Starting phenix.real_space_refine on Fri Mar 15 14:54:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlo_22375/03_2024/7jlo_22375.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlo_22375/03_2024/7jlo_22375.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/7jlo_22375/03_2024/7jlo_22375.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlo_22375/03_2024/7jlo_22375.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlo_22375/03_2024/7jlo_22375.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlo_22375/03_2024/7jlo_22375.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= 0.001 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 7881 2.51 5 N 2022 2.21 5 O 1992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A ASP 207": "OD1" <-> "OD2" 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 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 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 ASP 450": "OD1" <-> "OD2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A ASP 503": "OD1" <-> "OD2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 506": "NH1" <-> "NH2" Residue "A GLU 511": "OE1" <-> "OE2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B ASP 207": "OD1" <-> "OD2" 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 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 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 ASP 450": "OD1" <-> "OD2" Residue "B GLU 479": "OE1" <-> "OE2" Residue "B ASP 503": "OD1" <-> "OD2" Residue "B PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 506": "NH1" <-> "NH2" Residue "B GLU 511": "OE1" <-> "OE2" Residue "C PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C ASP 207": "OD1" <-> "OD2" 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 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 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 ASP 450": "OD1" <-> "OD2" Residue "C GLU 479": "OE1" <-> "OE2" Residue "C ASP 503": "OD1" <-> "OD2" Residue "C PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 506": "NH1" <-> "NH2" Residue "C GLU 511": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11964 Number of models: 1 Model: "" Number of chains: 3 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 Time building chain proxies: 6.30, per 1000 atoms: 0.53 Number of scatterers: 11964 At special positions: 0 Unit cell: (129.276, 123.606, 88.452, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 1992 8.00 N 2022 7.00 C 7881 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=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 122 " distance=2.04 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 122 " distance=2.04 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: 4.49 Conformation dependent library (CDL) restraints added in 2.0 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... Secondary structure from input PDB file: 78 helices and 9 sheets defined 72.0% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 42 through 56 Processing helix chain 'A' and resid 58 through 86 Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.934A pdb=" N ALA A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 116' Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 130 through 168 removed outlier: 4.045A pdb=" N ILE A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE A 160 " --> pdb=" O CYS A 156 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 168 " --> pdb=" O TYR A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 190 Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 213 through 226 removed outlier: 3.746A pdb=" N TYR A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.667A pdb=" N ARG A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 300 Processing helix chain 'A' and resid 300 through 317 removed outlier: 3.612A pdb=" N ALA A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 324 through 328 removed outlier: 4.270A pdb=" N LEU A 327 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 340 removed outlier: 3.591A pdb=" N CYS A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 357 removed outlier: 3.881A pdb=" N ARG A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 367 removed outlier: 3.559A pdb=" N MET A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 398 removed outlier: 3.605A pdb=" N VAL A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'A' and resid 406 through 422 Processing helix chain 'A' and resid 433 through 446 removed outlier: 3.581A pdb=" N