Starting phenix.real_space_refine on Sat Jul 20 05:12:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7y_18244/07_2024/8q7y_18244.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7y_18244/07_2024/8q7y_18244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7y_18244/07_2024/8q7y_18244.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7y_18244/07_2024/8q7y_18244.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7y_18244/07_2024/8q7y_18244.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7y_18244/07_2024/8q7y_18244.cif" } resolution = 2.6 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= 0.040 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 60 5.16 5 C 6412 2.51 5 N 1824 2.21 5 O 1736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 15": "OD1" <-> "OD2" Residue "A GLU 17": "OE1" <-> "OE2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A ASP 403": "OD1" <-> "OD2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A ASP 569": "OD1" <-> "OD2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "B ASP 403": "OD1" <-> "OD2" Residue "B TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 438": "OE1" <-> "OE2" Residue "B ASP 569": "OD1" <-> "OD2" Residue "C ASP 15": "OD1" <-> "OD2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C ASP 211": "OD1" <-> "OD2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C ASP 403": "OD1" <-> "OD2" Residue "C TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C ASP 569": "OD1" <-> "OD2" Residue "D ASP 15": "OD1" <-> "OD2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ASP 211": "OD1" <-> "OD2" Residue "D GLU 358": "OE1" <-> "OE2" Residue "D ASP 403": "OD1" <-> "OD2" Residue "D TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 438": "OE1" <-> "OE2" Residue "D ASP 569": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10032 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2508 Classifications: {'peptide': 303} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 284} Chain breaks: 11 Chain: "B" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2508 Classifications: {'peptide': 303} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 284} Chain breaks: 11 Chain: "C" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2508 Classifications: {'peptide': 303} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 284} Chain breaks: 11 Chain: "D" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2508 Classifications: {'peptide': 303} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 284} Chain breaks: 11 Time building chain proxies: 6.42, per 1000 atoms: 0.64 Number of scatterers: 10032 At special positions: 0 Unit cell: (126.99, 87.15, 80.51, 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 60 16.00 O 1736 8.00 N 1824 7.00 C 6412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.07 Conformation dependent library (CDL) restraints added in 1.9 seconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 20 sheets defined 34.7% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 192 through 196 removed outlier: 3.549A pdb=" N TYR A 196 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 368 through 382 removed outlier: 3.603A pdb=" N MET A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 406 removed outlier: 3.909A pdb=" N TYR A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 426 removed outlier: 3.942A pdb=" N LEU A 426 " --> pdb=" O MET A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 448 removed outlier: 3.701A pdb=" N ARG A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 479 removed outlier: 3.575A pdb=" N LEU A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 548 through 559 Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.550A pdb=" N TYR B 196 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 368 through 382 removed outlier: 3.602A pdb=" N MET B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 406 removed outlier: 3.909A pdb=" N TYR B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 removed outlier: 3.942A pdb=" N LEU B 426 " --> pdb=" O MET B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 448 removed outlier: 3.701A pdb=" N ARG B 442 " --> pdb=" O GLU B 438 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 479 removed outlier: 3.575A pdb=" N LEU B 471 " --> pdb=" O ASN B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 548 through 559 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 192 through 196 removed outlier: 3.550A pdb=" N TYR C 196 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 368 through 382 removed outlier: 3.603A pdb=" N MET C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 406 removed outlier: 3.908A pdb=" N TYR C 399 " --> pdb=" O HIS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 426 removed outlier: 3.943A pdb=" N LEU C 426 " --> pdb=" O MET C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 448 removed outlier: 3.701A pdb=" N ARG C 442 " --> pdb=" O GLU C 438 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 479 removed outlier: 3.576A pdb=" N LEU C 471 " --> pdb=" O ASN C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 548 through 559 Processing helix chain 'C' and resid 618 through 624 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 