Chirality : 0.041 0.153 2112 Planarity : 0.004 0.036 2432 Dihedral : 8.684 135.326 1915 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.63 % Favored : 95.13 % Rotamer: Outliers : 1.71 % Allowed : 14.96 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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 (0.21), residues: 1726 helix: 0.37 (0.21), residues: 644 sheet: -1.06 (0.30), residues: 266 loop : 0.27 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 323 HIS 0.004 0.001 HIS D 203 PHE 0.009 0.001 PHE A 324 TYR 0.009 0.001 TYR D 163 ARG 0.003 0.000 ARG D 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 2.410 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: B 387 SER cc_start: 0.9149 (OUTLIER) cc_final: 0.8882 (p) REVERT: D 173 MET cc_start: 0.8880 (mmm) cc_final: 0.8573 (mmm) REVERT: D 184 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8689 (mp) outliers start: 25 outliers final: 21 residues processed: 130 average time/residue: 0.4994 time to fit residues: 103.1152 Evaluate side-chains 137 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 13968 Z= 0.309 Angle : 0.553 7.148 18972 Z= 0.274 Chirality : 0.042 0.162 2112 Planarity : 0.004 0.038 2432 Dihedral : 8.574 118.846 1914 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.10 % Favored : 94.67 % Rotamer: Outliers : 1.98 % Allowed : 14.69 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.29 (0.21), residues: 1726 helix: 0.17 (0.20), residues: 660 sheet: -1.22 (0.30), residues: 264 loop : 0.08 (0.24), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 323 HIS 0.004 0.001 HIS A 203 PHE 0.011 0.001 PHE D 324 TYR 0.011 0.001 TYR D 163 ARG 0.003 0.000 ARG D 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 2.096 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: A 184 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8850 (mp) REVERT: B 387 SER cc_start: 0.9155 (OUTLIER) cc_final: 0.8898 (p) REVERT: D 173 MET cc_start: 0.8905 (mmm) cc_final: 0.8525 (mmm) REVERT: D 184 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8678 (mp) outliers start: 29 outliers final: 24 residues processed: 136 average time/residue: 0.5564 time to fit residues: 120.2565 Evaluate side-chains 140 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 501 HIS ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 13968 Z= 0.426 Angle : 0.612 8.338 18972 Z= 0.308 Chirality : 0.043 0.174 2112 Planarity : 0.004 0.042 2432 Dihedral : 8.635 101.043 1914 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.32 % Favored : 93.45 % Rotamer: Outliers : 2.39 % Allowed : 15.30 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.62 (0.21), residues: 1726 helix: -0.10 (0.20), residues: 664 sheet: -1.40 (0.30), residues: 256 loop : -0.14 (0.24), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 323 HIS 0.008 0.001 HIS C 501 PHE 0.014 0.002 PHE D 324 TYR 0.013 0.002 TYR D 163 ARG 0.004 0.000 ARG D 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 113 time to evaluate : 2.258 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: A 184 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8866 (mp) REVERT: B 387 SER cc_start: 0.9218 (OUTLIER) cc_final: 0.8969 (p) REVERT: C 479 VAL cc_start: 0.7519 (OUTLIER) cc_final: 0.7215 (p) REVERT: D 184 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8697 (mp) outliers start: 35 outliers final: 27 residues processed: 138 average time/residue: 0.4960 time to fit residues: 107.6806 Evaluate side-chains 138 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 107 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13968 Z= 0.239 Angle : 0.531 8.010 18972 Z= 0.260 Chirality : 0.041 0.153 2112 Planarity : 0.004 0.037 2432 Dihedral : 8.259 89.740 1914 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.87 % Favored : 94.90 % Rotamer: Outliers : 2.32 % Allowed : 15.71 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.41 (0.21), residues: 1726 helix: 0.09 (0.20), residues: 666 sheet: -1.29 (0.30), residues: 260 loop : -0.02 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 323 HIS 0.004 0.001 HIS D 203 PHE 0.008 0.001 PHE D 324 TYR 0.008 0.001 TYR C 233 ARG 0.002 0.000 ARG D 132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 113 time to evaluate : 2.460 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: A 184 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8831 (mp) REVERT: B 387 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8903 (p) REVERT: C 479 VAL cc_start: 0.7513 (OUTLIER) cc_final: 0.7219 (p) REVERT: D 184 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8656 (mp) outliers start: 34 outliers final: 28 residues processed: 138 average time/residue: 0.4986 time to fit residues: 108.3908 Evaluate side-chains 137 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 105 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 chunk 112 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13968 Z= 0.199 Angle : 0.513 6.437 18972 Z= 0.249 Chirality : 0.041 0.148 2112 Planarity : 0.004 0.036 2432 Dihedral : 8.092 88.950 1914 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.29 % Favored : 95.48 % Rotamer: Outliers : 2.19 % Allowed : 