LEU A 437 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N HIS A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 453 removed outlier: 3.525A pdb=" N TRP A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN A 453 " --> pdb=" O ASP A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 449 through 453' Processing helix chain 'A' and resid 460 through 466 Processing helix chain 'A' and resid 472 through 481 Processing helix chain 'A' and resid 481 through 492 Proline residue: A 487 - end of helix Processing helix chain 'A' and resid 497 through 508 removed outlier: 3.785A pdb=" N ILE A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 56 Processing helix chain 'B' and resid 58 through 86 Processing helix chain 'B' and resid 111 through 116 removed outlier: 3.935A pdb=" N ALA B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 116' Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 130 through 168 removed outlier: 4.045A pdb=" N ILE B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N CYS B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE B 160 " --> pdb=" O CYS B 156 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 190 Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 213 through 226 removed outlier: 3.746A pdb=" N TYR B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 270 through 275 removed outlier: 3.667A pdb=" N ARG B 275 " --> pdb=" O GLU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 300 Processing helix chain 'B' and resid 300 through 317 removed outlier: 3.612A pdb=" N ALA B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 323 Processing helix chain 'B' and resid 324 through 328 removed outlier: 4.270A pdb=" N LEU B 327 " --> pdb=" O PRO B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 340 removed outlier: 3.591A pdb=" N CYS B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 357 removed outlier: 3.880A pdb=" N ARG B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 367 removed outlier: 3.558A pdb=" N MET B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 398 removed outlier: 3.605A pdb=" N VAL B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'B' and resid 406 through 422 Processing helix chain 'B' and resid 433 through 446 removed outlier: 3.581A pdb=" N LEU B 437 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B 438 " --> pdb=" O PRO B 434 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N HIS B 444 " --> pdb=" O VAL B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 453 removed outlier: 3.525A pdb=" N TRP B 452 " --> pdb=" O PRO B 449 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN B 453 " --> pdb=" O ASP B 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 449 through 453' Processing helix chain 'B' and resid 460 through 466 Processing helix chain 'B' and resid 472 through 481 Processing helix chain 'B' and resid 481 through 492 Proline residue: B 487 - end of helix Processing helix chain 'B' and resid 497 through 508 removed outlier: 3.785A pdb=" N ILE B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 56 Processing helix chain 'C' and resid 58 through 86 Processing helix chain 'C' and resid 111 through 116 removed outlier: 3.933A pdb=" N ALA C 115 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 111 through 116' Processing helix chain 'C' and resid 118 through 128 Processing helix chain 'C' and resid 130 through 168 removed outlier: 4.045A pdb=" N ILE C 135 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE C 160 " --> pdb=" O CYS C 156 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 168 " --> pdb=" O TYR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 190 Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 213 through 226 removed outlier: 3.746A pdb=" N TYR C 218 " --> pdb=" O ARG C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 256 Processing helix chain 'C' and resid 270 through 275 removed outlier: 3.667A pdb=" N ARG C 275 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 300 Processing helix chain 'C' and resid 300 through 317 removed outlier: 3.612A pdb=" N ALA C 317 " --> pdb=" O PHE C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 323 Processing helix chain 'C' and resid 324 through 328 removed outlier: 4.270A pdb=" N LEU C 327 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 340 removed outlier: 3.590A pdb=" N CYS C 338 " --> pdb=" O LEU C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 357 removed outlier: 3.881A pdb=" N ARG