192 through 196 removed outlier: 3.549A pdb=" N TYR D 196 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 341 Processing helix chain 'D' and resid 368 through 382 removed outlier: 3.602A pdb=" N MET D 372 " --> pdb=" O ASP D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 406 removed outlier: 3.908A pdb=" N TYR D 399 " --> pdb=" O HIS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 426 removed outlier: 3.943A pdb=" N LEU D 426 " --> pdb=" O MET D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 448 removed outlier: 3.702A pdb=" N ARG D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 479 removed outlier: 3.575A pdb=" N LEU D 471 " --> pdb=" O ASN D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 548 through 559 Processing helix chain 'D' and resid 618 through 624 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 89 removed outlier: 3.796A pdb=" N ILE A 208 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 199 Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 336 Processing sheet with id=AA5, first strand: chain 'A' and resid 351 through 356 removed outlier: 3.647A pdb=" N ALA A 386 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU A 412 " --> pdb=" O CYS A 389 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL A 409 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N SER A 457 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP A 411 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLN A 485 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TRP A 456 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 498 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE A 499 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N CYS A 536 " --> pdb=" O ILE A 499 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU A 533 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N PHE A 566 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU A 535 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AA7, first strand: chain 'B' and resid 88 through 89 removed outlier: 3.794A pdb=" N ILE B 208 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 198 through 199 Processing sheet with id=AA9, first strand: chain 'B' and resid 335 through 336 Processing sheet with id=AB1, first strand: chain 'B' and resid 351 through 356 removed outlier: 3.647A pdb=" N ALA B 386 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU B 412 " --> pdb=" O CYS B 389 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL B 409 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N SER B 457 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASP B 411 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N GLN B 485 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TRP B 456 " --> pdb=" O GLN B 485 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 498 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE B 499 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N CYS B 536 " --> pdb=" O ILE B 499 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU B 533 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N PHE B 566 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU B 535 " --> pdb=" O PHE B 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 23 through 24 Processing sheet with id=AB3, first strand: chain 'C' and resid 88 through 89 removed outlier: 3.795A pdb=" N ILE C 208 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 198 through 199 Processing sheet with id=AB5, first strand: chain 'C' and resid 335 through 336 Processing sheet with id=AB6, first strand: chain 'C' and resid 351 through 356 removed outlier: 3.645A pdb=" N ALA C 386 " --> pdb=" O ARG C 352 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU C 412 " --> pdb=" O CYS C 389 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL C 409 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N SER C 457 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP C 411 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N GLN C 485 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TRP C 456 " --> pdb=" O GLN C 485 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 498 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE C 499 " --> pdb=" O ILE C 534 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N CYS C 536 " --> pdb=" O ILE C 499 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU C 533 " --> pdb=" O GLY C 564 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N PHE C 566 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU C 535 " --> pdb=" O PHE C 566 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 23 through 24 Processing sheet with id=AB8, first strand: chain 'D' and resid 88 through 89 removed outlier: 3.795A pdb=" N ILE D 208 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 198 through 199 Processing sheet with id=AC1, first strand: chain 'D' and resid 335 through 336 Processing sheet with id=AC2, first strand: chain 'D' and resid 351 through 356 removed outlier: 3.646A pdb=" N ALA D 386 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU D 412 " --> pdb=" O CYS D 389 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL D 409 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N