Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 17:07:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlp_22376/04_2023/7jlp_22376_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlp_22376/04_2023/7jlp_22376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlp_22376/04_2023/7jlp_22376.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlp_22376/04_2023/7jlp_22376.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlp_22376/04_2023/7jlp_22376_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlp_22376/04_2023/7jlp_22376_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 69 5.16 5 C 8643 2.51 5 N 2034 2.21 5 O 2133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 41": "OE1" <-> "OE2" Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 506": "NH1" <-> "NH2" Residue "A PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 527": "NH1" <-> "NH2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B ARG 322": "NH1" <-> "NH2" Residue "B TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 341": "NH1" <-> "NH2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 506": "NH1" <-> "NH2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 527": "NH1" <-> "NH2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 233": "NH1" <-> "NH2" Residue "C PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C ARG 322": "NH1" <-> "NH2" Residue "C TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 341": "NH1" <-> "NH2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 435": "OE1" <-> "OE2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 506": "NH1" <-> "NH2" Residue "C PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 527": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 12891 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3988 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 18, 'TRANS': 466} Chain breaks: 1 Chain: "B" Number of atoms: 3988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3988 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 18, 'TRANS': 466} Chain breaks: 1 Chain: "C" Number of atoms: 3988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3988 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 18, 'TRANS': 466} Chain breaks: 1 Chain: "A" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Unusual residues: {'POV': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 564 Unresolved non-hydrogen dihedrals: 353 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'POV:plan-3': 9, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Unusual residues: {'POV': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 564 Unresolved non-hydrogen dihedrals: 353 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'POV:plan-3': 9, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 84 Chain: "C" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Unusual residues: {'POV': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 564 Unresolved non-hydrogen dihedrals: 353 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'POV:plan-3': 9, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 84 Time building chain proxies: 7.08, per 1000 atoms: 0.55 Number of scatterers: 12891 At special positions: 0 Unit cell: (128.142, 123.606, 90.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 69 16.00 P 12 15.00 O 2133 8.00 N 2034 7.00 C 8643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 122 " distance=2.03 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: 5.49 Conformation dependent library (CDL) restraints added in 1.8 seconds 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2772 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 75 helices and 9 sheets defined 63.5% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.502A pdb=" N HIS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 85 Processing helix chain 'A' and resid 112 through 115 No H-bonds generated for 'chain 'A' and resid 112 through 115' Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 133 through 165 removed outlier: 3.784A pdb=" N ILE A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU A 159 " --> pdb=" O CYS A 155 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 160 " --> pdb=" O CYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 180 through 189 Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 214 through 224 removed outlier: 3.999A pdb=" N TYR A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 255 Processing helix chain 'A' and resid 271 through 274 Processing helix chain 'A' and resid 276 through 316 removed outlier: 3.711A pdb=" N ARG A 279 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU A 280 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 281 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS A 301 " --> pdb=" O PHE A 298 " (cutoff:3.500A) Proline residue: A 302 - end of helix removed outlier: 3.546A pdb=" N TYR A 316 " --> pdb=" O PHE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 322 No H-bonds generated for 'chain 'A' and resid 319 through 322' Processing helix chain 'A' and resid 324 through 327 removed outlier: 3.618A pdb=" N LEU A 327 " --> pdb=" O PRO A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 327' Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.678A pdb=" N CYS A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 removed outlier: 3.739A pdb=" N ARG A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 367 Processing helix chain 'A' and resid 371 through 397 removed outlier: 3.694A pdb=" N VAL A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 405 through 423 removed outlier: 4.396A pdb=" N LEU A 408 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR A 409 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 422 " --> pdb=" O THR A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 445 removed outlier: 3.683A pdb=" N HIS A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 465 Processing helix chain 'A' and resid 472 through 480 Processing helix chain 'A' and resid 482 through 492 Proline residue: A 487 - end of helix Processing helix chain 'A' and resid 495 through 507 removed outlier: 4.352A pdb=" N LEU A 499 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE A 501 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 505 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 55 removed outlier: 3.502A pdb=" N HIS B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 85 Processing helix chain 'B' and resid 112 through 115 No H-bonds generated for 'chain 'B' and resid 112 through 115' Processing helix chain 'B' and resid 119 through 128 Processing helix chain 'B' and resid 133 through 165 removed outlier: 3.784A pdb=" N ILE B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU B 159 " --> pdb=" O CYS B 155 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 160 " --> pdb=" O CYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 214 through 224 removed outlier: 3.999A pdb=" N TYR B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 255 Processing helix chain 'B' and resid 271 through 274 Processing helix chain 'B' and resid 276 through 316 removed outlier: 3.711A pdb=" N ARG B 279 " --> pdb=" O GLY B 276 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU B 280 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B 281 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS B 301 " --> pdb=" O PHE B 298 " (cutoff:3.500A) Proline residue: B 302 - end of helix removed outlier: 3.546A pdb=" N TYR B 316 " --> pdb=" O PHE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 322 No H-bonds generated for 'chain 'B' and resid 319 through 322' Processing helix chain 'B' and resid 324 through 327 removed outlier: 3.618A pdb=" N LEU B 327 " --> pdb=" O PRO B 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 324 through 327' Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.677A pdb=" N CYS B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 356 removed outlier: 3.739A pdb=" N ARG B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 367 Processing helix chain 'B' and resid 371 through 397 removed outlier: 3.695A pdb=" N VAL B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 403 Processing helix chain 'B' and resid 405 through 423 removed outlier: 4.395A pdb=" N LEU B 408 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR B 409 " --> pdb=" O HIS B 406 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 422 " --> pdb=" O THR B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 445 removed outlier: 3.683A pdb=" N HIS B 444 " --> pdb=" O VAL B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 465 Processing helix chain 'B' and resid 472 through 480 Processing helix chain 'B' and resid 482 through 492 Proline residue: B 487 - end of helix Processing helix chain 'B' and resid 495 through 507 removed outlier: 4.352A pdb=" N LEU B 499 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE B 501 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE B 505 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 55 removed outlier: 3.502A pdb=" N HIS C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 85 Processing helix chain 'C' and resid 112 through 115 No H-bonds generated for 'chain 'C' and resid 112 through 115' Processing helix chain 'C' and resid 119 through 128 Processing helix chain 'C' and resid 133 through 165 removed outlier: 3.784A pdb=" N ILE C 138 " --> pdb=" O THR C 134 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU C 159 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 160 " --> pdb=" O CYS C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 