C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 367 removed outlier: 3.558A pdb=" N MET C 365 " --> pdb=" O ALA C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 398 removed outlier: 3.605A pdb=" N VAL C 390 " --> pdb=" O SER C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 404 Processing helix chain 'C' and resid 406 through 422 Processing helix chain 'C' and resid 433 through 446 removed outlier: 3.581A pdb=" N LEU C 437 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU C 438 " --> pdb=" O PRO C 434 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 439 " --> pdb=" O GLU C 435 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL C 440 " --> pdb=" O GLN C 436 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS C 444 " --> pdb=" O VAL C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 453 removed outlier: 3.524A pdb=" N TRP C 452 " --> pdb=" O PRO C 449 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN C 453 " --> pdb=" O ASP C 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 449 through 453' Processing helix chain 'C' and resid 460 through 466 Processing helix chain 'C' and resid 472 through 481 Processing helix chain 'C' and resid 481 through 492 Proline residue: C 487 - end of helix Processing helix chain 'C' and resid 497 through 508 removed outlier: 3.785A pdb=" N ILE C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 231 through 234 Processing sheet with id=AA2, first strand: chain 'A' and resid 330 through 332 Processing sheet with id=AA3, first strand: chain 'A' and resid 509 through 512 Processing sheet with id=AA4, first strand: chain 'B' and resid 231 through 234 Processing sheet with id=AA5, first strand: chain 'B' and resid 330 through 332 Processing sheet with id=AA6, first strand: chain 'B' and resid 509 through 512 Processing sheet with id=AA7, first strand: chain 'C' and resid 231 through 234 Processing sheet with id=AA8, first strand: chain 'C' and resid 330 through 332 Processing sheet with id=AA9, first strand: chain 'C' and resid 509 through 512 699 hydrogen bonds defined for protein. 2025 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: 2.95 Time building geometry restraints manager: 4.90 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: 3759 1.34 - 1.46: 3117 1.46 - 1.58: 5331 1.58 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 12300 Sorted by residual: bond pdb=" C HIS A 451 " pdb=" N TRP A 452 " ideal model delta sigma weight residual 1.332 1.318 0.015 1.40e-02 5.10e+03 1.12e+00 bond pdb=" C HIS B 451 " pdb=" N TRP B 452 " ideal model delta sigma weight residual 1.332 1.318 0.014 1.40e-02 5.10e+03 1.01e+00 bond pdb=" C HIS C 451 " pdb=" N TRP C 452 " ideal model delta sigma weight residual 1.332 1.319 0.014 1.40e-02 5.10e+03 9.82e-01 bond pdb=" C TYR C 152 " pdb=" O TYR C 152 " ideal model delta sigma weight residual 1.236 1.246 -0.010 1.15e-02 7.56e+03 7.45e-01 bond pdb=" CB GLU C 399 " pdb=" CG GLU C 399 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 7.21e-01 ... (remaining 12295 not shown) Histogram of bond angle deviations from ideal: 99.94 - 106.75: 338 106.75 - 113.56: 6726 113.56 - 120.37: 5084 120.37 - 127.18: 4392 127.18 - 133.99: 167 Bond angle restraints: 16707 Sorted by residual: angle pdb=" N GLN C 528 " pdb=" CA GLN C 528 " pdb=" C GLN C 528 " ideal model delta sigma weight residual 111.02 115.45 -4.43 1.22e+00 6.72e-01 1.32e+01 angle pdb=" N GLN B 528 " pdb=" CA GLN B 528 " pdb=" C GLN B 528 " ideal model delta sigma weight residual 111.02 115.42 -4.40 1.22e+00 6.72e-01 1.30e+01 angle pdb=" N GLN A 528 " pdb=" CA GLN A 528 " pdb=" C GLN A 528 " ideal model delta sigma weight residual 111.02 115.42 -4.40 1.22e+00 6.72e-01 1.30e+01 angle pdb=" N ARG C 527 " pdb=" CA ARG C 527 " pdb=" C ARG C 527 " ideal model delta sigma weight residual 109.96 105.28 4.68 1.68e+00 3.54e-01 7.77e+00 angle pdb=" N ARG B 527 " pdb=" CA ARG B 527 " pdb=" C ARG B 527 " ideal model delta sigma weight residual 109.96 105.30 4.66 1.68e+00 3.54e-01 7.69e+00 ... (remaining 16702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 6455 17.83 - 35.67: 573 35.67 - 53.50: 112 53.50 - 71.33: 30 71.33 - 89.17: 12 Dihedral angle restraints: 7182 sinusoidal: 2904 harmonic: 4278 Sorted by residual: dihedral pdb=" CA ARG B 527 " pdb=" C ARG B 527 " pdb=" N GLN B 528 " pdb=" CA GLN B 528 " ideal model delta harmonic sigma weight residual -180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ARG A 527 " pdb=" C ARG A 527 " pdb=" N GLN A 528 " pdb=" CA GLN A 528 " ideal model delta harmonic sigma weight residual -180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ARG C 527 " pdb=" C ARG C 527 " pdb=" N GLN C 528 " pdb=" CA GLN C 528 " ideal model delta harmonic sigma weight residual -180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 7179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 846 0.024 - 0.047: 542 0.047 - 0.071: 328 0.071 - 0.095: 86 0.095 - 0.118: 67 Chirality restraints: 1869 Sorted by residual: chirality pdb=" CA ILE C 170 " pdb=" N ILE C 170 " pdb=" C ILE C 170 " pdb=" CB ILE C 170 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA ILE A 170 " pdb=" N ILE A 170 " pdb=" C ILE A 170 " pdb=" CB ILE A 170 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA ILE B 170 " pdb=" N ILE B 170 " pdb=" C ILE B 170 " pdb=" CB ILE B 170 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.45e-01 ... (remaining 1866 not shown) Planarity restraints: 2085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 117 " 0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO B 118 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 118 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 118 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 117 " 0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO C 118 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 118 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 118 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 117 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO A 118 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " -0.017 5.00e-02 4.00e+02 ... (remaining 2082 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1152 2.74 - 3.28: 11901 3.28 - 3.82: 19337 3.82 - 4.36: 22439 4.36 - 4.90: 39499 Nonbonded interactions: 94328 Sorted by model distance: nonbonded pdb=" O HIS C 406 " pdb=" OG1 THR C 410 " model vdw 2.203 2.440 nonbonded pdb=" O HIS B 406 " pdb=" OG1 THR B 410 " model vdw 2.203 2.440 nonbonded pdb=" O HIS A 406 " pdb=" OG1 THR A 410 " model vdw 2.203 2.440 nonbonded pdb=" NH2 ARG B 337 " pdb=" OE1 GLN B 351 " model vdw 2.230 2.520 nonbonded pdb=" NH2 ARG A 337 " pdb=" OE1 GLN A 351 " model vdw 2.231 2.520 ... (remaining 94323 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 2.270 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 31.430 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12300 Z= 0.285 Angle : 0.603 5.350 16707 Z= 0.361 Chirality : 0.041 0.118 1869 Planarity : 0.003 0.031 2085 Dihedral : 14.679 89.167 4401 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.46 % Allowed : 5.03 % Favored : 94.51 % 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: -2.15 (0.20), residues: 1443 helix: -0.55 (0.16), residues: 954 sheet: None (None), residues: 0 loop : -3.14 (0.21), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 180 HIS 0.003 0.001 HIS C 161 PHE 0.018 0.001 PHE C 79 TYR 0.012 0.001 TYR B 152 ARG 0.002 0.000 ARG A 495 *********************** 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 212 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 206 time to evaluate : 1.053 Fit side-chains REVERT: A 62 MET cc_start: 0.8289 (ttp) cc_final: 0.7877 (ttp) REVERT: A 69 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7350 (mm-30) REVERT: A 422 ARG cc_start: 0.7615 (tpt-90) cc_final: 0.7265 (mmm160) REVERT: B 69 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7668 (mm-30) REVERT: B 125 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.8004 (ttm110) REVERT: B 159 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7755 (tm-30) REVERT: B 372 LEU cc_start: 0.8587 (tp) cc_final: 0.8378 (tp) REVERT: B 427 ASP cc_start: 0.8598 (p0) cc_final: 0.8355 (p0) REVERT: C 89 TYR cc_start: 0.8861 (m-80) cc_final: 0.8585 (m-80) outliers start: 6 outliers final: 2 residues processed: 209 average time/residue: 0.3069 time to fit residues: 85.3056 Evaluate side-chains 133 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain B residue 137 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 109 optimal weight: 0.0980 chunk 60 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 HIS ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS A 467 GLN B 210 HIS ** B 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 GLN B 451 HIS B 467 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN C 210 HIS ** C 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS C 467 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 