SER D 457 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP D 411 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLN D 485 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TRP D 456 " --> pdb=" O GLN D 485 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 498 " --> pdb=" O VAL D 484 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE D 499 " --> pdb=" O ILE D 534 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N CYS D 536 " --> pdb=" O ILE D 499 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU D 533 " --> pdb=" O GLY D 564 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N PHE D 566 " --> pdb=" O LEU D 533 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU D 535 " --> pdb=" O PHE D 566 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 780 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: 2.70 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3279 1.34 - 1.46: 2431 1.46 - 1.58: 4502 1.58 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 10316 Sorted by residual: bond pdb=" CB ARG C 473 " pdb=" CG ARG C 473 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.88e+00 bond pdb=" CB ARG B 473 " pdb=" CG ARG B 473 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.84e+00 bond pdb=" CB ARG A 473 " pdb=" CG ARG A 473 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.78e+00 bond pdb=" CB ARG D 473 " pdb=" CG ARG D 473 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.71e+00 bond pdb=" CD ARG D 473 " pdb=" NE ARG D 473 " ideal model delta sigma weight residual 1.458 1.443 0.015 1.40e-02 5.10e+03 1.09e+00 ... (remaining 10311 not shown) Histogram of bond angle deviations from ideal: 95.14 - 102.93: 113 102.93 - 110.72: 3157 110.72 - 118.51: 4694 118.51 - 126.30: 5652 126.30 - 134.09: 344 Bond angle restraints: 13960 Sorted by residual: angle pdb=" C TYR A 472 " pdb=" N ARG A 473 " pdb=" CA ARG A 473 " ideal model delta sigma weight residual 122.38 113.87 8.51 1.81e+00 3.05e-01 2.21e+01 angle pdb=" C TYR C 472 " pdb=" N ARG C 473 " pdb=" CA ARG C 473 " ideal model delta sigma weight residual 122.38 113.93 8.45 1.81e+00 3.05e-01 2.18e+01 angle pdb=" C TYR B 472 " pdb=" N ARG B 473 " pdb=" CA ARG B 473 " ideal model delta sigma weight residual 122.38 113.96 8.42 1.81e+00 3.05e-01 2.17e+01 angle pdb=" C TYR D 472 " pdb=" N ARG D 473 " pdb=" CA ARG D 473 " ideal model delta sigma weight residual 122.38 113.96 8.42 1.81e+00 3.05e-01 2.16e+01 angle pdb=" N PRO C 480 " pdb=" CD PRO C 480 " pdb=" CG PRO C 480 " ideal model delta sigma weight residual 103.20 96.74 6.46 1.50e+00 4.44e-01 1.85e+01 ... (remaining 13955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4943 17.72 - 35.43: 689 35.43 - 53.15: 246 53.15 - 70.87: 74 70.87 - 88.58: 16 Dihedral angle restraints: 5968 sinusoidal: 2492 harmonic: 3476 Sorted by residual: dihedral pdb=" CA ARG C 473 " pdb=" C ARG C 473 " pdb=" N TRP C 474 " pdb=" CA TRP C 474 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ARG D 473 " pdb=" C ARG D 473 " pdb=" N TRP D 474 " pdb=" CA TRP D 474 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ARG A 473 " pdb=" C ARG A 473 " pdb=" N TRP A 474 " pdb=" CA TRP A 474 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 5965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 781 0.026 - 0.051: 327 0.051 - 0.077: 142 0.077 - 0.103: 106 0.103 - 0.128: 56 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA ILE C 415 " pdb=" N ILE C 415 " pdb=" C ILE C 415 " pdb=" CB ILE C 415 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA ILE B 415 " pdb=" N ILE B 415 " pdb=" C ILE B 415 " pdb=" CB ILE B 415 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE A 415 " pdb=" N ILE A 415 " pdb=" C ILE A 415 " pdb=" CB ILE A 415 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 1409 not shown) Planarity restraints: 1780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 63 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO C 64 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 63 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO D 64 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 64 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 64 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 63 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO A 64 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " -0.018 5.00e-02 4.00e+02 ... (remaining 1777 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 164 2.64 - 3.21: 8427 3.21 - 3.77: 16021 3.77 - 4.34: 23289 4.34 - 4.90: 36076 Nonbonded interactions: 83977 Sorted by model distance: nonbonded pdb=" NH2 ARG C 473 " pdb=" O ASP D 469 " model vdw 2.081 2.520 nonbonded pdb=" O ASP C 469 " pdb=" NH2 ARG D 473 " model vdw 2.085 2.520 nonbonded pdb=" NH2 ARG A 473 " pdb=" O ASP B 469 " model vdw 2.096 2.520 nonbonded pdb=" O ASP A 469 " pdb=" NH2 ARG B 473 " model vdw 2.099 2.520 nonbonded pdb=" OD2 ASP D 368 " pdb=" OG1 THR D 371 " model vdw 2.137 2.440 ... (remaining 83972 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' selection = chain 'D' } 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: 7.580 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.130 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 