180 through 189 Processing helix chain 'C' and resid 205 through 212 Processing helix chain 'C' and resid 214 through 224 removed outlier: 3.998A pdb=" N TYR C 218 " --> pdb=" O ARG C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 255 Processing helix chain 'C' and resid 271 through 274 Processing helix chain 'C' and resid 276 through 316 removed outlier: 3.710A pdb=" N ARG C 279 " --> pdb=" O GLY C 276 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU C 280 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU C 281 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS C 301 " --> pdb=" O PHE C 298 " (cutoff:3.500A) Proline residue: C 302 - end of helix removed outlier: 3.547A pdb=" N TYR C 316 " --> pdb=" O PHE C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 322 No H-bonds generated for 'chain 'C' and resid 319 through 322' Processing helix chain 'C' and resid 324 through 327 removed outlier: 3.618A pdb=" N LEU C 327 " --> pdb=" O PRO C 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 324 through 327' Processing helix chain 'C' and resid 334 through 339 removed outlier: 3.677A pdb=" N CYS C 338 " --> pdb=" O LEU C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 356 removed outlier: 3.739A pdb=" N ARG C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 367 Processing helix chain 'C' and resid 371 through 397 removed outlier: 3.695A pdb=" N VAL C 390 " --> pdb=" O SER C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 403 Processing helix chain 'C' and resid 405 through 423 removed outlier: 4.396A pdb=" N LEU C 408 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR C 409 " --> pdb=" O HIS C 406 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG C 422 " --> pdb=" O THR C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 445 removed outlier: 3.683A pdb=" N HIS C 444 " --> pdb=" O VAL C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 465 Processing helix chain 'C' and resid 472 through 480 Processing helix chain 'C' and resid 482 through 492 Proline residue: C 487 - end of helix Processing helix chain 'C' and resid 495 through 507 removed outlier: 4.351A pdb=" N LEU C 499 " --> pdb=" O PRO C 496 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE C 501 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE C 505 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 231 through 234 Processing sheet with id= B, first strand: chain 'A' and resid 330 through 332 Processing sheet with id= C, first strand: chain 'A' and resid 509 through 512 Processing sheet with id= D, first strand: chain 'B' and resid 231 through 234 Processing sheet with id= E, first strand: chain 'B' and resid 330 through 332 Processing sheet with id= F, first strand: chain 'B' and resid 509 through 512 Processing sheet with id= G, first strand: chain 'C' and resid 231 through 234 Processing sheet with id= H, first strand: chain 'C' and resid 330 through 332 Processing sheet with id= I, first strand: chain 'C' and resid 509 through 512 591 hydrogen bonds defined for protein. 1278 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: 3.67 Time building geometry restraints manager: 5.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3735 1.34 - 1.46: 2104 1.46 - 1.58: 7226 1.58 - 1.69: 12 1.69 - 1.81: 105 Bond restraints: 13182 Sorted by residual: bond pdb=" C29 POV B 615 " pdb="C210 POV B 615 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" C29 POV C 602 " pdb="C210 POV C 602 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.94e+01 bond pdb=" C29 POV C 612 " pdb="C210 POV C 612 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.94e+01 bond pdb=" C29 POV B 610 " pdb="C210 POV B 610 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.94e+01 bond pdb=" C29 POV A 615 " pdb="C210 POV A 615 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.94e+01 ... (remaining 13177 not shown) Histogram of bond angle deviations from ideal: 95.35 - 103.09: 103 103.09 - 110.83: 5112 110.83 - 118.56: 5300 118.56 - 126.30: 6912 126.30 - 134.04: 243 Bond angle restraints: 17670 Sorted by residual: angle pdb=" C28 POV B 605 " pdb=" C29 POV B 605 " pdb="C210 POV B 605 " ideal model delta sigma weight residual 127.79 109.78 18.01 3.00e+00 1.11e-01 3.60e+01 angle pdb=" C28 POV C 607 " pdb=" C29 POV C 607 " pdb="C210 POV C 607 " ideal model delta sigma weight residual 127.79 109.81 17.98 3.00e+00 1.11e-01 3.59e+01 angle pdb=" C28 POV A 605 " pdb=" C29 POV A 605 " pdb="C210 POV A 605 " ideal model delta sigma weight residual 127.79 109.84 17.95 3.00e+00 1.11e-01 3.58e+01 angle pdb=" C28 POV C 613 " pdb=" C29 POV C 613 " pdb="C210 POV C 613 " ideal model delta sigma weight residual 127.79 109.91 17.88 3.00e+00 1.11e-01 3.55e+01 angle pdb=" C28 POV A 611 " pdb=" C29 POV A 611 " pdb="C210 