12300 Z= 0.140 Angle : 0.478 5.435 16707 Z= 0.248 Chirality : 0.037 0.119 1869 Planarity : 0.004 0.054 2085 Dihedral : 4.337 22.855 1595 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.54 % Allowed : 11.68 % Favored : 87.78 % 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: -0.41 (0.22), residues: 1443 helix: 0.83 (0.18), residues: 936 sheet: -1.28 (0.83), residues: 30 loop : -2.49 (0.23), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 180 HIS 0.003 0.001 HIS C 161 PHE 0.008 0.001 PHE C 465 TYR 0.017 0.001 TYR A 152 ARG 0.006 0.000 ARG A 125 *********************** 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 143 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 1.394 Fit side-chains REVERT: A 62 MET cc_start: 0.8086 (ttp) cc_final: 0.7819 (ttp) REVERT: A 300 LEU cc_start: 0.8528 (mm) cc_final: 0.8287 (mt) REVERT: B 125 ARG cc_start: 0.8222 (ttm-80) cc_final: 0.7981 (ttm110) REVERT: B 159 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7752 (tm-30) REVERT: B 396 ILE cc_start: 0.8470 (mt) cc_final: 0.8269 (mm) REVERT: C 159 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7746 (tm-30) outliers start: 7 outliers final: 4 residues processed: 141 average time/residue: 0.3019 time to fit residues: 58.4917 Evaluate side-chains 124 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain C residue 266 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 12300 Z= 0.169 Angle : 0.468 6.876 16707 Z= 0.243 Chirality : 0.038 0.192 1869 Planarity : 0.003 0.033 2085 Dihedral : 4.200 22.158 1593 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.16 % Allowed : 14.23 % Favored : 84.61 % 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: 0.15 (0.22), residues: 1443 helix: 1.24 (0.18), residues: 933 sheet: -1.31 (0.83), residues: 30 loop : -2.15 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 180 HIS 0.003 0.001 HIS A 161 PHE 0.010 0.001 PHE C 79 TYR 0.015 0.001 TYR A 152 ARG 0.003 0.000 ARG A 146 *********************** 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 139 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 1.394 Fit side-chains REVERT: A 62 MET cc_start: 0.8104 (ttp) cc_final: 0.7832 (ttp) REVERT: A 300 LEU cc_start: 0.8510 (mm) cc_final: 0.8273 (mt) REVERT: B 125 ARG cc_start: 0.8224 (ttm-80) cc_final: 0.7986 (ttm110) REVERT: B 159 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7857 (tm-30) REVERT: B 298 PHE cc_start: 0.8210 (t80) cc_final: 0.8009 (t80) REVERT: C 524 MET cc_start: 0.5750 (pmm) cc_final: 0.5280 (pmm) outliers start: 15 outliers final: 12 residues processed: 136 average time/residue: 0.2483 time to fit residues: 48.7338 Evaluate side-chains 126 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 199 HIS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 431 VAL 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: 5.9990 chunk 67 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN B 379 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12300 Z= 0.324 Angle : 0.537 6.692 16707 Z= 0.278 Chirality : 0.041 0.123 1869 Planarity : 0.004 0.042 2085 Dihedral : 4.506 23.080 1593 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.55 % Allowed : 15.08 % Favored : 82.37 % 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: 0.00 (0.22), residues: 1443 helix: 1.08 (0.18), residues: 957 sheet: None (None), residues: 0 loop : -2.26 (0.23), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 180 HIS 0.004 0.001 HIS B 531 PHE 0.015 0.001 PHE B 79 TYR 0.016 0.001 TYR A 152 ARG 0.002 0.000 ARG A 330 *********************** 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 153 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 120 time to evaluate : 1.441 Fit side-chains REVERT: A 62 MET cc_start: 0.8295 (ttp) cc_final: 0.7899 (ttp) REVERT: A 526 VAL cc_start: 0.5020 (OUTLIER) cc_final: 0.4781 (m) REVERT: B 125 ARG cc_start: 0.8232 (ttm-80) cc_final: 0.7980 (ttm110) REVERT: B 320 LEU cc_start: 0.8484 (mm) cc_final: 0.8160 (mp) outliers start: 33 outliers final: 24 residues processed: 150 average time/residue: 0.2443 time to fit residues: 52.9406 Evaluate side-chains 141 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 526 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 12300 Z= 0.184 Angle : 0.474 6.142 16707 Z= 0.248 Chirality : 0.038 0.118 1869 Planarity : 0.003 0.041 2085 Dihedral : 4.330 22.135 1593 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.62 % Allowed : 17.09 % Favored : 81.28 % 