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 : 0.003 0.066 10316 Z= 0.188 Angle : 0.685 10.959 13960 Z= 0.371 Chirality : 0.044 0.128 1412 Planarity : 0.005 0.033 1780 Dihedral : 19.409 88.583 3712 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.87 % Allowed : 27.64 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % 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: -1.10 (0.23), residues: 1116 helix: 0.19 (0.28), residues: 316 sheet: -0.19 (0.58), residues: 64 loop : -1.26 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 568 HIS 0.003 0.001 HIS C 357 PHE 0.003 0.001 PHE B 566 TYR 0.021 0.001 TYR B 472 ARG 0.007 0.001 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 204 time to evaluate : 1.306 Fit side-chains outliers start: 41 outliers final: 28 residues processed: 236 average time/residue: 1.4626 time to fit residues: 365.8874 Evaluate side-chains 214 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 186 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 500 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.0030 chunk 90 optimal weight: 0.0270 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 overall best weight: 0.6650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN ** B 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN C 381 GLN ** C 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN D 381 GLN ** D 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 10316 Z= 0.242 Angle : 0.664 9.523 13960 Z= 0.344 Chirality : 0.049 0.261 1412 Planarity : 0.006 0.060 1780 Dihedral : 7.194 55.795 1364 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 7.17 % Allowed : 25.94 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -0.81 (0.23), residues: 1116 helix: 0.40 (0.28), residues: 316 sheet: -0.23 (0.58), residues: 64 loop : -1.03 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 553 HIS 0.007 0.001 HIS A 450 PHE 0.005 0.001 PHE A 566 TYR 0.016 0.002 TYR B 559 ARG 0.014 0.001 ARG D 473 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 204 time to evaluate : 1.108 Fit side-chains REVERT: A 365 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.6897 (mt0) REVERT: B 365 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.6893 (mt0) REVERT: B 439 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8503 (mtt-85) REVERT: C 365 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.6902 (mt0) REVERT: C 439 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8500 (mtt-85) REVERT: D 365 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.6908 (mt0) REVERT: D 439 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8499 (mtt-85) REVERT: D 551 LYS cc_start: 0.7207 (mtpp) cc_final: 0.6913 (mttp) outliers start: 76 outliers final: 30 residues processed: 250 average time/residue: 1.4508 time to fit residues: 384.1020 Evaluate side-chains 221 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 184 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 520 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 0.0470 chunk 30 optimal weight: 0.1980 chunk 109 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 97 optimal weight: 0.0670 chunk 108 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN ** B 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN C 381 GLN ** C 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN D 381 GLN ** D 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10316 Z= 0.168 Angle : 0.591 7.915 13960 Z= 0.302 Chirality : 0.045 0.154 1412 Planarity : 0.005 0.045 1780 Dihedral : 5.971 55.291 1340 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.92 % Allowed : 30.66 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % 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: -0.65 (0.23), residues: 1116 helix: 0.62 (0.28), residues: 320 sheet: -0.25 (0.58), residues: 64 loop : -0.96 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 553 HIS 0.004 0.001 HIS A 395 PHE 0.003 0.001 PHE D 150 TYR 0.013 0.001 TYR A 559 ARG 0.007 0.001 ARG B 473 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 196 time to evaluate : 1.113 Fit side-chains REVERT: A 439 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8465 (mtt-85) outliers start: 31 outliers final: 20 residues processed: 215 average time/residue: 1.4423 time to fit residues: 329.1198 Evaluate side-chains 204 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 183 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 476 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 0.0070 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN ** B 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN C 381 GLN ** C 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN ** D 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10316 Z= 0.234 Angle : 0.670 8.219 13960 Z= 0.342 Chirality : 0.048 0.145 1412 Planarity : 0.005 0.044 1780 Dihedral : 5.885 56.010 1332 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 6.51 % Allowed : 26.60 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % 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: -0.68 (0.24), residues: 1116 helix: 0.62 (0.28), residues: 320 sheet: -0.14 (0.59), residues: 64 loop : -1.00 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 