Starting phenix.real_space_refine on Sat Jul 20 16:49:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy1_33507/07_2024/7xy1_33507.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy1_33507/07_2024/7xy1_33507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy1_33507/07_2024/7xy1_33507.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy1_33507/07_2024/7xy1_33507.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy1_33507/07_2024/7xy1_33507.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy1_33507/07_2024/7xy1_33507.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 48 5.16 5 C 7143 2.51 5 N 2076 2.21 5 O 2283 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 582": "OE1" <-> "OE2" Residue "A GLU 727": "OE1" <-> "OE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 582": "OE1" <-> "OE2" Residue "B GLU 727": "OE1" <-> "OE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 582": "OE1" <-> "OE2" Residue "C GLU 727": "OE1" <-> "OE2" 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: 11550 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3850 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 16, 'TRANS': 495} Chain: "B" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3850 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 16, 'TRANS': 495} Chain: "C" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3850 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 16, 'TRANS': 495} Time building chain proxies: 6.95, per 1000 atoms: 0.60 Number of scatterers: 11550 At special positions: 0 Unit cell: (83.7876, 80.565, 150.388, 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 48 16.00 O 2283 8.00 N 2076 7.00 C 7143 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: 4.78 Conformation dependent library (CDL) restraints added in 2.4 seconds 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2730 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 27 sheets defined 9.0% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 283 through 292 removed outlier: 3.515A pdb=" N LEU A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 301 Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 319 through 329 removed outlier: 4.064A pdb=" N GLY A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 removed outlier: 4.217A pdb=" N PHE A 370 " --> pdb=" O ASP A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 283 through 292 removed outlier: 3.515A pdb=" N LEU B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 302 through 312 Processing helix chain 'B' and resid 319 through 329 removed outlier: 4.064A pdb=" N GLY B 329 " --> pdb=" O ALA B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 removed outlier: 4.217A pdb=" N PHE B 370 " --> pdb=" O ASP B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 276 Processing helix chain 'C' and resid 283 through 292 removed outlier: 3.515A pdb=" N LEU C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 301 Processing helix chain 'C' and resid 302 through 312 Processing helix chain 'C' and resid 319 through 329 removed outlier: 4.064A pdb=" N GLY C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 370 removed outlier: 4.217A pdb=" N PHE C 370 " --> pdb=" O ASP C 367 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 295 through 296 removed outlier: 6.594A pdb=" N VAL A 295 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE A 333 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 353 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ALA A 395 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N CYS A 425 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 398 " --> pdb=" O GLY A 426 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N TYR A 428 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE A 400 " --> pdb=" O TYR A 428 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE A 377 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 295 through 296 removed outlier: 6.594A pdb=" N VAL A 295 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE A 333 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 353 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ALA A 395 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N CYS A 425 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N GLY A 421 " --> pdb=" O PHE A 445 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N PHE A 447 " --> pdb=" O GLY A 421 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N PHE A 423 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASN A 449 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N CYS A 425 " --> pdb=" O ASN A 449 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ASN A 451 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE A 427 " --> pdb=" O ASN A 451 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 346 removed outlier: 6.732A pdb=" N VAL A 345 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLN A 411 " --> pdb=" O PHE A 387 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 457 through 458 removed outlier: 5.575A pdb=" N ILE A 457 " --> pdb=" O MET A 479 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE A 555 " --> pdb=" O ARG A 590 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ALA A 592 " --> pdb=" O ILE A 555 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N PHE A 557 " --> pdb=" O ALA A 592 