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: 0.35 (0.23), residues: 1443 helix: 1.23 (0.18), residues: 957 sheet: -1.16 (0.86), residues: 30 loop : -1.83 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 180 HIS 0.004 0.001 HIS C 161 PHE 0.009 0.001 PHE A 465 TYR 0.014 0.001 TYR A 152 ARG 0.002 0.000 ARG A 146 *********************** 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 147 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 1.415 Fit side-chains REVERT: A 62 MET cc_start: 0.8108 (ttp) cc_final: 0.7852 (ttp) REVERT: B 125 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7972 (ttm110) REVERT: B 320 LEU cc_start: 0.8453 (mm) cc_final: 0.8106 (mp) outliers start: 21 outliers final: 17 residues processed: 144 average time/residue: 0.2322 time to fit residues: 48.8517 Evaluate side-chains 137 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 10.0000 chunk 125 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN C 57 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12300 Z= 0.266 Angle : 0.505 6.039 16707 Z= 0.263 Chirality : 0.039 0.117 1869 Planarity : 0.004 0.042 2085 Dihedral : 4.425 21.343 1593 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.24 % Allowed : 16.78 % Favored : 80.97 % 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: 0.35 (0.23), residues: 1443 helix: 1.22 (0.18), residues: 957 sheet: -1.15 (0.88), residues: 30 loop : -1.81 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 180 HIS 0.004 0.001 HIS A 161 PHE 0.011 0.001 PHE B 79 TYR 0.015 0.001 TYR A 152 ARG 0.002 0.000 ARG C 330 *********************** 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 153 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 124 time to evaluate : 1.472 Fit side-chains REVERT: A 62 MET cc_start: 0.8234 (ttp) cc_final: 0.7842 (ttp) REVERT: B 125 ARG cc_start: 0.8207 (ttm-80) cc_final: 0.7959 (ttm110) REVERT: B 442 LEU cc_start: 0.8945 (tp) cc_final: 0.8743 (tt) REVERT: C 524 MET cc_start: 0.5536 (pmm) cc_final: 0.5144 (pmm) outliers start: 29 outliers final: 24 residues processed: 149 average time/residue: 0.2443 time to fit residues: 52.7244 Evaluate side-chains 147 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 520 SER 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: 1.9990 chunk 101 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 117 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 86 optimal weight: 0.1980 chunk 84 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12300 Z= 0.191 Angle : 0.474 5.786 16707 Z= 0.249 Chirality : 0.038 0.118 1869 Planarity : 0.003 0.043 2085 Dihedral : 4.314 20.900 1593 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.70 % Allowed : 17.63 % Favored : 80.67 % 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: 0.47 (0.23), residues: 1443 helix: 1.29 (0.18), residues: 957 sheet: -1.23 (0.87), residues: 30 loop : -1.71 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 180 HIS 0.004 0.001 HIS A 161 PHE 0.009 0.001 PHE A 465 TYR 0.014 0.001 TYR A 152 ARG 0.002 0.000 ARG A 146 *********************** 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 142 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 1.494 Fit side-chains REVERT: A 448 MET cc_start: 0.7830 (mtp) cc_final: 0.7596 (mtm) REVERT: B 125 ARG cc_start: 0.8187 (ttm-80) cc_final: 0.7956 (ttm110) REVERT: B 442 LEU cc_start: 0.8930 (tp) cc_final: 0.8725 (tt) REVERT: C 524 MET cc_start: 0.5626 (pmm) cc_final: 0.5230 (pmm) outliers start: 22 outliers final: 19 residues processed: 139 average time/residue: 0.2318 time to fit residues: 46.9456 Evaluate side-chains 138 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 463 ASP Chi-restraints excluded: chain C residue 520 SER 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: 3.9990 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 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 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12300 Z= 0.149 Angle : 0.449 5.822 16707 Z= 0.235 Chirality : 0.037 0.117 1869 Planarity : 0.003 0.043 2085 Dihedral : 4.117 19.875 1593 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.78 % Allowed : 18.10 % Favored : 80.12 % 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: 0.66 (0.23), residues: 1443 helix: 1.45 (0.18), residues: 951 sheet: -1.29 (0.86), residues: 30 loop : -1.62 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 180 HIS 0.004 0.001 HIS C 161 PHE 0.009 0.001 PHE A 465 TYR 0.014 0.001 TYR A 152 ARG 0.002 