Starting phenix.real_space_refine on Thu Feb 15 17:19:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlp_22376/02_2024/7jlp_22376_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlp_22376/02_2024/7jlp_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_22376/02_2024/7jlp_22376.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlp_22376/02_2024/7jlp_22376.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlp_22376/02_2024/7jlp_22376_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlp_22376/02_2024/7jlp_22376_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 425 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: 425 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: 425 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: 7.22, per 1000 atoms: 0.56 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: 5.01 Conformation dependent library (CDL) restraints added in 2.3 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: 2.50 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: 3.58 Time building geometry restraints manager: 5.42 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: 6849 18.36 - 36.73: 726 36.73 - 55.09: 198 55.09 - 73.46: 48 73.46 - 91.82: 42 Dihedral angle restraints: 7863 sinusoidal: 3585 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 7860 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: 0.400 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: 0.000 Extract box with map and model: 2.370 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 36.130 Find NCS groups from input model: 0.870 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.970 ------------------------------------------------------------------------------- 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 : 17.666 91.820 5082 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 % Allowed : 2.09 % Favored : 97.22 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 180 HIS 0.004 0.001 HIS A 161 PHE 0.014 0.001 PHE A 163 TYR 0.005 0.001 TYR C 177 ARG 0.002 0.000 ARG A 458 *********************** 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 : 1.458 Fit side-chains REVERT: B 62 MET cc_start: 0.7912 (ttp) cc_final: 0.7626 (ttp) REVERT: B 91 ILE cc_start: 0.8718 (pt) cc_final: 0.8516 (pt) REVERT: B 191 GLN cc_start: 0.8041 (pp30) cc_final: 0.7740 (pp30) REVERT: B 306 ILE cc_start: 0.8944 (mt) cc_final: 0.8709 (mt) REVERT: B 524 MET cc_start: 0.4129 (ptp) cc_final: 0.3515 (ptp) REVERT: C 91 ILE cc_start: 0.8666 (pt) cc_final: 0.8438 (pt) REVERT: C 121 VAL cc_start: 0.7418 (p) cc_final: 0.7156 (t) outliers start: 9 outliers final: 7 residues processed: 168 average time/residue: 0.2959 time to fit residues: 69.3754 Evaluate side-chains 130 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 GLN 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: 0.8980 chunk 58 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN A 406 HIS 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1108 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= 0.183 Angle : 0.469 6.139 17670 Z= 0.250 Chirality : 0.037 0.135 1878 Planarity : 0.005 0.040 2154 Dihedral : 15.752 84.241 2287 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.01 % Allowed : 7.66 % Favored : 91.34 % 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: -1.28 (0.21), residues: 1443 helix: 0.06 (0.17), residues: 936 sheet: -1.72 (0.91), residues: 30 loop : -2.60 (0.24), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 292 HIS 0.004 0.001 HIS A 161 PHE 0.012 0.001 PHE C 469 TYR 0.011 0.001 TYR A 152 ARG 0.007 0.000 ARG C 231 *********************** 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 128 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 1.409 Fit side-chains REVERT: A 233 ARG cc_start: 0.7577 (mmm-85) cc_final: 0.7242 (tpp80) REVERT: B 62 MET cc_start: 0.7681 (ttp) cc_final: 0.7444 (ttp) REVERT: B 91 ILE cc_start: 0.8698 (pt) cc_final: 0.8449 (pt) REVERT: B 306 ILE cc_start: 0.8808 (mt) cc_final: 0.8597 (mt) REVERT: B 375 LEU cc_start: 0.8900 (mt) cc_final: 0.8609 (mt) REVERT: B 524 MET cc_start: 0.4085 (ptp) cc_final: 0.3292 (ptp) REVERT: C 91 ILE cc_start: 0.8680 (pt) cc_final: 0.8459 (pt) outliers start: 13 outliers final: 9 residues processed: 126 average time/residue: 0.2957 time to fit residues: 52.3764 Evaluate side-chains 113 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 379 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13182 