POV A 611 " ideal model delta sigma weight residual 127.79 109.92 17.87 3.00e+00 1.11e-01 3.55e+01 ... (remaining 17665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.36: 6846 18.36 - 36.73: 714 36.73 - 55.09: 177 55.09 - 73.46: 33 73.46 - 91.82: 39 Dihedral angle restraints: 7809 sinusoidal: 3531 harmonic: 4278 Sorted by residual: dihedral pdb=" CB CYS A 86 " pdb=" SG CYS A 86 " pdb=" SG CYS A 122 " pdb=" CB CYS A 122 " ideal model delta sinusoidal sigma weight residual -86.00 -121.29 35.29 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" CB CYS B 86 " pdb=" SG CYS B 86 " pdb=" SG CYS B 122 " pdb=" CB CYS B 122 " ideal model delta sinusoidal sigma weight residual -86.00 -121.29 35.29 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" CB CYS C 86 " pdb=" SG CYS C 86 " pdb=" SG CYS C 122 " pdb=" CB CYS C 122 " ideal model delta sinusoidal sigma weight residual -86.00 -121.28 35.28 1 1.00e+01 1.00e-02 1.76e+01 ... (remaining 7806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1050 0.028 - 0.055: 554 0.055 - 0.083: 199 0.083 - 0.111: 69 0.111 - 0.138: 6 Chirality restraints: 1878 Sorted by residual: chirality pdb=" CA ILE A 425 " pdb=" N ILE A 425 " pdb=" C ILE A 425 " pdb=" CB ILE A 425 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA ILE C 425 " pdb=" N ILE C 425 " pdb=" C ILE C 425 " pdb=" CB ILE C 425 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ILE B 425 " pdb=" N ILE B 425 " pdb=" C ILE B 425 " pdb=" CB ILE B 425 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1875 not shown) Planarity restraints: 2154 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B 605 " -0.158 2.00e-02 2.50e+03 3.01e-01 9.07e+02 pdb=" C29 POV B 605 " 0.392 2.00e-02 2.50e+03 pdb="C210 POV B 605 " -0.397 2.00e-02 2.50e+03 pdb="C211 POV B 605 " 0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C 607 " -0.158 2.00e-02 2.50e+03 3.01e-01 9.07e+02 pdb=" C29 POV C 607 " 0.392 2.00e-02 2.50e+03 pdb="C210 POV C 607 " -0.397 2.00e-02 2.50e+03 pdb="C211 POV C 607 " 0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 605 " -0.158 2.00e-02 2.50e+03 3.01e-01 9.06e+02 pdb=" C29 POV A 605 " 0.392 2.00e-02 2.50e+03 pdb="C210 POV A 605 " -0.397 2.00e-02 2.50e+03 pdb="C211 POV A 605 " 0.162 2.00e-02 2.50e+03 ... (remaining 2151 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2766 2.78 - 3.31: 11428 3.31 - 3.84: 19740 3.84 - 4.37: 24145 4.37 - 4.90: 42052 Nonbonded interactions: 100131 Sorted by model distance: nonbonded pdb=" NH2 ARG C 337 " pdb=" OE1 GLN C 351 " model vdw 2.252 2.520 nonbonded pdb=" NH2 ARG B 337 " pdb=" OE1 GLN B 351 " model vdw 2.252 2.520 nonbonded pdb=" NH2 ARG A 337 " pdb=" OE1 GLN A 351 " model vdw 2.252 2.520 nonbonded pdb=" O HIS A 406 " pdb=" OG1 THR A 410 " model vdw 2.273 2.440 nonbonded pdb=" O HIS C 406 " pdb=" OG1 THR C 410 " model vdw 2.273 2.440 ... (remaining 100126 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 36 through 532 or resid 603 or (resid 604 and (name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8 or name C39 or name C310 or name C311 or name C312 or name C313 or name C314)) \ or (resid 605 and (name C21 or name C22 or name C23 or name C24 or name C25 or \ name C26 or name C27 or name C28)) or resid 611 or (resid 613 and (name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name O21 or name O22 or name C210 or name C211 or name C212 or na \ me C213 or name C214 or name C215)) or resid 615)) selection = (chain 'B' and (resid 36 through 532 or resid 603 or (resid 604 and (name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8 or name C39 or name C310 or name C311 or name C312 or name C313 or name C314)) \ or (resid 605 and (name C21 or name C22 or name C23 or name C24 or name C25 or \ name C26 or name C27 or name C28)) or resid 611 or (resid 613 and (name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name O21 or name O22 or name C210 or name C211 or name C212 or na \ me C213 or name C214 or name C215)) or resid 615)) selection = (chain 'C' and (resid 36 through 532 or (resid 603 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name O11 or name O12 or name O13 or n \ ame O14 or name O21 or name O22 or name O31 or name O32 or name P )) or resid 60 \ 4 or (resid 605 and (name C21 or name C22 or name C23 or name C24 or name C25 or \ name C26 or name C27 or name C28)) or (resid 611 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name O21 or name O22 or name C210 or name C211 or name C212 or name C213 or n \ ame C214 or name C215)) or resid 613 or (resid 615 and (name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name O21 or name O22 or name C210 or name C211 or name C212 or name C213 or \ name C214 or name C215 or name C216)))) } 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: 0.390 