0.000 ARG A 146 *********************** 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 141 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 1.363 Fit side-chains REVERT: A 448 MET cc_start: 0.7855 (mtp) cc_final: 0.7613 (mtm) REVERT: B 125 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7966 (ttm110) REVERT: B 298 PHE cc_start: 0.8306 (t80) cc_final: 0.8093 (t80) REVERT: C 323 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5890 (tt0) REVERT: C 524 MET cc_start: 0.5588 (pmm) cc_final: 0.5210 (pmm) outliers start: 23 outliers final: 18 residues processed: 138 average time/residue: 0.2376 time to fit residues: 47.6135 Evaluate side-chains 135 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 520 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12300 Z= 0.129 Angle : 0.443 6.804 16707 Z= 0.231 Chirality : 0.037 0.191 1869 Planarity : 0.003 0.044 2085 Dihedral : 4.012 19.263 1593 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.62 % Allowed : 18.25 % Favored : 80.12 % 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: 0.83 (0.23), residues: 1443 helix: 1.68 (0.18), residues: 927 sheet: -1.28 (0.86), residues: 30 loop : -1.61 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 180 HIS 0.004 0.001 HIS C 161 PHE 0.009 0.001 PHE B 469 TYR 0.014 0.001 TYR A 152 ARG 0.002 0.000 ARG A 146 *********************** 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 133 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 1.109 Fit side-chains REVERT: A 224 ASN cc_start: 0.8063 (m110) cc_final: 0.7794 (m-40) REVERT: A 448 MET cc_start: 0.7861 (mtp) cc_final: 0.7583 (mtm) REVERT: B 125 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7969 (ttm110) REVERT: B 298 PHE cc_start: 0.8291 (t80) cc_final: 0.8077 (t80) REVERT: C 323 GLU cc_start: 0.6092 (OUTLIER) cc_final: 0.5881 (tt0) outliers start: 21 outliers final: 16 residues processed: 130 average time/residue: 0.2410 time to fit residues: 44.7880 Evaluate side-chains 125 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 463 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 143 optimal weight: 0.0770 chunk 132 optimal weight: 0.9980 chunk 114 optimal weight: 0.0870 chunk 11 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12300 Z= 0.119 Angle : 0.436 5.956 16707 Z= 0.227 Chirality : 0.036 0.123 1869 Planarity : 0.003 0.044 2085 Dihedral : 3.923 18.575 1593 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.24 % Allowed : 18.79 % Favored : 79.97 % 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: 1.03 (0.23), residues: 1443 helix: 1.79 (0.18), residues: 924 sheet: -1.28 (0.85), residues: 30 loop : -1.41 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 180 HIS 0.004 0.001 HIS C 161 PHE 0.009 0.001 PHE B 469 TYR 0.013 0.001 TYR A 152 ARG 0.002 0.000 ARG A 146 ********************** 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 133 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.419 Fit side-chains REVERT: A 448 MET cc_start: 0.7856 (mtp) cc_final: 0.7584 (mtm) REVERT: B 125 ARG cc_start: 0.8195 (ttm-80) cc_final: 0.7975 (ttm110) REVERT: B 298 PHE cc_start: 0.8216 (t80) cc_final: 0.7972 (t80) outliers start: 16 outliers final: 14 residues processed: 131 average time/residue: 0.2338 time to fit residues: 44.6440 Evaluate side-chains 121 residues out of total 1293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 463 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 100 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN C 161 HIS ** C 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.125544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.102170 restraints weight = 16150.228| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.78 r_work: 0.2889 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12300 Z= 0.140 Angle : 0.446 6.033 16707 Z= 0.233 Chirality : 0.037 0.118 1869 Planarity : 0.003 0.044 2085 Dihedral : 3.957 18.715 1593 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.55 % Allowed : 18.79 % Favored : 79.66 % 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: 1.06 (0.23), residues: 1443 helix: 1.82 (0.18), residues: 924 sheet: -1.31 (0.84), residues: 30 loop : -1.40 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 180 HIS 0.004 0.001 HIS A 161 PHE 0.027 0.001 PHE A 298 TYR 0.013 0.001 TYR A 152 ARG 0.002 0.000 ARG A 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2244.93 seconds wall clock time: 41 minutes 20.73 seconds (2480.73 seconds total)