Starting phenix.real_space_refine on Sun Feb 18 15:50:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2k_28818/02_2024/8f2k_28818_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2k_28818/02_2024/8f2k_28818.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2k_28818/02_2024/8f2k_28818_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2k_28818/02_2024/8f2k_28818_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2k_28818/02_2024/8f2k_28818_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2k_28818/02_2024/8f2k_28818.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2k_28818/02_2024/8f2k_28818.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2k_28818/02_2024/8f2k_28818_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2k_28818/02_2024/8f2k_28818_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.184 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: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 32 5.16 5 C 14164 2.51 5 N 3908 2.21 5 O 4278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 52": "OE1" <-> "OE2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A ASP 124": "OD1" <-> "OD2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A ASP 335": "OD1" <-> "OD2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "A GLU 401": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B ASP 172": "OD1" <-> "OD2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B ASP 272": "OD1" <-> "OD2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B ASP 335": "OD1" <-> "OD2" Residue "B GLU 442": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C ASP 196": "OD1" <-> "OD2" Residue "C ASP 226": "OD1" <-> "OD2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "C GLU 330": "OE1" <-> "OE2" Residue "C ASP 349": "OD1" <-> "OD2" Residue "C GLU 401": "OE1" <-> "OE2" Residue "C ASP 456": "OD1" <-> "OD2" Residue "C TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 22": "OD1" <-> "OD2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D GLU 169": "OE1" <-> "OE2" Residue "D GLU 246": "OE1" <-> "OE2" Residue "D ASP 288": "OD1" <-> "OD2" Residue "D ASP 315": "OD1" <-> "OD2" Residue "D PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 330": "OD1" <-> "OD2" Residue "D ASP 352": "OD1" <-> "OD2" Residue "D TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 436": "OD1" <-> "OD2" Residue "D GLU 454": "OE1" <-> "OE2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E ASP 120": "OD1" <-> "OD2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E ASP 250": "OD1" <-> "OD2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 341": "OE1" <-> "OE2" Residue "E ASP 352": "OD1" <-> "OD2" Residue "E TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 436": "OD1" <-> "OD2" Residue "E GLU 454": "OE1" <-> "OE2" Residue "E TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 68": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "F GLU 200": "OE1" <-> "OE2" Residue "F ASP 330": "OD1" <-> "OD2" Residue "F GLU 341": "OE1" <-> "OE2" Residue "F ASP 352": "OD1" <-> "OD2" Residue "F GLU 366": "OE1" <-> "OE2" Residue "F GLU 376": "OE1" <-> "OE2" Residue "F GLU 422": "OE1" <-> "OE2" Residue "G GLU 5": "OE1" <-> "OE2" Residue "G GLU 7": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22402 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3657 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3641 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3666 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 465} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3472 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 446} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 45 Chain: "E" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3485 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 446} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 48 Chain: "F" Number of atoms: 3490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3490 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 446} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "G" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 747 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Unusual residues: {' MG': 1, 'ATP': 1, 'XBC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Unusual residues: {' MG': 1, 'ATP': 1, 'XBC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 12.48, per 1000 atoms: 0.56 Number of scatterers: 22402 At special positions: 0 Unit cell: (133.916, 124.5, 126.593, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 15 15.00 Mg 5 11.99 O 4278 8.00 N 3908 7.00 C 14164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.03 Conformation dependent library (CDL) restraints added in 4.7 seconds 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5366 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 21 sheets defined 42.9% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.16 Creating SS restraints... Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.939A pdb=" N GLN A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ARG A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TRP A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 227 through 230 removed outlier: 3.744A pdb=" N TYR A 230 " --> pdb=" O ALA A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 242 through 262 Proline residue: A 249 - end of helix removed outlier: 3.632A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 300 through 310 removed outlier: 4.438A pdb=" N ARG A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 356 through 360 Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 383 through 408 removed outlier: 3.821A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ALA A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N PHE A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLN A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 Processing helix chain 'A' and resid 440 through 452 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 462 through 477 removed outlier: 3.600A pdb=" N SER A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 488 Processing helix chain 'A' and resid 493 through 509 Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 177 through 192 removed outlier: 3.730A pdb=" N GLN B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LYS B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ARG B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TRP B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 224 Processing helix chain 'B' and resid 227 through 230 removed outlier: 3.841A pdb=" N TYR B 230 " --> pdb=" O ALA B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 242 through 261 Proline residue: B 249 - end of helix removed outlier: 3.521A pdb=" N TRP B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 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 310 removed outlier: 4.093A pdb=" N PHE B 301 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 305 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG B 306 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU B 309 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 339 through 345 Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 377 through 379 No H-bonds generated for 'chain 'B' and resid 377 through 379' Processing helix chain 'B' and resid 383 through 389 Processing helix chain 'B' and resid 392 through 406 removed outlier: 3.592A pdb=" N PHE B 405 " --> pdb=" O GLU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 430 Processing helix chain 'B' and resid 440 through 451 Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 454 through 457 removed outlier: 4.198A pdb=" N GLY B 457 " --> pdb=" O HIS B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 