Z= 0.257 Angle : 0.485 5.422 17670 Z= 0.253 Chirality : 0.039 0.133 1878 Planarity : 0.005 0.030 2154 Dihedral : 15.437 89.673 2277 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.24 % Allowed : 9.36 % Favored : 89.40 % 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: -1.04 (0.21), residues: 1443 helix: 0.19 (0.17), residues: 936 sheet: -1.47 (0.91), residues: 30 loop : -2.37 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 292 HIS 0.004 0.001 HIS A 161 PHE 0.014 0.001 PHE B 469 TYR 0.012 0.001 TYR A 152 ARG 0.005 0.000 ARG C 231 *********************** 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: 16 poor density : 112 time to evaluate : 1.349 Fit side-chains REVERT: A 233 ARG cc_start: 0.7516 (mmm-85) cc_final: 0.7187 (tpp80) REVERT: B 62 MET cc_start: 0.7844 (ttp) cc_final: 0.7555 (ttp) REVERT: B 91 ILE cc_start: 0.8688 (pt) cc_final: 0.8374 (pt) REVERT: B 191 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.6646 (pt0) REVERT: B 306 ILE cc_start: 0.8816 (mt) cc_final: 0.8579 (mt) REVERT: B 524 MET cc_start: 0.3940 (ptp) cc_final: 0.3066 (ptp) REVERT: C 460 GLN cc_start: 0.8005 (tt0) cc_final: 0.7513 (pt0) outliers start: 16 outliers final: 12 residues processed: 124 average time/residue: 0.2904 time to fit residues: 50.6099 Evaluate side-chains 117 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 430 MET 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: 0.6980 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8465 moved from start: 0.1654 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= 0.166 Angle : 0.431 5.258 17670 Z= 0.227 Chirality : 0.037 0.132 1878 Planarity : 0.004 0.028 2154 Dihedral : 14.740 89.613 2277 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.39 % Allowed : 10.60 % Favored : 88.01 % 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: -0.71 (0.22), residues: 1443 helix: 0.39 (0.17), residues: 936 sheet: -1.31 (0.90), residues: 30 loop : -2.11 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 292 HIS 0.004 0.001 HIS B 161 PHE 0.010 0.001 PHE A 469 TYR 0.011 0.001 TYR C 152 ARG 0.004 0.000 ARG C 231 *********************** 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 131 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 1.540 Fit side-chains REVERT: A 233 ARG cc_start: 0.7497 (mmm-85) cc_final: 0.7194 (tpp80) REVERT: B 91 ILE cc_start: 0.8638 (pt) cc_final: 0.8279 (pt) REVERT: B 191 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6890 (pt0) REVERT: B 306 ILE cc_start: 0.8795 (mt) cc_final: 0.8531 (mt) REVERT: B 524 MET cc_start: 0.3995 (ptp) cc_final: 0.3142 (ptp) REVERT: C 460 GLN cc_start: 0.7967 (tt0) cc_final: 0.7488 (pt0) outliers start: 18 outliers final: 11 residues processed: 126 average time/residue: 0.2812 time to fit residues: 50.2276 Evaluate side-chains 122 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 430 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 2 optimal weight: 0.0470 chunk 103 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.1484 ------------------------------------------------------------------------------- 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 ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13182 Z= 0.248 Angle : 0.471 5.801 17670 Z= 0.243 Chirality : 0.039 0.132 1878 Planarity : 0.004 0.029 2154 Dihedral : 14.706 87.530 2277 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.39 % Allowed : 11.60 % Favored : 87.01 % 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: -0.60 (0.22), residues: 1443 helix: 0.45 (0.18), residues: 936 sheet: -1.29 (0.91), residues: 30 loop : -1.99 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 180 HIS 0.004 0.001 HIS B 161 PHE 0.010 0.001 PHE C 469 TYR 0.011 0.001 TYR C 152 ARG 0.003 0.000 ARG C 231 *********************** 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 132 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 1.439 Fit side-chains REVERT: A 233 ARG cc_start: 0.7541 (mmm-85) cc_final: 0.7226 (tpp80) REVERT: B 91 ILE cc_start: 0.8592 (pt) cc_final: 0.8144 (pt) REVERT: B 191 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6906 (pt0) REVERT: B 306 ILE cc_start: 0.8785 (mt) cc_final: 0.8521 (mt) REVERT: B 524 MET cc_start: 0.4010 (ptp) cc_final: 0.3205 (ptp) REVERT: C 91 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8319 (pt) REVERT: C 460 GLN cc_start: 0.8001 (tt0) cc_final: 0.7505 (pt0) outliers start: 18 outliers final: 13 residues