Starting phenix.real_space_refine on Sat Nov 18 09:19:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2k_28818/11_2023/8f2k_28818_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2k_28818/11_2023/8f2k_28818.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2k_28818/11_2023/8f2k_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_28818/11_2023/8f2k_28818_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2k_28818/11_2023/8f2k_28818_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2k_28818/11_2023/8f2k_28818.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2k_28818/11_2023/8f2k_28818.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2k_28818/11_2023/8f2k_28818_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2k_28818/11_2023/8f2k_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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 11.01, per 1000 atoms: 0.49 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: 9.36 Conformation dependent library (CDL) restraints added in 4.6 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: 5.04 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: 8.56 Time building geometry restraints manager: 10.10 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: 12658 19.15 - 38.30: 750 38.30 - 57.44: 199 57.44 - 76.59: 58 76.59 - 95.74: 20 Dihedral angle restraints: 13685 sinusoidal: 5290 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 13682 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: 1.610 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: 13.670 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 60.040 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.120 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:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.450 ------------------------------------------------------------------------------- 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 : 14.750 95.738 8319 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 *********************** 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 : 2.940 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 259 average time/residue: 1.3522 time to fit residues: 402.1901 Evaluate side-chains 198 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 187 time to evaluate : 2.865 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 3.6352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 246 optimal weight: 3.9990 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: 0.6980 chunk 228 optimal weight: 0.4980 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: 1.8386 ------------------------------------------------------------------------------- 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: 0.8214 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 22748 Z= 0.347 Angle : 0.607 8.290 30880 Z= 0.311 Chirality : 0.047 0.193 3654 Planarity : 0.004 0.077 3978 Dihedral : 7.487 99.169 3243 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.32 % Favored : 98.64 % Rotamer: Outliers : 2.13 % Allowed : 10.15 % Favored : 87.72 % 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: 0.95 (0.16), residues: 2946 helix: 1.11 (0.15), residues: 1216 sheet: 0.42 (0.23), residues: 482 loop : 0.42 (0.18), residues: 1248 *********************** 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 265 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 216 time to evaluate : 2.614 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 20 residues processed: 246 average time/residue: 1.4304 time to fit residues: 403.3914 Evaluate side-chains 212 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 192 time to evaluate : 2.613 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 8 average time/residue: 0.6641 time to fit residues: 10.4034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 147 optimal weight: 0.0170 chunk 82 optimal weight: 0.9990 chunk 220 optimal weight: 0.6980 chunk 180 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 265 optimal weight: 0.8980 chunk 286 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 chunk 263 optimal weight: 0.0270 chunk 90 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 304 HIS B 26 ASN C 428 GLN D 208 ASN D 263 GLN E 375 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 22748 Z= 0.150 Angle : 0.502 8.005 30880 Z= 0.255 Chirality : 0.042 0.192 3654 Planarity : 0.003 0.054 3978 Dihedral : 7.060 97.408 3243 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.74 % Allowed : 11.97 % Favored : 86.29 % 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: 1.29 (0.16), residues: 2946 helix: 1.45 (0.15), residues: 1231 sheet: 0.57 (0.24), residues: 482 loop : 0.54 (0.18), residues: 1233 *********************** 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 264 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 224 time to evaluate : 2.578 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 14 residues processed: 249 average time/residue: 1.4365 time to fit residues: 408.6774 Evaluate side-chains 202 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 188 time to evaluate : 2.722 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 5 average time/residue: 0.6178 time to fit residues: 7.6486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 262 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 126 optimal weight: 0.0270 chunk 178 optimal weight: 0.8980 chunk 266 optimal weight: 3.9990 chunk 282 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 252 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN B 26 ASN C 210 GLN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN D 263 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: 0.8164 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22748 Z= 0.145 Angle : 0.474 8.730 30880 Z= 0.240 Chirality : 0.042 0.208 3654 Planarity : 0.003 0.051 3978 Dihedral : 6.730 95.903 3243 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.82 % Allowed : 12.58 % Favored : 85.60 % 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: 1.40 (0.16), residues: 2946 helix: 1.59 (0.15), residues: 1234 sheet: 0.66 (0.24), residues: 488 loop : 0.50 (0.18), residues: 1224 *********************** 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 251 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 209 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 19 residues processed: 241 average time/residue: 1.5270 time to fit residues: 417.7590 Evaluate side-chains 201 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 182 time to evaluate : 2.656 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 13 residues processed: 6 average time/residue: 0.7567 time to fit residues: 9.0966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 235 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 240 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 144 optimal weight: 0.6980 chunk 253 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN C 428 GLN D 263 GLN E 293 GLN F 53 HIS F 223 ASN G 265 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1864 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= 0.307 Angle : 0.532 7.988 30880 Z= 0.269 Chirality : 0.045 0.215 3654 Planarity : 0.004 0.052 3978 Dihedral : 6.980 99.470 3243 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.17 % Allowed : 12.97 % Favored : 84.86 % 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: 1.17 (0.16), residues: 2946 helix: 1.47 (0.15), residues: 1218 sheet: 0.46 (0.23), residues: 534 loop : 0.37 (0.19), residues: 1194 *********************** 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 240 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 190 time to evaluate : 2.713 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 21 residues processed: 226 average