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: 0.010 Extract box with map and model: 2.840 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 34.480 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 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 : 0.009 0.189 13182 Z= 0.533 Angle : 1.271 18.010 17670 Z= 0.493 Chirality : 0.038 0.138 1878 Planarity : 0.018 0.301 2154 Dihedral : 17.049 91.820 5028 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.21), residues: 1443 helix: -0.55 (0.16), residues: 957 sheet: -1.93 (0.89), residues: 30 loop : -3.02 (0.24), residues: 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 159 time to evaluate : 1.515 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 168 average time/residue: 0.2847 time to fit residues: 67.0812 Evaluate side-chains 129 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 1.373 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1232 time to fit residues: 3.3790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 428 GLN B 184 GLN B 250 ASN B 406 HIS B 507 ASN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS C 428 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 13182 Z= 0.204 Angle : 0.477 6.304 17670 Z= 0.254 Chirality : 0.038 0.139 1878 Planarity : 0.005 0.040 2154 Dihedral : 14.700 86.273 2220 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.21), residues: 1443 helix: 0.05 (0.17), residues: 936 sheet: -1.72 (0.91), residues: 30 loop : -2.60 (0.24), residues: 477 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 1.586 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 123 average time/residue: 0.3095 time to fit residues: 54.0556 Evaluate side-chains 111 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 1.366 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1330 time to fit residues: 3.4725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 0.0000 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 191 GLN A 406 HIS ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 13182 Z= 0.163 Angle : 0.434 5.404 17670 Z= 0.229 Chirality : 0.037 0.127 1878 Planarity : 0.005 0.028 2154 Dihedral : 13.786 81.899 2220 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.22), residues: 1443 helix: 0.27 (0.17), residues: 936 sheet: -1.43 (0.91), residues: 30 loop : -2.31 (0.25), residues: 477 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 1.565 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 124 average time/residue: 0.2804 time to fit residues: 50.1926 Evaluate side-chains 118 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 1.509 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1351 time to fit residues: 3.1974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 0.0980 chunk 62 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 131 optimal weight: 0.3980 chunk 139 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 191 GLN A 379 ASN B 191 GLN B 284 GLN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN C 428 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 13182 Z= 0.116 Angle : 0.407 5.974 17670 Z= 0.214 Chirality : 0.036 0.138 1878 Planarity : 0.004 0.029 2154 Dihedral : 12.878 84.541 2220 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.22), residues: 1443 helix: 0.55 (0.18), residues: 924 sheet: -1.16 (0.92), residues: 30 loop : -2.05 (0.25), residues: 489 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 1.477 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 132 average time/residue: 0.2586 time to fit residues: 49.8474 Evaluate side-chains 112 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 1.427 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1166 time to fit residues: 2.4960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 103 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 184 GLN A 191 GLN A 284 GLN B 57 ASN B 191 GLN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 13182 Z= 0.158 Angle : 0.429 6.326 17670 Z= 0.222 Chirality : 0.037 0.130 1878 Planarity : 0.004 0.029 2154 Dihedral : 12.737 87.826 2220 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.22), residues: 1443 helix: 0.61 (0.18), residues: 936 sheet: -1.03 (0.92), residues: 30 loop : -1.90 (0.27), residues: 477 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 1.553 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 123 average time/residue: 0.2775 time to fit residues: 49.2264 Evaluate side-chains 114 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 1.576 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1326 time to fit residues: 2.7734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 0.2980 chunk 134 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 13182 Z= 0.200 Angle : 0.451 6.682 17670 Z= 0.232 Chirality : 0.038 0.129 1878 Planarity : 0.004 0.030 2154 Dihedral : 12.901 87.216 2220 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.22), residues: 1443 helix: 0.60 (0.18), residues: 939 sheet: -1.03 (0.92), residues: 30 loop : -1.79 (0.27), residues: 474 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 1.460 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 122 average time/residue: 0.2910 time to fit residues: 50.8781 Evaluate side-chains 118 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 1.479 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1147 time to fit residues: 2.6287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 10.0000 chunk 79 optimal weight: 0.5980 chunk 101 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 428 GLN B 38 HIS C 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 13182 Z= 0.163 Angle : 0.434 7.026 17670 Z= 0.224 Chirality : 0.037 0.130 1878 Planarity : 0.004 0.028 2154 Dihedral : 12.715 88.160 2220 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.23), residues: 1443 helix: 0.69 (0.18), residues: 936 sheet: -1.00 (0.92), residues: 30 loop : -1.74 (0.27), residues: 477 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 1.538 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 121 average time/residue: 0.2940 time to fit residues: 50.7907 Evaluate side-chains 120 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 1.529 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1207 time to fit residues: 2.2995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 88 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 428 GLN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 13182 Z= 0.201 Angle : 0.453 6.416 17670 Z= 0.233 Chirality : 0.038 0.131 1878 Planarity : 0.004 0.028 2154 Dihedral : 12.813 88.437 2220 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.23), residues: 1443 helix: 0.64 (0.18), residues: 942 sheet: -0.95 (0.93), residues: 30 loop : -1.73 (0.27), residues: 471 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 1.491 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 124 average time/residue: 0.3020 time to fit residues: 52.8650 Evaluate side-chains 122 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 1.528 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1156 time to fit residues: 2.4589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN C 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 13182 Z= 0.160 Angle : 0.432 5.999 17670 Z= 0.223 Chirality : 0.037 0.133 1878 Planarity : 0.004 0.028 2154 Dihedral : 12.519 89.018 2220 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.23), residues: 1443 helix: 0.72 (0.18), residues: 939 sheet: -0.90 (0.94), residues: 30 loop : -1.69 (0.27), residues: 474 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 1.601 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 129 average time/residue: 0.2880 time to fit residues: 53.4950 Evaluate side-chains 123 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 1.461 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1300 time to fit residues: 2.3874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN B 57 ASN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 13182 Z= 0.143 Angle : 0.426 7.695 17670 Z= 0.221 Chirality : 0.036 0.133 1878 Planarity : 0.004 0.030 2154 Dihedral : 12.211 86.790 2220 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.23), residues: 1443 helix: 0.81 (0.18), residues: 930 sheet: -0.90 (0.94), residues: 30 loop : -1.67 (0.27), residues: 483 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2886 Ramachandran restraints generated. 1443 Oldfield, 0 Emsley, 1443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.386 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2943 time to fit residues: 51.0545 Evaluate side-chains 120 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.369 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 117 optimal weight: 0.0270 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 216 GLN A 428 GLN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.111987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.090981 restraints weight = 16009.756| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.33 r_work: 0.2650 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 13182 Z= 0.206 Angle : 0.459 7.683 17670 Z= 0.236 Chirality : 0.038 0.133 1878 Planarity : 0.004 0.029 2154 Dihedral : 12.462 84.111 2220 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.23), residues: 1443 helix: 0.70 (0.18), residues: 945 sheet: -0.91 (0.94), residues: 30 loop : -1.63 (0.28), residues: 468 =============================================================================== Job complete usr+sys time: 2333.74 seconds wall clock time: 43 minutes 29.88 seconds (2609.88 seconds total)