processed: 124 average time/residue: 0.2897 time to fit residues: 50.4643 Evaluate side-chains 124 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 430 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 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 184 GLN B 38 HIS ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN C 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13182 Z= 0.157 Angle : 0.424 5.208 17670 Z= 0.222 Chirality : 0.037 0.130 1878 Planarity : 0.004 0.028 2154 Dihedral : 14.005 89.554 2277 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.70 % Allowed : 11.76 % Favored : 86.54 % 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: -0.37 (0.22), residues: 1443 helix: 0.60 (0.18), residues: 936 sheet: -1.22 (0.91), residues: 30 loop : -1.84 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 180 HIS 0.003 0.000 HIS B 161 PHE 0.009 0.001 PHE A 469 TYR 0.011 0.001 TYR C 152 ARG 0.003 0.000 ARG C 231 *********************** 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 144 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 1.492 Fit side-chains REVERT: A 233 ARG cc_start: 0.7499 (mmm-85) cc_final: 0.7205 (tpp80) REVERT: A 369 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8404 (pt) REVERT: B 91 ILE cc_start: 0.8531 (pt) cc_final: 0.8294 (pt) REVERT: B 191 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.6950 (pt0) REVERT: B 524 MET cc_start: 0.3955 (ptp) cc_final: 0.3096 (ptp) REVERT: C 91 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8220 (pt) REVERT: C 193 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.6055 (mp0) outliers start: 22 outliers final: 14 residues processed: 136 average time/residue: 0.2778 time to fit residues: 53.8154 Evaluate side-chains 133 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain C residue 455 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13182 Z= 0.289 Angle : 0.492 5.801 17670 Z= 0.253 Chirality : 0.040 0.132 1878 Planarity : 0.004 0.030 2154 Dihedral : 14.414 89.034 2277 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.70 % Allowed : 12.61 % Favored : 85.69 % 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: -0.46 (0.22), residues: 1443 helix: 0.51 (0.18), residues: 939 sheet: -1.19 (0.92), residues: 30 loop : -1.84 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 180 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE B 475 TYR 0.010 0.001 TYR C 152 ARG 0.003 0.000 ARG C 353 *********************** 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 139 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 1.586 Fit side-chains REVERT: A 233 ARG cc_start: 0.7522 (mmm-85) cc_final: 0.7209 (tpp80) REVERT: B 91 ILE cc_start: 0.8556 (pt) cc_final: 0.8301 (pt) REVERT: B 191 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6945 (pt0) REVERT: B 524 MET cc_start: 0.4005 (ptp) cc_final: 0.3199 (ptp) REVERT: C 193 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6003 (mp0) REVERT: C 460 GLN cc_start: 0.8138 (tt0) cc_final: 0.7814 (pt0) outliers start: 22 outliers final: 16 residues processed: 133 average time/residue: 0.2862 time to fit residues: 53.5272 Evaluate side-chains 134 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 455 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN C 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13182 Z= 0.154 Angle : 0.433 5.579 17670 Z= 0.226 Chirality : 0.037 0.133 1878 Planarity : 0.004 0.029 2154 Dihedral : 13.802 88.729 2277 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.86 % Allowed : 12.53 % Favored : 85.61 % 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: -0.25 (0.23), residues: 1443 helix: 0.64 (0.18), residues: 939 sheet: -1.13 (0.92), residues: 30 loop : -1.68 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 292 HIS 0.003 0.001 HIS B 161 PHE 0.008 0.001 PHE A 469 TYR 0.011 0.001 TYR C 152 ARG 0.003 0.000 ARG C 231 *********************** 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 146 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.441 Fit side-chains REVERT: A 233 ARG cc_start: 0.7488 (mmm-85) cc_final: 0.7187 (tpp80) REVERT: B 91 ILE cc_start: 0.8505 (pt) cc_final: 0.8249 (pt) REVERT: B 524 MET cc_start: 0.4006 (ptp) cc_final: 0.3215 (ptp) REVERT: C 91 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8172 (pt) REVERT: C 193 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6033 (mp0) REVERT: C 460 GLN cc_start: 0.8101 (tt0) cc_final: 