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 464 through 465 removed outlier: 6.176A pdb=" N LEU A 562 " --> pdb=" O GLU A 600 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N SER A 602 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N MET A 564 " --> pdb=" O SER A 602 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA7, first strand: chain 'A' and resid 640 through 643 Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.559A pdb=" N ASP A 682 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N GLY A 697 " --> pdb=" O SER A 720 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N SER A 720 " --> pdb=" O GLY A 697 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE A 699 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL A 718 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR A 701 " --> pdb=" O VAL A 716 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 664 through 669 Processing sheet with id=AB1, first strand: chain 'B' and resid 295 through 296 removed outlier: 6.595A pdb=" N VAL B 295 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE B 333 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B 353 " --> pdb=" O GLU B 396 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ALA B 395 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N CYS B 425 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL B 398 " --> pdb=" O GLY B 426 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N TYR B 428 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE B 400 " --> pdb=" O TYR B 428 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE B 377 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 295 through 296 removed outlier: 6.595A pdb=" N VAL B 295 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE B 333 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B 353 " --> pdb=" O GLU B 396 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ALA B 395 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N CYS B 425 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N GLY B 421 " --> pdb=" O PHE B 445 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N PHE B 447 " --> pdb=" O GLY B 421 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N PHE B 423 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASN B 449 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N CYS B 425 " --> pdb=" O ASN B 449 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ASN B 451 " --> pdb=" O CYS B 425 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE B 427 " --> pdb=" O ASN B 451 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.732A pdb=" N VAL B 345 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLN B 411 " --> pdb=" O PHE B 387 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 457 through 458 removed outlier: 5.575A pdb=" N ILE B 457 " --> pdb=" O MET B 479 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE B 555 " --> pdb=" O ARG B 590 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ALA B 592 " --> pdb=" O ILE B 555 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N PHE B 557 " --> pdb=" O ALA B 592 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 464 through 465 removed outlier: 6.176A pdb=" N LEU B 562 " --> pdb=" O GLU B 600 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N SER B 602 " --> pdb=" O LEU B 562 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N MET B 564 " --> pdb=" O SER B 602 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 538 through 539 Processing sheet with id=AB7, first strand: chain 'B' and resid 640 through 643 Processing sheet with id=AB8, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.559A pdb=" N ASP B 682 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N GLY B 697 " --> pdb=" O SER B 720 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N SER B 720 " --> pdb=" O GLY B 697 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE B 699 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL B 718 " --> pdb=" O ILE B 699 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR B 701 " --> pdb=" O VAL B 716 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 664 through 669 Processing sheet with id=AC1, first strand: chain 'C' and resid 295 through 296 removed outlier: 6.594A pdb=" N VAL C 295 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE C 333 " --> pdb=" O PHE C 354 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU C 353 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ALA C 395 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N CYS C 425 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL C 398 " --> pdb=" O GLY C 426 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N TYR C 428 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE C 400 " --> pdb=" O TYR C 428 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE C 377 " --> pdb=" O ASP C 401 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 295 through 296 removed outlier: 6.594A pdb=" N VAL C 295 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE C 333 " --> pdb=" O PHE C 354 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU C 353 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ALA C 395 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N CYS C 425 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N GLY C 421 " --> pdb=" O PHE C 445 