454 through 457' Processing helix chain 'B' and resid 460 through 477 removed outlier: 3.839A pdb=" N ILE B 463 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY B 464 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 468 " --> pdb=" O GLU B 465 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE B 470 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 471 " --> pdb=" O SER B 468 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS B 475 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN B 477 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 488 Processing helix chain 'B' and resid 493 through 509 Processing helix chain 'C' and resid 81 through 83 No H-bonds generated for 'chain 'C' and resid 81 through 83' Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 177 through 192 removed outlier: 3.748A pdb=" N GLN C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ARG C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TRP C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 224 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 242 through 262 Proline residue: C 249 - end of helix removed outlier: 3.653A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 298 through 310 removed outlier: 4.142A pdb=" N PHE C 301 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 303 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER C 305 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG C 306 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU C 309 " --> pdb=" O ARG C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 345 Processing helix chain 'C' and resid 356 through 360 Processing helix chain 'C' and resid 377 through 379 No H-bonds generated for 'chain 'C' and resid 377 through 379' Processing helix chain 'C' and resid 383 through 408 removed outlier: 6.749A pdb=" N SER C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU C 392 " --> pdb=" O VAL C 388 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LYS C 393 " --> pdb=" O ALA C 389 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU C 394 " --> pdb=" O GLY C 390 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N PHE C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 430 removed outlier: 3.551A pdb=" N THR C 419 " --> pdb=" O THR C 416 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG C 422 " --> pdb=" O THR C 419 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY C 423 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C 426 " --> pdb=" O GLY C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 451 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 454 through 457 removed outlier: 3.695A pdb=" N GLY C 457 " --> pdb=" O HIS C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 454 through 457' Processing helix chain 'C' and resid 460 through 477 removed outlier: 3.629A pdb=" N ILE C 463 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLY C 464 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER C 469 " --> pdb=" O PHE C 466 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE C 470 " --> pdb=" O GLU C 467 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 471 " --> pdb=" O SER C 468 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 474 " --> pdb=" O LEU C 471 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS C 475 " --> pdb=" O SER C 472 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN C 477 " --> pdb=" O LEU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 488 Processing helix chain 'C' and resid 493 through 509 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 163 through 178 Processing helix chain 'D' and resid 191 through 204 Processing helix chain 'D' and resid 226 through 247 removed outlier: 4.776A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 272 Processing helix chain 'D' and resid 285 through 295 removed outlier: 4.461A pdb=" N ARG D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 326 Processing helix chain 'D' and resid 337 through 341 Processing helix chain 'D' and resid 360 through 363 No H-bonds generated for 'chain 'D' and resid 360 through 363' Processing helix chain 'D' and resid 365 through 391 removed outlier: 4.459A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 413 Processing helix chain 'D' and resid 421 through 425 removed outlier: 3.765A pdb=" N THR D 425 " --> pdb=" O GLU D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 445 Processing helix chain 'D' and resid 454 through 456 No H-bonds generated for 'chain 'D' and resid 454 through 456' Processing helix chain 'D' and resid 463 through 475 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 139 through 144 Processing helix chain 'E' and resid 163 through 174 Processing helix chain 'E' and resid 191 through 204 Processing helix chain 'E' and resid 226 through 245 removed outlier: 4.892A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 272 removed outlier: 3.766A pdb=" N GLN E 263 " --> pdb=" O ARG E 260 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL E 268 " --> pdb=" O GLY E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 293 Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 320 through 328 removed outlier: 4.088A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N HIS E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 341 Processing helix chain 'E' and resid 360 through 363 No H-bonds generated for 'chain 'E' and resid 360 through 363' Processing helix chain 'E' and resid 365 through 391 removed outlier: 4.737A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 395 No H-bonds generated for 'chain 'E' and resid 393 through 395' Processing helix chain 'E' and resid 398 through 413 Processing helix chain 'E' and resid 419 through 425 removed outlier: 3.664A pdb=" N GLU E 422 " --> pdb=" O ALA E 419 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N VAL E 423 " --> pdb=" O VAL E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 445 Processing helix chain 'E' and resid 454 through 457 No H-bonds generated for 'chain 'E' and resid 454 through 457' Processing helix chain 'E' and resid 463 through 475 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 139 through 144 Processing helix chain 'F' and resid 163 through 174 Processing helix chain 'F' and resid 191 through 203 Processing helix chain 'F' and resid 226 through 229 No H-bonds generated for 'chain 'F' and resid 226 through 229' Processing helix chain 'F' and resid 232 through 245 Processing helix chain 'F' and resid 258 through 272 removed outlier: 3.734A pdb=" N GLN F 263 " --> pdb=" O ARG F 260 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA F 264 " --> pdb=" O PHE F 261 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL F 268 " --> pdb=" O GLY F 265 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA F 270 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 293 removed outlier: 4.505A pdb=" N ALA F 286 " --> pdb=" O PRO F 283 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP F 288 " --> pdb=" O LEU F 285 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET F 289 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN F 293 " --> pdb=" O GLY F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 328 removed outlier: 4.227A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N HIS F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 341 Processing helix chain 'F' and resid 365 through 390 removed outlier: 3.543A pdb=" N GLN F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 395 No H-bonds generated for 'chain 'F' and resid 393 through 395' Processing helix chain 'F' and resid 398 through 413 Processing helix chain 'F' and resid 420 through 425 removed outlier: 3.726A pdb=" N THR F 425 " --> pdb=" O GLU