15.92 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.22 (0.21), residues: 1726 helix: 0.26 (0.21), residues: 664 sheet: -1.14 (0.31), residues: 260 loop : 0.05 (0.24), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 323 HIS 0.004 0.001 HIS D 203 PHE 0.006 0.001 PHE D 310 TYR 0.008 0.001 TYR C 233 ARG 0.002 0.000 ARG D 369 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 108 time to evaluate : 2.278 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: A 184 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8813 (mp) REVERT: B 387 SER cc_start: 0.9188 (OUTLIER) cc_final: 0.8967 (p) REVERT: C 169 MET cc_start: 0.6747 (mtt) cc_final: 0.6319 (ttm) REVERT: C 479 VAL cc_start: 0.7547 (OUTLIER) cc_final: 0.7266 (p) REVERT: D 184 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8669 (mp) outliers start: 32 outliers final: 28 residues processed: 131 average time/residue: 0.4967 time to fit residues: 103.3500 Evaluate side-chains 137 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 105 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 380 ASN Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 146 optimal weight: 0.4980 chunk 153 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13968 Z= 0.168 Angle : 0.497 6.525 18972 Z= 0.239 Chirality : 0.041 0.148 2112 Planarity : 0.003 0.038 2432 Dihedral : 7.954 87.552 1914 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.88 % Favored : 95.89 % Rotamer: Outliers : 2.12 % Allowed : 15.92 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.03 (0.21), residues: 1726 helix: 0.45 (0.21), residues: 660 sheet: -0.96 (0.31), residues: 260 loop : 0.19 (0.24), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 323 HIS 0.005 0.001 HIS C 501 PHE 0.005 0.001 PHE D 324 TYR 0.007 0.001 TYR C 233 ARG 0.002 0.000 ARG D 369 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 113 time to evaluate : 1.987 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: A 184 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8799 (mp) REVERT: D 184 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8653 (mp) outliers start: 31 outliers final: 26 residues processed: 135 average time/residue: 0.4956 time to fit residues: 104.9378 Evaluate side-chains 134 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 380 ASN Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 171 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 145 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 HIS ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13968 Z= 0.226 Angle : 0.516 7.351 18972 Z= 0.249 Chirality : 0.041 0.157 2112 Planarity : 0.004 0.039 2432 Dihedral : 7.994 87.736 1914 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.81 % Favored : 94.96 % Rotamer: Outliers : 1.91 % Allowed : 16.39 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.09 (0.21), residues: 1726 helix: 0.34 (0.21), residues: 672 sheet: -1.04 (0.31), residues: 256 loop : 0.13 (0.24), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 390 HIS 0.004 0.001 HIS D 203 PHE 0.007 0.001 PHE D 324 TYR 0.007 0.001 TYR C 233 ARG 0.003 0.000 ARG B 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3452 Ramachandran restraints generated. 1726 Oldfield, 0 Emsley, 1726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 119 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 2.302 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: A 184 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8812 (mp) REVERT: C 479 VAL cc_start: 0.7564 (OUTLIER) cc_final: 0.7292 (p) REVERT: D 184 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8669 (mp) outliers start: 28 outliers final: 25 residues processed: 129 average time/residue: 0.5329 time to fit residues: 106.6110 Evaluate side-chains 134 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 501 HIS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 380 ASN Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 501 HIS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 378 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 501 HIS ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.104810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.087632 restraints weight = 86430.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.091451 restraints weight = 43645.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.094015 restraints weight = 27553.844| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 13968 Z= 0.353 Angle : 0.576 7.383 18972 Z= 0.284 Chirality : 0.042 0.163 2112 Planarity : 0.004 0.039 2432 Dihedral : 8.205 89.543 1914 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.26 % Favored : 93.51 % Rotamer: Outliers : 2.05 % Allowed : 16.39 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.33 (0.21), residues: 1726 helix: 0.20 (0.20), residues: 666 sheet: -1.31 (0.31), residues: 256 loop : -0.00 (0.24), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 323 HIS 0.010 0.001 HIS C 501 PHE 0.012 0.002 PHE D 324 TYR 0.011 0.002 TYR D 233 ARG 0.004 0.000 ARG D 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5209.81 seconds wall clock time: 94 minutes 56.39 seconds (5696.39 seconds total)