time/residue: 1.4745 time to fit residues: 380.3537 Evaluate side-chains 200 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 179 time to evaluate : 2.451 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 15 residues processed: 6 average time/residue: 0.2758 time to fit residues: 6.0844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 69 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 234 optimal weight: 0.1980 chunk 130 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 B 478 HIS C 276 GLN C 428 GLN D 249 GLN D 263 GLN F 223 ASN G 265 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22748 Z= 0.357 Angle : 0.557 8.126 30880 Z= 0.282 Chirality : 0.046 0.210 3654 Planarity : 0.004 0.054 3978 Dihedral : 7.175 102.170 3243 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.60 % Allowed : 13.19 % Favored : 84.21 % 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: 1.25 (0.15), residues: 1222 sheet: 0.30 (0.23), residues: 529 loop : 0.17 (0.18), residues: 1195 *********************** 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 247 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 187 time to evaluate : 2.842 Fit side-chains revert: symmetry clash outliers start: 60 outliers final: 27 residues processed: 235 average time/residue: 1.4625 time to fit residues: 392.0712 Evaluate side-chains 206 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 179 time to evaluate : 2.769 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 20 residues processed: 7 average time/residue: 0.8126 time to fit residues: 10.5573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 272 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 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 ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN D 249 GLN D 263 GLN E 375 GLN F 293 GLN G 265 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22748 Z= 0.250 Angle : 0.512 7.931 30880 Z= 0.260 Chirality : 0.044 0.215 3654 Planarity : 0.004 0.054 3978 Dihedral : 7.074 102.432 3243 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.21 % Allowed : 14.36 % Favored : 83.43 % 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: 0.95 (0.16), residues: 2946 helix: 1.31 (0.15), residues: 1236 sheet: 0.30 (0.23), residues: 519 loop : 0.22 (0.18), residues: 1191 *********************** 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 239 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 188 time to evaluate : 2.664 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 29 residues processed: 227 average time/residue: 1.5489 time to fit residues: 401.3098 Evaluate side-chains 209 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 180 time to evaluate : 2.793 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 21 residues processed: 9 average time/residue: 0.4159 time to fit residues: 9.3409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0980 chunk 168 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 191 optimal weight: 0.3980 chunk 139 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 221 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 263 GLN E 375 GLN G 265 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22748 Z= 0.148 Angle : 0.466 9.054 30880 Z= 0.237 Chirality : 0.042 0.196 3654 Planarity : 0.003 0.055 3978 Dihedral : 6.764 100.684 3243 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.56 % Allowed : 15.14 % Favored : 83.30 % 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: 1.52 (0.15), residues: 1236 sheet: 0.45 (0.23), residues: 512 loop : 0.32 (0.18), residues: 1198 *********************** 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 240 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 204 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 21 residues processed: 236 average time/residue: 1.4565 time to fit residues: 392.4655 Evaluate side-chains 207 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 186 time to evaluate : 2.931 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 1.1655 time to fit residues: 6.3469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 256 optimal weight: 4.9990 chunk 269 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 236 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 428 GLN D 249 GLN D 263 GLN E 375 GLN F 223 ASN G 265 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 22748 Z= 0.505 Angle : 0.623 8.078 30880 Z= 0.315 Chirality : 0.049 0.298 3654 Planarity : 0.005 0.061 3978 Dihedral : 7.246 103.396 3243 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.78 % Allowed : 15.27 % Favored : 82.95 % 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: 1.10 (0.15), residues: 1232 sheet: 0.06 (0.23), residues: 536 loop : 0.08 (0.18), residues: 1178 *********************** 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 224 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 183 time to evaluate : 2.800 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 24 residues processed: 216 average time/residue: 1.4544 time to fit residues: 359.9905 Evaluate side-chains 204 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 180 time to evaluate : 2.710 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 19 residues processed: 5 average time/residue: 0.3527 time to fit residues: 6.3535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 172 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 192 optimal weight: 3.9990 chunk 290 optimal weight: 2.9990 chunk 267 optimal weight: 0.7980 chunk 231 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 178 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN D 263 GLN E 375 GLN E 455 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2274 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= 0.192 Angle : 0.507 10.457 30880 Z= 0.255 Chirality : 0.043 0.303 3654 Planarity : 0.004 0.116 3978 Dihedral : 7.065 103.377 3243 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.21 % Allowed : 16.01 % Favored : 82.78 % 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: 0.91 (0.16), residues: 2946 helix: 1.32 (0.15), residues: 1236 sheet: 0.27 (0.23), residues: 514 loop : 0.15 (0.18), residues: 1196 ********************** 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 212 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 184 time to evaluate : 2.878 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 19 residues processed: 210 average time/residue: 1.5287 time to fit residues: 365.7631 Evaluate side-chains 198 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 179 time to evaluate : 2.674 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 1.0063 time to fit residues: 6.2270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 184 optimal weight: 0.9990 chunk 246 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 97 optimal weight: 0.3980 chunk 238 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 42 optimal weight: 0.0370 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN D 263 GLN E 375 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.091127 restraints weight = 30429.025| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.05 r_work: 0.2891 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22748 Z= 0.165 Angle : 0.487 9.864 30880 Z= 0.245 Chirality : 0.042 0.291 3654 Planarity : 0.004 0.057 3978 Dihedral : 6.825 101.773 3243 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.30 % Allowed : 16.10 % Favored : 82.60 % 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: 1.09 (0.16), residues: 2946 helix: 1.48 (0.15), residues: 1236 sheet: 0.31 (0.23), residues: 520 loop : 0.27 (0.18), residues: 1190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6968.47 seconds wall clock time: 125 minutes 28.96 seconds (7528.96 seconds total)