F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 445 Processing helix chain 'F' and resid 454 through 457 Processing helix chain 'F' and resid 463 through 475 Processing helix chain 'G' and resid 3 through 41 Processing helix chain 'G' and resid 219 through 274 Processing sheet with id= A, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.658A pdb=" N GLY A 74 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LEU A 68 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLN A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N PHE A 44 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL A 33 " --> pdb=" O PHE A 44 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 98 through 101 Processing sheet with id= C, first strand: chain 'A' and resid 350 through 354 Processing sheet with id= D, first strand: chain 'A' and resid 231 through 236 removed outlier: 6.584A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N SER A 322 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE A 268 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR A 324 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N TYR A 270 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU A 326 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 30 through 32 removed outlier: 6.979A pdb=" N GLY B 74 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU B 68 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLN B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N PHE B 44 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL B 33 " --> pdb=" O PHE B 44 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 98 through 101 Processing sheet with id= G, first strand: chain 'B' and resid 109 through 111 removed outlier: 8.641A pdb=" N VAL B 110 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE B 233 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS B 203 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL B 234 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N SER B 322 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE B 268 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 324 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N TYR B 270 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU B 326 " --> pdb=" O TYR B 270 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 351 through 354 removed outlier: 6.498A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU B 354 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE B 170 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.541A pdb=" N GLY C 74 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU C 68 " --> pdb=" O GLN C 72 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLN C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 35 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE C 44 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL C 33 " --> pdb=" O PHE C 44 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 98 through 101 Processing sheet with id= K, first strand: chain 'C' and resid 351 through 354 removed outlier: 6.406A pdb=" N LEU C 168 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU C 354 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE C 170 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 231 through 236 removed outlier: 8.913A pdb=" N ILE C 232 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N HIS C 265 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N VAL C 204 " --> pdb=" O HIS C 265 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU C 267 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL C 206 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL C 269 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL C 208 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER C 322 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ILE C 268 " --> pdb=" O SER C 322 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR C 324 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N TYR C 270 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU C 326 " --> pdb=" O TYR C 270 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.471A pdb=" N ASP D 22 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL D 16 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= O, first strand: chain 'D' and resid 331 through 334 removed outlier: 8.411A pdb=" N ILE D 153 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER D 306 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU D 155 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN D 308 " --> pdb=" O LEU D 155 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.955A pdb=" N LYS E 75 " --> pdb=" O LYS E 40 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS E 40 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N HIS E 24 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL E 13 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 87 removed outlier: 4.830A pdb=" N LEU E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 331 through 335 removed outlier: 7.779A pdb=" N ILE E 153 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER E 306 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU E 155 " --> pdb=" O SER E 306 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN E 308 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLY E 157 " --> pdb=" O GLN E 308 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL E 310 " --> pdb=" O GLY E 157 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL E 251 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL E 307 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU E 253 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ALA E 309 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE E 255 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N TYR E 311 " --> pdb=" O ILE E 255 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 75 through 77 removed outlier: 6.642A pdb=" N ASP F 22 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL F 16 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 84 through 87 removed outlier: 4.555A pdb=" N LEU F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 331 through 334 removed outlier: 7.755A pdb=" N ILE F 153 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N SER F 306 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU F 155 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN F 308 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLY F 157 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL F 310 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL F 251 " --> pdb=" O THR F 305 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL F 307 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU F 253 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ALA F 309 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE F 255 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N TYR F 311 " --> pdb=" O ILE F 255 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2523 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: 7.76 Time building geometry restraints manager: 9.