0.7770 (pt0) outliers start: 24 outliers final: 17 residues processed: 136 average time/residue: 0.2843 time to fit residues: 54.5647 Evaluate side-chains 138 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain C residue 455 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 B 191 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13182 Z= 0.231 Angle : 0.471 6.188 17670 Z= 0.242 Chirality : 0.038 0.132 1878 Planarity : 0.004 0.029 2154 Dihedral : 13.957 88.363 2277 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.62 % Allowed : 12.92 % Favored : 85.46 % 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: -0.28 (0.23), residues: 1443 helix: 0.61 (0.18), residues: 939 sheet: -1.15 (0.92), residues: 30 loop : -1.68 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 180 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE C 469 TYR 0.011 0.001 TYR C 152 ARG 0.002 0.000 ARG C 231 *********************** 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 140 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 1.433 Fit side-chains REVERT: A 233 ARG cc_start: 0.7518 (mmm-85) cc_final: 0.7206 (tpp80) REVERT: A 369 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8406 (pt) REVERT: B 91 ILE cc_start: 0.8497 (pt) cc_final: 0.8225 (pt) REVERT: B 375 LEU cc_start: 0.8901 (mt) cc_final: 0.8637 (mt) REVERT: B 524 MET cc_start: 0.4055 (ptp) cc_final: 0.3225 (ptp) REVERT: C 91 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8186 (pt) REVERT: C 193 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.5992 (mp0) REVERT: C 460 GLN cc_start: 0.8119 (tt0) cc_final: 0.7782 (pt0) outliers start: 21 outliers final: 18 residues processed: 132 average time/residue: 0.2921 time to fit residues: 54.7431 Evaluate side-chains 139 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 430 MET Chi-restraints excluded: chain C residue 455 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 143 optimal weight: 0.2980 chunk 132 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13182 Z= 0.131 Angle : 0.428 5.829 17670 Z= 0.223 Chirality : 0.036 0.133 1878 Planarity : 0.004 0.030 2154 Dihedral : 13.393 86.744 2277 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.39 % Allowed : 13.30 % Favored : 85.31 % 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: -0.13 (0.23), residues: 1443 helix: 0.74 (0.18), residues: 939 sheet: -1.11 (0.92), residues: 30 loop : -1.66 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 292 HIS 0.003 0.000 HIS B 161 PHE 0.009 0.001 PHE A 469 TYR 0.012 0.001 TYR C 152 ARG 0.003 0.000 ARG C 231 ********************** 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 142 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 1.453 Fit side-chains REVERT: A 233 ARG cc_start: 0.7484 (mmm-85) cc_final: 0.7190 (tpp80) REVERT: A 369 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8394 (pt) REVERT: A 524 MET cc_start: 0.4444 (ptp) cc_final: 0.3697 (ptp) REVERT: B 91 ILE cc_start: 0.8427 (pt) cc_final: 0.8189 (pt) REVERT: B 524 MET cc_start: 0.4021 (ptp) cc_final: 0.3187 (ptp) REVERT: C 91 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8118 (pt) REVERT: C 460 GLN cc_start: 0.8073 (tt0) cc_final: 0.7698 (pt0) outliers start: 18 outliers final: 14 residues processed: 135 average time/residue: 0.2985 time to fit residues: 56.5520 Evaluate side-chains 135 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 455 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 284 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.111116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.090189 restraints weight = 16000.656| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 1.32 r_work: 0.2635 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13182 Z= 0.228 Angle : 0.475 5.933 17670 Z= 0.244 Chirality : 0.038 0.133 1878 Planarity : 0.004 0.029 2154 Dihedral : 13.670 87.394 2277 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.39 % Allowed : 13.38 % Favored : 85.23 % 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: -0.19 (0.23), residues: 1443 helix: 0.68 (0.18), residues: 939 sheet: -1.12 (0.93), residues: 30 loop : -1.63 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 292 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE B 475 TYR 0.014 0.001 TYR B 177 ARG 0.002 0.000 ARG C 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2522.80 seconds wall clock time: 47 minutes 1.65 seconds (2821.65 seconds total)