553 HIS 0.005 0.001 HIS C 395 PHE 0.005 0.001 PHE C 566 TYR 0.012 0.002 TYR B 559 ARG 0.009 0.001 ARG D 473 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 202 time to evaluate : 1.064 Fit side-chains REVERT: A 17 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.5339 (mt-10) REVERT: A 420 MET cc_start: 0.7503 (mmm) cc_final: 0.6943 (mmm) REVERT: A 439 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8536 (mtt-85) REVERT: B 17 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.5337 (mt-10) REVERT: B 420 MET cc_start: 0.7497 (mmm) cc_final: 0.6949 (mmm) REVERT: C 17 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.5336 (mt-10) REVERT: D 17 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.5349 (mt-10) REVERT: D 420 MET cc_start: 0.7508 (mmm) cc_final: 0.6932 (mmm) REVERT: D 551 LYS cc_start: 0.7253 (mtpp) cc_final: 0.6946 (mttp) outliers start: 69 outliers final: 29 residues processed: 250 average time/residue: 1.3581 time to fit residues: 361.0375 Evaluate side-chains 222 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 188 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 520 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 80 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 0.0000 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 0.0470 overall best weight: 0.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10316 Z= 0.165 Angle : 0.557 5.055 13960 Z= 0.286 Chirality : 0.045 0.126 1412 Planarity : 0.004 0.028 1780 Dihedral : 5.603 55.879 1332 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.66 % Allowed : 28.02 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % 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: -0.57 (0.24), residues: 1116 helix: 0.74 (0.28), residues: 320 sheet: -0.16 (0.58), residues: 64 loop : -0.94 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 553 HIS 0.003 0.001 HIS B 395 PHE 0.003 0.001 PHE D 150 TYR 0.011 0.001 TYR D 559 ARG 0.006 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 190 time to evaluate : 1.141 Fit side-chains REVERT: A 193 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.7132 (t70) REVERT: A 365 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.6858 (mt0) REVERT: A 420 MET cc_start: 0.7491 (mmm) cc_final: 0.6953 (mmm) REVERT: A 439 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8493 (mtt-85) REVERT: B 193 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.7144 (t70) REVERT: B 365 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.6827 (mt0) REVERT: B 420 MET cc_start: 0.7489 (mmm) cc_final: 0.6924 (mmm) REVERT: B 439 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8485 (mtt-85) REVERT: C 193 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7212 (t70) REVERT: C 365 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6842 (mt0) REVERT: C 439 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8481 (mtt-85) REVERT: D 365 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.6834 (mt0) REVERT: D 420 MET cc_start: 0.7513 (mmm) cc_final: 0.6945 (mmm) REVERT: D 439 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8474 (mtt-85) outliers start: 60 outliers final: 20 residues processed: 236 average time/residue: 1.4688 time to fit residues: 367.1264 Evaluate side-chains 205 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 174 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 423 MET Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 476 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 1.9990 chunk 104 optimal weight: 0.0270 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 116 optimal weight: 0.0870 chunk 96 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10316 Z= 0.204 Angle : 0.592 6.020 13960 Z= 0.304 Chirality : 0.046 0.137 1412 Planarity : 0.004 0.031 1780 Dihedral : 5.631 54.346 1332 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 4.91 % Allowed : 28.77 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % 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: -0.63 (0.24), residues: 1116 helix: 0.72 (0.28), residues: 320 sheet: -0.16 (0.58), residues: 64 loop : -1.00 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 553 HIS 0.004 0.001 HIS B 395 PHE 0.005 0.001 PHE D 566 TYR 0.010 0.001 TYR A 559 ARG 0.003 0.000 ARG D 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 181 time to evaluate : 1.139 Fit side-chains REVERT: A 193 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7204 (t70) REVERT: A 365 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6880 (mt0) REVERT: A 420 MET cc_start: 0.7546 (mmm) cc_final: 0.6937 (mmm) REVERT: A 439 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8528 (mtt-85) REVERT: B 365 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.6889 (mt0) REVERT: B 420 MET cc_start: 0.7540 (mmm) cc_final: 0.6935 (mmm) REVERT: B 439 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8517 (mtt-85) REVERT: C 193 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7228 (t70) REVERT: C 365 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.6891 (mt0) REVERT: C 439 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8520 (mtt-85) REVERT: D 365 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.6884 (mt0) REVERT: D 439 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8512 (mtt-85) outliers start: 52 outliers final: 24 residues processed: 218 average time/residue: 1.5458 time to fit residues: 355.8776 Evaluate side-chains 210 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 176 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 520 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 HIS ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN B 391 HIS ** B 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** C 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 HIS ** D 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 10316 Z= 0.438 Angle : 0.789 7.164 13960 Z= 0.408 Chirality : 0.054 0.187 1412 Planarity : 0.006 0.040 1780 Dihedral : 5.780 54.140 1324 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 5.38 % Allowed : 28.58 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % 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: -0.98 (0.23), residues: 1116 helix: 0.06 (0.26), residues: 320 sheet: -0.22 (0.55), residues: 64 loop : -1.04 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP D 90 HIS 0.008 0.002 HIS B 395 PHE 0.012 0.002 PHE A 566 TYR 0.015 0.003 TYR B 486 ARG 0.004 0.001 ARG C 561 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 192 time to evaluate : 1.031 Fit side-chains REVERT: A 17 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.5389 (mt-10) REVERT: A 365 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7256 (mt0) REVERT: A 439 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8586 (mtt-85) REVERT: B 17 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.5382 (mt-10) REVERT: B 365 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7255 (mt0) REVERT: B 439 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8587 (mtt-85) REVERT: C 17 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.5390 (mt-10) REVERT: C 193 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7364 (t70) REVERT: C 365 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7258 (mt0) REVERT: C 439 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8583 (mtt-85) REVERT: C 551 LYS cc_start: 0.7327 (mtpp) cc_final: 0.7010 (mttp) REVERT: D 17 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.5396 (mt-10) REVERT: D 365 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7264 (mt0) REVERT: D 439 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8568 (mtt-85) REVERT: D 551 LYS cc_start: 0.7290 (mtpp) cc_final: 0.6972 (mttp) outliers start: 57 outliers final: 28 residues processed: 227 average time/residue: 1.5808 time to fit residues: 378.4397 Evaluate side-chains 225 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 184 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 428 ASP Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 520 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 90 optimal weight: 0.2980 chunk 105 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10316 Z= 0.225 Angle : 0.623 5.907 13960 Z= 0.321 Chirality : 0.047 0.132 1412 Planarity : 0.005 0.035 1780 Dihedral : 5.306 54.549 1324 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 6.23 % Allowed : 28.02 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.24), residues: 1116 helix: 0.45 (0.27), residues: 320 sheet: -0.21 (0.56), residues: 64 loop : -1.04 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 553 HIS 0.004 0.001 HIS C 395 PHE 0.006 0.001 PHE A 566 TYR 0.009 0.002 TYR D 559 ARG 0.004 0.000 ARG D 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 183 time to evaluate : 1.241 Fit side-chains REVERT: A 193 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7280 (t70) REVERT: A 365 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7046 (mt0) REVERT: A 439 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8555 (mtt-85) REVERT: B 365 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7096 (mt0) REVERT: B 420 MET cc_start: 0.7397 (mmm) cc_final: 0.6811 (mmm) REVERT: B 439 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8556 (mtt-85) REVERT: C 193 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7294 (t70) REVERT: C 365 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7095 (mt0) REVERT: C 439 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8554 (mtt-85) REVERT: D 365 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7039 (mt0) REVERT: D 439 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8544 (mtt-85) REVERT: D 551 LYS cc_start: 0.7315 (mtpp) cc_final: 0.7000 (mttp) outliers start: 66 outliers final: 25 residues processed: 232 average time/residue: 1.5608 time to fit residues: 382.6825 Evaluate side-chains 217 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 182 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 520 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10316 Z= 0.262 Angle : 0.656 5.955 13960 Z= 0.338 Chirality : 0.048 0.149 1412 Planarity : 0.005 0.035 1780 Dihedral : 5.419 53.394 1324 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 5.47 % Allowed : 28.21 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % 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: 1116 helix: 0.42 (0.27), residues: 320 sheet: -0.24 (0.55), residues: 64 loop : -1.07 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 90 HIS 0.005 0.001 HIS B 395 PHE 0.008 0.001 PHE A 566 TYR 0.011 0.002 TYR B 486 ARG 0.004 0.001 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 179 time to evaluate : 1.170 Fit side-chains REVERT: A 17 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.5379 (mt-10) REVERT: A 193 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7273 (t70) REVERT: A 365 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7114 (mt0) REVERT: A 439 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8552 (mtt-85) REVERT: A 537 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8102 (mt-10) REVERT: B 365 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7151 (mt0) REVERT: B 420 MET cc_start: 0.7361 (mmm) cc_final: 0.6767 (mmm) REVERT: B 439 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8541 (mtt-85) REVERT: B 537 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8107 (mt-10) REVERT: C 365 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7143 (mt0) REVERT: C 439 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8543 (mtt-85) REVERT: C 537 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8064 (mt-10) REVERT: C 551 LYS cc_start: 0.7278 (mtpp) cc_final: 0.6996 (mtmm) REVERT: D 365 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7141 (mt0) REVERT: D 439 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8535 (mtt-85) REVERT: D 537 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8111 (mt-10) outliers start: 58 outliers final: 27 residues processed: 219 average time/residue: 1.5545 time to fit residues: 359.3987 Evaluate side-chains 222 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 181 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 GLU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 537 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10316 Z= 0.261 Angle : 0.661 5.720 13960 Z= 0.341 Chirality : 0.048 0.146 1412 Planarity : 0.005 0.035 1780 Dihedral : 5.428 53.696 1324 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 4.25 % Allowed : 29.34 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % 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: -0.85 (0.23), residues: 1116 helix: 0.37 (0.27), residues: 320 sheet: -0.20 (0.55), residues: 64 loop : -1.07 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 90 HIS 0.005 0.001 HIS C 395 PHE 0.007 0.001 PHE A 566 TYR 0.011 0.002 TYR B 486 ARG 0.004 0.001 ARG B 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 181 time to evaluate : 1.202 Fit side-chains REVERT: A 17 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.5373 (mt-10) REVERT: A 193 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7293 (t70) REVERT: A 365 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7093 (mt0) REVERT: A 439 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8550 (mtt-85) REVERT: A 537 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: B 17 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.5364 (mt-10) REVERT: B 365 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7092 (mt0) REVERT: B 439 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8545 (mtt-85) REVERT: B 537 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8103 (mt-10) REVERT: C 17 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.5364 (mt-10) REVERT: C 193 ASP cc_start: 0.7694 (t70) cc_final: 0.7327 (t70) REVERT: C 365 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7102 (mt0) REVERT: C 439 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8548 (mtt-85) REVERT: D 17 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.5362 (mt-10) REVERT: D 365 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7130 (mt0) REVERT: D 439 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8542 (mtt-85) REVERT: D 537 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8102 (mt-10) REVERT: D 551 LYS cc_start: 0.7277 (mtpp) cc_final: 0.6986 (mtmm) outliers start: 45 outliers final: 27 residues processed: 210 average time/residue: 1.5941 time to fit residues: 353.4774 Evaluate side-chains 228 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 185 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 365 GLN Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 537 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.208816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.187278 restraints weight = 8372.072| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.16 r_work: 0.3610 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10316 Z= 0.275 Angle : 0.672 5.733 13960 Z= 0.347 Chirality : 0.049 0.150 1412 Planarity : 0.005 0.036 1780 Dihedral : 5.474 53.481 1324 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 5.09 % Allowed : 28.49 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.23), residues: 1116 helix: 0.27 (0.27), residues: 320 sheet: -0.18 (0.55), residues: 64 loop : -1.08 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 90 HIS 0.005 0.001 HIS A 395 PHE 0.007 0.001 PHE B 209 TYR 0.012 0.002 TYR D 486 ARG 0.004 0.001 ARG A 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5553.32 seconds wall clock time: 97 minutes 32.78 seconds (5852.78 seconds total)