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3782 1.31 - 1.44: 5433 1.44 - 1.56: 13446 1.56 - 1.69: 26 1.69 - 1.81: 61 Bond restraints: 22748 Sorted by residual: bond pdb=" C06 XBC F 503 " pdb=" C07 XBC F 503 " ideal model delta sigma weight residual 1.563 1.341 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C06 XBC E 503 " pdb=" C07 XBC E 503 " ideal model delta sigma weight residual 1.563 1.341 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" CB PRO E 42 " pdb=" CG PRO E 42 " ideal model delta sigma weight residual 1.492 1.641 -0.149 5.00e-02 4.00e+02 8.94e+00 bond pdb=" N PRO E 42 " pdb=" CA PRO E 42 " ideal model delta sigma weight residual 1.471 1.439 0.031 1.32e-02 5.74e+03 5.63e+00 bond pdb=" C40 XBC F 503 " pdb=" C41 XBC F 503 " ideal model delta sigma weight residual 1.596 1.549 0.047 2.00e-02 2.50e+03 5.61e+00 ... (remaining 22743 not shown) Histogram of bond angle deviations from ideal: 96.59 - 105.23: 534 105.23 - 113.86: 13145 113.86 - 122.49: 14509 122.49 - 131.12: 2648 131.12 - 139.76: 44 Bond angle restraints: 30880 Sorted by residual: angle pdb=" CA PRO E 42 " pdb=" N PRO E 42 " pdb=" CD PRO E 42 " ideal model delta sigma weight residual 112.00 97.17 14.83 1.40e+00 5.10e-01 1.12e+02 angle pdb=" C14 XBC E 503 " pdb=" C15 XBC E 503 " pdb=" C16 XBC E 503 " ideal model delta sigma weight residual 152.65 121.77 30.88 3.00e+00 1.11e-01 1.06e+02 angle pdb=" C14 XBC F 503 " pdb=" C15 XBC F 503 " pdb=" C16 XBC F 503 " ideal model delta sigma weight residual 152.65 124.46 28.19 3.00e+00 1.11e-01 8.83e+01 angle pdb=" C15 XBC F 503 " pdb=" C16 XBC F 503 " pdb=" C17 XBC F 503 " ideal model delta sigma weight residual 112.21 137.24 -25.03 3.00e+00 1.11e-01 6.96e+01 angle pdb=" C15 XBC E 503 " pdb=" C16 XBC E 503 " pdb=" C17 XBC E 503 " ideal model delta sigma weight residual 112.21 133.90 -21.69 3.00e+00 1.11e-01 5.22e+01 ... (remaining 30875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.15: 12707 19.15 - 38.30: 788 38.30 - 57.44: 239 57.44 - 76.59: 79 76.59 - 95.74: 27 Dihedral angle restraints: 13840 sinusoidal: 5445 harmonic: 8395 Sorted by residual: dihedral pdb=" CA ASP A 271 " pdb=" C ASP A 271 " pdb=" N ASP A 272 " pdb=" CA ASP A 272 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA GLN E 282 " pdb=" C GLN E 282 " pdb=" N PRO E 283 " pdb=" CA PRO E 283 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA VAL F 312 " pdb=" C VAL F 312 " pdb=" N PRO F 313 " pdb=" CA PRO F 313 " ideal model delta harmonic sigma weight residual -180.00 -151.87 -28.13 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 13837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3062 0.062 - 0.124: 504 0.124 - 0.186: 72 0.186 - 0.247: 2 0.247 - 0.309: 14 Chirality restraints: 3654 Sorted by residual: chirality pdb=" C2' ATP E 501 " pdb=" C1' ATP E 501 " pdb=" C3' ATP E 501 " pdb=" O2' ATP E 501 " both_signs ideal model delta sigma weight residual False -2.68 -2.99 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C3' ATP B 600 " pdb=" C2' ATP B 600 " pdb=" C4' ATP B 600 " pdb=" O3' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C2' ATP A 600 " pdb=" C1' ATP A 600 " pdb=" C3' ATP A 600 " pdb=" O2' ATP A 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 3651 not shown) Planarity restraints: 3978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 41 " -0.124 5.00e-02 4.00e+02 1.73e-01 4.80e+01 pdb=" N PRO E 42 " 0.299 5.00e-02 4.00e+02 pdb=" CA PRO E 42 " -0.091 5.00e-02 4.00e+02 pdb=" CD PRO E 42 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 166 " -0.417 9.50e-02 1.11e+02 1.88e-01 2.59e+01 pdb=" NE ARG C 166 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG C 166 " -0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG C 166 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG C 166 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 191 " -0.043 2.00e-02 2.50e+03 3.05e-02 2.32e+01 pdb=" CG TRP C 191 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP C 191 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP C 191 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 191 " 0.050 2.00e-02 2.50e+03 pdb=" CE2 TRP C 191 " -0.019 2.00e-02 2.50e+03 pdb=" CE3 TRP C 191 " 0.054 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 191 " -0.026 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 191 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 191 " -0.026 2.00e-02 2.50e+03 ... (remaining 3975 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 128 2.55 - 3.14: 18822 3.14 - 3.72: 34897 3.72 - 4.31: 52432 4.31 - 4.90: 87189 Nonbonded interactions: 193468 Sorted by model distance: nonbonded pdb=" O3G ATP C 600 " pdb="MG MG C 601 " model vdw 1.959 2.170 nonbonded pdb=" O1G ATP E 501 " pdb="MG MG E 502 " model vdw 1.961 2.170 nonbonded pdb=" O2B ATP F 501 " pdb="MG MG F 502 " model vdw 1.992 2.170 nonbonded pdb=" OG1 THR C 178 " pdb="MG MG C 601 " model vdw 2.034 2.170 nonbonded pdb=" OG1 THR E 164 " pdb="MG MG E 502 " model vdw 2.037 2.170 ... (remaining 193463 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 26 through 194 or (resid 195 and (name N or name CA or nam \ e C or name O or name CB )) or resid 196 through 315 or (resid 316 and (name N o \ r name CA or name C or name O or name CB )) or resid 317 through 356 or (resid 3 \ 57 and (name N or name CA or name C or name O or name CB )) or resid 358 through \ 406 or (resid 407 through 408 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 409 through 411 and (name N or name CA or name C or name O or \ name CB )) or resid 412 or (resid 413 through 414 and (name N or name CA or name \ C or name O or name CB )) or resid 415 through 458 or (resid 459 and (name N or \ name CA or name C or name O or name CB )) or resid 460 through 476 or (resid 47 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 478 through \ 486 or (resid 487 and (name N or name CA or name C or name O or name CB )) or re \ sid 488 through 489 or (resid 490 and (name N or name CA or name C or name O or \ name CB )) or resid 491 through 492 or (resid 493 through 494 and (name N or nam \ e CA or name C or name O or name CB )) or resid 495 through 510 or resid 600 thr \ ough 601)) selection = (chain 'B' and (resid 26 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 68 or (resid 69 and (name N or nam \ e CA or name C or name O or name CB )) or resid 70 through 171 or (resid 172 and \ (name N or name CA or name C or name O or name CB )) or resid 173 through 182 o \ r (resid 183 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 84 through 293 or (resid 294 through 295 and (name N or name CA or name C or nam \ e O or name CB )) or resid 296 through 392 or (resid 393 and (name N or name CA \ or name C or name O or name CB )) or resid 394 through 407 or (resid 408 and (na \ me N or name CA or name C or name O or name CB )) or resid 409 through 423 or (r \ esid 424 and (name N or name CA or name C or name O or name CB )) or resid 425 t \ hrough 510 or resid 600 through 601)) selection = (chain 'C' and (resid 26 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 37 or (resid 38 and (name N or nam \ e CA or name C or name O or name CB )) or resid 39 through 68 or (resid 69 and ( \ name N or name CA or name C or name O or name CB )) or resid 70 through 171 or ( \ resid 172 and (name N or name CA or name C or name O or name CB )) or resid 173 \ through 182 or (resid 183 and (name N or name CA or name C or name O or name CB \ )) or resid 184 through 194 or (resid 195 and (name N or name CA or name C or na \ me O or name CB )) or resid 196 through 293 or (resid 294 through 295 and (name \ N or name CA or name C or name O or name CB )) or resid 296 through 356 or (resi \ d 357 and (name N or name CA or name C or name O or name CB )) or resid 358 thro \ ugh 392 or (resid 393 and (name N or name CA or name C or name O or name CB )) o \ r resid 394 through 406 or (resid 407 through 408 and (name N or name CA or name \ C or name O or name CB )) or resid 409 through 423 or (resid 424 and (name N or \ name CA or name C or name O or name CB )) or resid 425 through 458 or (resid 45 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 460 through \ 476 or (resid 477 and (name N or name CA or name C or name O or name CB )) or re \ sid 478 through 479 or (resid 480 and (name N or name CA or name C or name O or \ name CB )) or resid 481 through 486 or (resid 487 and (name N or name CA or name \ C or name O or name CB )) or resid 488 through 489 or (resid 490 and (name N or \ name CA or name C or name O or name CB )) or resid 491 through 510 or resid 600 \ through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 39 or (resid 40 and (name N or name CA or name C \ or name O or name CB )) or resid 41 through 42 or (resid 43 and (name N or name \ CA or name C or name O or name CB )) or resid 44 through 104 or (resid 105 and \ (name N or name CA or name C or name O or name CB )) or resid 106 through 111 or \ (resid 112 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 3 through 188 or (resid 189 and (name N or name CA or name C or name O or name C \ B )) or resid 190 through 199 or (resid 200 and (name N or name CA or name C or \ name O or name CB )) or resid 201 through 209 or (resid 210 and (name N or name \ CA or name C or name O or name CB )) or resid 211 through 245 or (resid 246 and \ (name N or name CA or name C or name O or name CB )) or resid 247 through 372 or \ (resid 373 and (name N or name CA or name C or name O or name CB )) or resid 37 \ 4 through 375 or (resid 376 and (name N or name CA or name C or name O or name C \ B )) or resid 377 through 398 or (resid 399 and (name N or name CA or name C or \ name O or name CB )) or resid 400 through 470 or (resid 471 through 472 and (nam \ e N or name CA or name C or name O or name CB )) or resid 473 through 476)) selection = (chain 'E' and (resid 8 through 25 or (resid 26 through 27 and (name N or name C \ A or name C or name O or name CB )) or resid 28 through 175 or (resid 176 throug \ h 177 and (name N or name CA or name C or name O or name CB )) or resid 178 thro \ ugh 188 or (resid 189 and (name N or name CA or name C or name O or name CB )) o \ r resid 190 through 358 or (resid 359 through 361 and (name N or name CA or name \ C or name O or name CB )) or resid 362 through 384 or (resid 385 through 386 an \ d (name N or name CA or name C or name O or name CB )) or resid 387 through 389 \ or (resid 390 through 391 and (name N or name CA or name C or name O or name CB \ )) or resid 392 or (resid 393 through 396 and (name N or name CA or name C or na \ me O or name CB )) or resid 397 through 398 or (resid 399 and (name N or name CA \ or name C or name O or name CB )) or resid 400 or (resid 401 and (name N or nam \ e CA or name C or name O or name CB )) or resid 402 through 434 or (resid 435 an \ d (name N or name CA or name C or name O or name CB )) or resid 436 through 463 \ or (resid 464 and (name N or name CA or name C or name O or name CB )) or resid \ 465 through 471 or (resid 472 and (name N or name CA or name C or name O or name \ CB )) or resid 473 through 476)) selection = (chain 'F' and (resid 8 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 111 or (resid 112 and (name N or na \ me CA or name C or name O or name CB )) or resid 113 through 175 or (resid 176 t \ hrough 177 and (name N or name CA or name C or name O or name CB )) or resid 178 \ through 199 or (resid 200 and (name N or name CA or name C or name O or name CB \ )) or resid 201 through 358 or (resid 359 through 361 and (name N or name CA or \ name C or name O or name CB )) or resid 362 through 375 or (resid 376 and (name \ N or name CA or name C or name O or name CB )) or resid 377 through 384 or (res \ id 385 through 386 and (name N or name CA or name C or name O or name CB )) or r \ esid 387 through 389 or (resid 390 through 391 and (name N or name CA or name C \ or name O or name CB )) or resid 392 or (resid 393 through 396 and (name N or na \ me CA or name C or name O or name CB )) or resid 397 through 400 or (resid 401 a \ nd (name N or name CA or name C or name O or name CB )) or resid 402 through 434 \ or (resid 435 and (name N or name CA or name C or name O or name CB )) or resid \ 436 through 463 or (resid 464 and (name N or name CA or name C or name O or nam \ e CB )) or resid 465 through 470 or (resid 471 through 472 and (name N or name C \ A or name C or name O or name CB )) or resid 473 through 475 or (resid 476 and ( \ name N or name CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 0.020 Extract box with map and model: 8.190 Check model and map are aligned: 0.390 Set scattering table: 0.210 Process input model: 62.850 Find NCS groups from input model: 1.710 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 : 0.004 0.222 22748 Z= 0.270 Angle : 0.821 30.880 30880 Z= 0.445 Chirality : 0.050 0.309 3654 Planarity : 0.011 0.188 3978 Dihedral : 15.674 95.738 8474 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.60 % Favored : 98.37 % Rotamer: Outliers : 0.74 % Allowed : 9.07 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.08 (0.15), residues: 2946 helix: -0.20 (0.13), residues: 1240 sheet: 0.22 (0.23), residues: 496 loop : 0.25 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.016 TRP C 191 HIS 0.010 0.002 HIS A 265 PHE 0.027 0.005 PHE B 395 TYR 0.028 0.005 TYR E 368 ARG 0.037 0.004 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 247 time to evaluate : 2.744 Fit side-chains revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7996 (tt0) cc_final: 0.7784 (tt0) REVERT: B 448 TYR cc_start: 0.8405 (t80) cc_final: 0.7969 (t80) REVERT: C 64 MET cc_start: 0.8816 (ttt) cc_final: 0.8465 (ttm) REVERT: C 257 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7828 (mt-10) REVERT: D 172 ASN cc_start: 0.8595 (t0) cc_final: 0.8189 (t0) REVERT: E 386 ASP cc_start: 0.8286 (p0) cc_final: 0.8040 (p0) REVERT: F 212 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7576 (tp30) outliers start: 17 outliers final: 11 residues processed: 259 average time/residue: 1.3196 time to fit residues: 390.9893 Evaluate side-chains 201 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 190 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain G residue 32 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 246 optimal weight: 4.9990 chunk 221 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN B 26 ASN D 208 ASN E 455 HIS F 195 ASN F 223 ASN F 385 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 22748 Z= 0.435 Angle : 0.647 7.687 30880 Z= 0.333 Chirality : 0.049 0.208 3654 Planarity : 0.005 0.072 3978 Dihedral : 10.330 100.529 3413 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.46 % Favored : 98.51 % Rotamer: Outliers : 2.17 % Allowed : 10.02 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.80 (0.15), residues: 2946 helix: 0.95 (0.15), residues: 1215 sheet: 0.33 (0.23), residues: 512 loop : 0.38 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 191 HIS 0.006 0.001 HIS A 454 PHE 0.033 0.002 PHE B 405 TYR 0.022 0.002 TYR F 311 ARG 0.007 0.001 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 216 time to evaluate : 2.648 Fit side-chains revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8327 (mtm-85) REVERT: C 257 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7708 (mt-10) REVERT: D 263 GLN cc_start: 0.7833 (tt0) cc_final: 0.7592 (tt0) REVERT: E 382 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8775 (ttmm) REVERT: F 212 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7611 (tp30) REVERT: F 250 ASP cc_start: 0.7506 (m-30) cc_final: 0.7149 (m-30) REVERT: F 385 GLN cc_start: 0.7367 (mm-40) cc_final: 0.7162 (mm-40) outliers start: 50 outliers final: 19 residues processed: 245 average time/residue: 1.4065 time to fit residues: 392.4640 Evaluate side-chains 220 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 199 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 382 LYS Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 270 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 147 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 265 optimal weight: 4.9990 chunk 286 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 263 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 213 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN B 478 HIS C 428 GLN D 208 ASN E 375 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22748 Z= 0.253 Angle : 0.539 7.700 30880 Z= 0.276 Chirality : 0.044 0.218 3654 Planarity : 0.004 0.053 3978 Dihedral : 9.917 100.368 3401 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.17 % Allowed : 11.37 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.01 (0.16), residues: 2946 helix: 1.25 (0.15), residues: 1219 sheet: 0.37 (0.23), residues: 512 loop : 0.37 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 191 HIS 0.004 0.001 HIS D 367 PHE 0.024 0.002 PHE B 405 TYR 0.017 0.001 TYR D 458 ARG 0.008 0.000 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 217 time to evaluate : 2.484 Fit side-chains revert: symmetry clash REVERT: A 173 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8442 (ptt90) REVERT: A 418 GLN cc_start: 0.7821 (tp40) cc_final: 0.7480 (tp40) REVERT: A 467 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7200 (tt0) REVERT: B 199 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7838 (mtpm) REVERT: B 451 VAL cc_start: 0.8557 (t) cc_final: 0.8124 (m) REVERT: C 257 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7634 (mt-10) REVERT: C 500 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7449 (tttm) REVERT: D 263 GLN cc_start: 0.7762 (tt0) cc_final: 0.7536 (tt0) REVERT: D 345 TYR cc_start: 0.6487 (OUTLIER) cc_final: 0.6188 (m-80) REVERT: E 38 GLU cc_start: 0.7881 (tt0) cc_final: 0.7680 (tt0) REVERT: E 74 GLU cc_start: 0.8867 (tt0) cc_final: 0.8581 (tt0) REVERT: F 385 GLN cc_start: 0.7350 (mm-40) cc_final: 0.7145 (mm-40) REVERT: F 435 LYS cc_start: 0.7828 (mtpm) cc_final: 0.7496 (mmtt) REVERT: G 265 ASN cc_start: 0.8736 (m-40) cc_final: 0.8330 (m-40) outliers start: 50 outliers final: 18 residues processed: 245 average time/residue: 1.4554 time to fit residues: 403.8388 Evaluate side-chains 218 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 196 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain D residue 345 TYR Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 402 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 262 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 126 optimal weight: 0.0020 chunk 178 optimal weight: 0.4980 chunk 266 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 252 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN C 210 GLN C 428 GLN D 208 ASN E 375 GLN F 53 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22748 Z= 0.181 Angle : 0.488 8.392 30880 Z= 0.250 Chirality : 0.043 0.207 3654 Planarity : 0.004 0.050 3978 Dihedral : 9.221 99.808 3400 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.65 % Allowed : 13.10 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.19 (0.16), residues: 2946 helix: 1.42 (0.15), residues: 1233 sheet: 0.49 (0.23), residues: 512 loop : 0.42 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 191 HIS 0.003 0.001 HIS D 367 PHE 0.013 0.001 PHE E 25 TYR 0.016 0.001 TYR D 458 ARG 0.009 0.000 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 218 time to evaluate : 2.608 Fit side-chains revert: symmetry clash REVERT: A 95 ASN cc_start: 0.8317 (m-40) cc_final: 0.8035 (m-40) REVERT: A 133 VAL cc_start: 0.8925 (p) cc_final: 0.8689 (m) REVERT: A 173 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8428 (ptt90) REVERT: A 303 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8059 (tp) REVERT: A 357 GLU cc_start: 0.8024 (tt0) cc_final: 0.7793 (tm-30) REVERT: A 418 GLN cc_start: 0.7902 (tp40) cc_final: 0.7475 (tp40) REVERT: A 467 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7182 (tt0) REVERT: B 66 LEU cc_start: 0.9085 (tp) cc_final: 0.8868 (tt) REVERT: B 69 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7918 (mt-10) REVERT: B 199 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7848 (mtpm) REVERT: B 442 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7961 (mt-10) REVERT: B 451 VAL cc_start: 0.8582 (t) cc_final: 0.8160 (m) REVERT: C 257 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7643 (mt-10) REVERT: C 500 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7441 (tttm) REVERT: D 9 ILE cc_start: 0.8415 (mp) cc_final: 0.7952 (tp) REVERT: D 345 TYR cc_start: 0.6469 (OUTLIER) cc_final: 0.6016 (m-80) REVERT: E 74 GLU cc_start: 0.8814 (tt0) cc_final: 0.8559 (mt-10) REVERT: E 77 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8027 (mp) REVERT: F 281 TYR cc_start: 0.9228 (m-80) cc_final: 0.8881 (m-80) REVERT: F 293 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8885 (mm110) REVERT: F 435 LYS cc_start: 0.7831 (mtpm) cc_final: 0.7553 (mmtt) outliers start: 38 outliers final: 15 residues processed: 242 average time/residue: 1.4370 time to fit residues: 394.8330 Evaluate side-chains 217 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 195 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 345 TYR Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 293 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 235 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 144 optimal weight: 0.0670 chunk 253 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN C 276 GLN C 428 GLN D 263 GLN E 293 GLN E 375 GLN F 223 ASN G 265 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 22748 Z= 0.356 Angle : 0.560 7.609 30880 Z= 0.285 Chirality : 0.046 0.221 3654 Planarity : 0.004 0.050 3978 Dihedral : 9.398 102.000 3400 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.73 % Allowed : 12.71 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.92 (0.16), residues: 2946 helix: 1.30 (0.15), residues: 1213 sheet: 0.30 (0.23), residues: 529 loop : 0.19 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 191 HIS 0.005 0.001 HIS D 367 PHE 0.021 0.002 PHE B 405 TYR 0.016 0.001 TYR F 147 ARG 0.008 0.001 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 197 time to evaluate : 2.463 Fit side-chains revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6635 (tt0) REVERT: A 95 ASN cc_start: 0.8284 (m-40) cc_final: 0.7994 (m-40) REVERT: A 173 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8403 (mtm-85) REVERT: A 303 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8168 (tp) REVERT: A 357 GLU cc_start: 0.8051 (tt0) cc_final: 0.7839 (tm-30) REVERT: A 373 VAL cc_start: 0.8460 (p) cc_final: 0.8124 (m) REVERT: A 418 GLN cc_start: 0.8057 (tp40) cc_final: 0.7710 (tp40) REVERT: A 467 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7190 (tt0) REVERT: B 69 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8048 (mt-10) REVERT: B 199 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7947 (mtpm) REVERT: B 467 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7486 (mt-10) REVERT: C 257 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7660 (mt-10) REVERT: D 345 TYR cc_start: 0.6507 (OUTLIER) cc_final: 0.6067 (m-80) REVERT: E 74 GLU cc_start: 0.8826 (tt0) cc_final: 0.8604 (mt-10) REVERT: E 385 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7059 (mt0) REVERT: F 293 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8884 (mm110) REVERT: F 354 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8209 (mttm) REVERT: F 385 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.6314 (mp10) REVERT: F 435 LYS cc_start: 0.7891 (mtpm) cc_final: 0.7569 (mmtt) REVERT: G 257 ARG cc_start: 0.8248 (mtm-85) cc_final: 0.8028 (mtm-85) outliers start: 63 outliers final: 26 residues processed: 242 average time/residue: 1.4600 time to fit residues: 399.6881 Evaluate side-chains 227 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 191 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 345 TYR Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 385 GLN Chi-restraints excluded: chain G residue 270 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 94 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 282 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN B 26 ASN C 428 GLN D 208 ASN D 249 GLN D 263 GLN E 375 GLN G 265 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 22748 Z= 0.416 Angle : 0.582 7.980 30880 Z= 0.297 Chirality : 0.047 0.221 3654 Planarity : 0.004 0.050 3978 Dihedral : 9.543 102.497 3400 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.04 % Allowed : 12.84 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.66 (0.16), residues: 2946 helix: 1.09 (0.15), residues: 1230 sheet: 0.13 (0.23), residues: 535 loop : 0.05 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 191 HIS 0.005 0.001 HIS D 367 PHE 0.017 0.002 PHE C 506 TYR 0.020 0.002 TYR F 147 ARG 0.008 0.000 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 202 time to evaluate : 3.175 Fit side-chains revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6606 (tt0) REVERT: A 95 ASN cc_start: 0.8289 (m-40) cc_final: 0.7961 (m-40) REVERT: A 173 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8405 (mtm-85) REVERT: A 303 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8215 (tp) REVERT: A 357 GLU cc_start: 0.8082 (tt0) cc_final: 0.7858 (tm-30) REVERT: A 373 VAL cc_start: 0.8494 (p) cc_final: 0.8147 (m) REVERT: A 418 GLN cc_start: 0.8099 (tp40) cc_final: 0.7758 (tp40) REVERT: A 467 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7192 (tt0) REVERT: B 199 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7977 (mtpm) REVERT: B 451 VAL cc_start: 0.8612 (t) cc_final: 0.8167 (m) REVERT: C 257 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7720 (mt-10) REVERT: D 68 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: D 345 TYR cc_start: 0.6559 (OUTLIER) cc_final: 0.6065 (m-80) REVERT: E 178 HIS cc_start: 0.5837 (OUTLIER) cc_final: 0.5606 (t-90) REVERT: F 354 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8239 (mttm) REVERT: F 385 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.6275 (mp10) REVERT: F 435 LYS cc_start: 0.7891 (mtpm) cc_final: 0.7569 (mmtt) outliers start: 70 outliers final: 33 residues processed: 254 average time/residue: 1.4629 time to fit residues: 421.7487 Evaluate side-chains 232 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 190 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 345 TYR Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 385 GLN Chi-restraints excluded: chain G residue 270 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 272 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 206 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 237 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 281 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN D 208 ASN D 263 GLN E 375 GLN G 265 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22748 Z= 0.209 Angle : 0.502 10.910 30880 Z= 0.256 Chirality : 0.043 0.197 3654 Planarity : 0.004 0.051 3978 Dihedral : 9.195 102.569 3400 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.21 % Allowed : 14.14 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.90 (0.16), residues: 2946 helix: 1.29 (0.15), residues: 1239 sheet: 0.30 (0.23), residues: 529 loop : 0.15 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 258 HIS 0.003 0.001 HIS D 367 PHE 0.023 0.001 PHE B 405 TYR 0.016 0.001 TYR D 458 ARG 0.008 0.000 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 201 time to evaluate : 2.747 Fit side-chains revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6635 (tt0) REVERT: A 95 ASN cc_start: 0.8290 (m-40) cc_final: 0.7960 (m-40) REVERT: A 173 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8411 (ptt90) REVERT: A 303 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8099 (tp) REVERT: A 357 GLU cc_start: 0.8073 (tt0) cc_final: 0.7842 (tm-30) REVERT: A 373 VAL cc_start: 0.8503 (p) cc_final: 0.8150 (m) REVERT: A 418 GLN cc_start: 0.8140 (tp40) cc_final: 0.7812 (tp40) REVERT: A 467 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7181 (tt0) REVERT: B 69 GLU cc_start: 0.8238 (mt-10) cc_final: 0.8036 (mt-10) REVERT: B 199 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7965 (mtpm) REVERT: B 451 VAL cc_start: 0.8603 (t) cc_final: 0.8207 (m) REVERT: C 257 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7704 (mt-10) REVERT: D 68 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: D 345 TYR cc_start: 0.6381 (OUTLIER) cc_final: 0.5970 (m-80) REVERT: E 77 LEU cc_start: 0.8450 (tp) cc_final: 0.8185 (mp) REVERT: E 412 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7943 (ttm170) REVERT: F 281 TYR cc_start: 0.9201 (m-80) cc_final: 0.8982 (m-80) REVERT: F 354 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8229 (mttp) REVERT: F 385 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6201 (mp10) REVERT: F 435 LYS cc_start: 0.7867 (mtpm) cc_final: 0.7546 (mmtt) outliers start: 51 outliers final: 24 residues processed: 242 average time/residue: 1.4775 time to fit residues: 404.1213 Evaluate side-chains 222 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 189 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 345 TYR Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 412 ARG Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 354 LYS Chi-restraints excluded: chain F residue 385 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 174 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 178 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN D 263 GLN E 375 GLN E 379 GLN F 293 GLN G 265 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22748 Z= 0.272 Angle : 0.522 10.504 30880 Z= 0.266 Chirality : 0.044 0.216 3654 Planarity : 0.004 0.054 3978 Dihedral : 9.123 102.664 3400 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.08 % Allowed : 14.53 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.89 (0.16), residues: 2946 helix: 1.31 (0.15), residues: 1233 sheet: 0.28 (0.23), residues: 529 loop : 0.13 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 258 HIS 0.005 0.001 HIS D 455 PHE 0.015 0.001 PHE E 25 TYR 0.015 0.001 TYR F 147 ARG 0.009 0.000 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 195 time to evaluate : 2.603 Fit side-chains revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6689 (tt0) REVERT: A 95 ASN cc_start: 0.8276 (m-40) cc_final: 0.7949 (m-40) REVERT: A 173 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8430 (mtm-85) REVERT: A 303 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8124 (tp) REVERT: A 357 GLU cc_start: 0.8097 (tt0) cc_final: 0.7859 (tm-30) REVERT: A 373 VAL cc_start: 0.8520 (p) cc_final: 0.8179 (m) REVERT: A 418 GLN cc_start: 0.8170 (tp40) cc_final: 0.7842 (tp40) REVERT: A 467 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7183 (tt0) REVERT: B 199 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7983 (mtpm) REVERT: B 451 VAL cc_start: 0.8614 (t) cc_final: 0.8206 (m) REVERT: B 484 GLU cc_start: 0.7481 (tt0) cc_final: 0.7140 (tt0) REVERT: C 64 MET cc_start: 0.8902 (ttt) cc_final: 0.8698 (ttt) REVERT: C 257 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7704 (mt-10) REVERT: C 417 LYS cc_start: 0.7879 (mttp) cc_final: 0.7358 (mmmm) REVERT: D 68 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: D 345 TYR cc_start: 0.6381 (OUTLIER) cc_final: 0.5896 (m-80) REVERT: E 77 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8199 (mp) REVERT: E 412 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7970 (ttm170) REVERT: F 354 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8246 (mttp) REVERT: F 435 LYS cc_start: 0.7879 (mtpm) cc_final: 0.7553 (mmtt) outliers start: 48 outliers final: 24 residues processed: 232 average time/residue: 1.4745 time to fit residues: 388.4633 Evaluate side-chains 222 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 189 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 345 TYR Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain E residue 412 ARG Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 354 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 256 optimal weight: 0.7980 chunk 269 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 236 optimal weight: 4.9990 chunk 248 optimal weight: 0.5980 chunk 261 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN D 208 ASN D 263 GLN E 375 GLN F 293 GLN F 308 GLN G 265 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22748 Z= 0.202 Angle : 0.493 10.245 30880 Z= 0.251 Chirality : 0.043 0.206 3654 Planarity : 0.004 0.055 3978 Dihedral : 8.896 102.263 3400 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.91 % Allowed : 14.84 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.02 (0.16), residues: 2946 helix: 1.41 (0.15), residues: 1239 sheet: 0.32 (0.23), residues: 525 loop : 0.21 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 258 HIS 0.004 0.001 HIS E 178 PHE 0.024 0.001 PHE B 405 TYR 0.017 0.001 TYR D 458 ARG 0.009 0.000 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 206 time to evaluate : 2.545 Fit side-chains revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6745 (tt0) REVERT: A 95 ASN cc_start: 0.8267 (m-40) cc_final: 0.7942 (m-40) REVERT: A 133 VAL cc_start: 0.8934 (p) cc_final: 0.8670 (m) REVERT: A 173 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8405 (ptt90) REVERT: A 303 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8115 (tp) REVERT: A 357 GLU cc_start: 0.8087 (tt0) cc_final: 0.7848 (tm-30) REVERT: A 373 VAL cc_start: 0.8535 (p) cc_final: 0.8190 (m) REVERT: A 418 GLN cc_start: 0.8162 (tp40) cc_final: 0.7827 (tp40) REVERT: A 467 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7183 (tt0) REVERT: B 199 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7975 (mtpm) REVERT: B 451 VAL cc_start: 0.8605 (t) cc_final: 0.8220 (m) REVERT: B 484 GLU cc_start: 0.7346 (tt0) cc_final: 0.7019 (tt0) REVERT: C 64 MET cc_start: 0.8950 (ttt) cc_final: 0.8727 (ttp) REVERT: C 257 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7653 (mt-10) REVERT: C 417 LYS cc_start: 0.7904 (mttp) cc_final: 0.7380 (mmmm) REVERT: D 345 TYR cc_start: 0.6300 (OUTLIER) cc_final: 0.5900 (m-80) REVERT: D 454 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7454 (pt0) REVERT: E 77 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8242 (mp) REVERT: E 178 HIS cc_start: 0.5947 (OUTLIER) cc_final: 0.5595 (t-90) REVERT: E 412 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7878 (ttm170) REVERT: F 281 TYR cc_start: 0.9184 (m-80) cc_final: 0.8927 (m-80) REVERT: F 354 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8272 (mttp) REVERT: F 435 LYS cc_start: 0.7851 (mtpm) cc_final: 0.7530 (mmtt) outliers start: 44 outliers final: 22 residues processed: 241 average time/residue: 1.4339 time to fit residues: 391.5989 Evaluate side-chains 227 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 195 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain D residue 345 TYR Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 412 ARG Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 354 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 172 optimal weight: 4.9990 chunk 277 optimal weight: 0.0770 chunk 169 optimal weight: 4.9990 chunk 131 optimal weight: 0.0670 chunk 192 optimal weight: 3.9990 chunk 290 optimal weight: 3.9990 chunk 267 optimal weight: 0.3980 chunk 231 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 overall best weight: 1.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 428 GLN D 263 GLN E 375 GLN F 223 ASN F 293 GLN G 265 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22748 Z= 0.313 Angle : 0.544 10.758 30880 Z= 0.276 Chirality : 0.045 0.208 3654 Planarity : 0.004 0.055 3978 Dihedral : 9.035 103.051 3400 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.87 % Allowed : 15.23 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.88 (0.16), residues: 2946 helix: 1.31 (0.15), residues: 1233 sheet: 0.23 (0.23), residues: 535 loop : 0.11 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 258 HIS 0.005 0.001 HIS F 455 PHE 0.015 0.001 PHE E 25 TYR 0.020 0.001 TYR F 147 ARG 0.009 0.000 ARG D 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 195 time to evaluate : 2.652 Fit side-chains revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6670 (tt0) REVERT: A 95 ASN cc_start: 0.8255 (m-40) cc_final: 0.7927 (m-40) REVERT: A 173 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8431 (mtm-85) REVERT: A 303 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8118 (tp) REVERT: A 357 GLU cc_start: 0.8107 (tt0) cc_final: 0.7858 (tm-30) REVERT: A 373 VAL cc_start: 0.8525 (p) cc_final: 0.8187 (m) REVERT: A 418 GLN cc_start: 0.8176 (tp40) cc_final: 0.7839 (tp40) REVERT: A 467 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7191 (tt0) REVERT: B 199 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7987 (mtpm) REVERT: B 451 VAL cc_start: 0.8612 (t) cc_final: 0.8182 (m) REVERT: B 484 GLU cc_start: 0.7432 (tt0) cc_final: 0.7092 (tt0) REVERT: C 257 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7718 (mt-10) REVERT: C 417 LYS cc_start: 0.7918 (mttp) cc_final: 0.7390 (mmmm) REVERT: D 345 TYR cc_start: 0.6383 (OUTLIER) cc_final: 0.5935 (m-80) REVERT: D 454 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7554 (pt0) REVERT: E 77 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8251 (mp) REVERT: E 412 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8003 (ttm170) REVERT: F 281 TYR cc_start: 0.9201 (m-80) cc_final: 0.8977 (m-80) REVERT: F 354 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8263 (mttp) REVERT: F 435 LYS cc_start: 0.7882 (mtpm) cc_final: 0.7558 (mmtt) outliers start: 43 outliers final: 26 residues processed: 229 average time/residue: 1.5033 time to fit residues: 390.7123 Evaluate side-chains 226 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 191 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 345 TYR Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 412 ARG Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 354 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 184 optimal weight: 0.8980 chunk 246 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 232 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 238 optimal weight: 0.0980 chunk 29 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN D 168 GLN D 263 GLN E 375 GLN F 293 GLN G 265 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.108909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.090769 restraints weight = 30442.272| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.05 r_work: 0.2883 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22748 Z= 0.173 Angle : 0.492 11.610 30880 Z= 0.248 Chirality : 0.042 0.200 3654 Planarity : 0.004 0.055 3978 Dihedral : 8.724 101.970 3400 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.56 % Allowed : 15.62 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.11 (0.16), residues: 2946 helix: 1.48 (0.15), residues: 1234 sheet: 0.37 (0.23), residues: 525 loop : 0.25 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 258 HIS 0.003 0.001 HIS E 178 PHE 0.027 0.001 PHE B 405 TYR 0.012 0.001 TYR F 147 ARG 0.008 0.000 ARG D 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7087.13 seconds wall clock time: 127 minutes 16.65 seconds (7636.65 seconds total)