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N PHE C 447 " --> pdb=" O GLY C 421 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N PHE C 423 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ASN C 449 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N CYS C 425 " --> pdb=" O ASN C 449 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ASN C 451 " --> pdb=" O CYS C 425 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE C 427 " --> pdb=" O ASN C 451 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.733A pdb=" N VAL C 345 " --> pdb=" O LEU C 388 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLN C 411 " --> pdb=" O PHE C 387 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 457 through 458 removed outlier: 5.575A pdb=" N ILE C 457 " --> pdb=" O MET C 479 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 555 " --> pdb=" O ARG C 590 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ALA C 592 " --> pdb=" O ILE C 555 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N PHE C 557 " --> pdb=" O ALA C 592 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 464 through 465 removed outlier: 6.177A pdb=" N LEU C 562 " --> pdb=" O GLU C 600 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N SER C 602 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N MET C 564 " --> pdb=" O SER C 602 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 538 through 539 Processing sheet with id=AC7, first strand: chain 'C' and resid 640 through 643 Processing sheet with id=AC8, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.559A pdb=" N ASP C 682 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N GLY C 697 " --> pdb=" O SER C 720 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N SER C 720 " --> pdb=" O GLY C 697 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE C 699 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL C 718 " --> pdb=" O ILE C 699 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR C 701 " --> pdb=" O VAL C 716 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 664 through 669 264 hydrogen bonds defined for protein. 702 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: 4.51 Time building geometry restraints manager: 5.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1992 1.32 - 1.44: 3269 1.44 - 1.56: 6427 1.56 - 1.68: 3 1.68 - 1.81: 72 Bond restraints: 11763 Sorted by residual: bond pdb=" CA CYS C 468 " pdb=" C CYS C 468 " ideal model delta sigma weight residual 1.527 1.477 0.050 1.35e-02 5.49e+03 1.36e+01 bond pdb=" CA CYS A 468 " pdb=" C CYS A 468 " ideal model delta sigma weight residual 1.527 1.477 0.050 1.35e-02 5.49e+03 1.36e+01 bond pdb=" CA CYS B 468 " pdb=" C CYS B 468 " ideal model delta sigma weight residual 1.527 1.477 0.050 1.35e-02 5.49e+03 1.36e+01 bond pdb=" CA SER A 530 " pdb=" C SER A 530 " ideal model delta sigma weight residual 1.521 1.479 0.043 1.19e-02 7.06e+03 1.29e+01 bond pdb=" CA SER C 530 " pdb=" C SER C 530 " ideal model delta sigma weight residual 1.521 1.479 0.043 1.19e-02 7.06e+03 1.29e+01 ... (remaining 11758 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.54: 258 106.54 - 113.39: 6202 113.39 - 120.24: 3984 120.24 - 127.09: 5431 127.09 - 133.94: 76 Bond angle restraints: 15951 Sorted by residual: angle pdb=" N HIS B 476 " pdb=" CA HIS B 476 " pdb=" C HIS B 476 " ideal model delta sigma weight residual 111.28 122.48 -11.20 1.09e+00 8.42e-01 1.06e+02 angle pdb=" N HIS C 476 " pdb=" CA HIS C 476 " pdb=" C HIS C 476 " ideal model delta sigma weight residual 111.28 122.48 -11.20 1.09e+00 8.42e-01 1.06e+02 angle pdb=" N HIS A 476 " pdb=" CA HIS A 476 " pdb=" C HIS A 476 " ideal model delta sigma weight residual 111.28 122.47 -11.19 1.09e+00 8.42e-01 1.05e+02 angle pdb=" N SER B 486 " pdb=" CA SER B 486 " pdb=" CB SER B 486 " ideal model delta sigma weight residual 110.49 117.65 -7.16 1.69e+00 3.50e-01 1.80e+01 angle pdb=" N SER A 486 " pdb=" CA SER A 486 " pdb=" CB SER A 486 " ideal model delta sigma weight residual 110.49 117.60 -7.11 1.69e+00 3.50e-01 1.77e+01 ... (remaining 15946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 6255 16.83 - 33.66: 534 33.66 - 50.49: 105 50.49 - 67.31: 9 67.31 - 84.14: 9 Dihedral angle restraints: 6912 sinusoidal: 2595 harmonic: 4317 Sorted by residual: dihedral pdb=" N VAL A 661 " pdb=" C VAL A 661 " pdb=" CA VAL A 661 " pdb=" CB VAL A 661 " ideal model delta harmonic sigma weight residual 123.40 135.83 -12.43 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" N VAL B 661 " pdb=" C VAL B 661 " pdb=" CA VAL B 661 " pdb=" CB VAL B 661 " ideal model delta harmonic sigma weight residual 123.40 135.83 -12.43 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" N VAL C 661 " pdb=" C VAL C 661 " pdb=" CA VAL C 661 " pdb=" CB VAL C 661 " ideal model delta harmonic sigma weight residual 123.40 135.78 -12.38 0 2.50e+00 1.60e-01 2.45e+01 ... (remaining 6909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1568 0.093 - 0.186: 169 0.186 - 0.279: 18 0.279 - 0.373: 4 0.373 - 0.466: 8 Chirality restraints: 1767 Sorted by residual: chirality pdb=" CB VAL B 661 " pdb=" CA VAL B 661 " pdb=" CG1 VAL B 661 " pdb=" CG2 VAL B 661 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" CB VAL C 661 " pdb=" CA VAL C 661 " pdb=" CG1 VAL C 661 " pdb=" CG2 VAL C 661 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CB VAL A 661 " pdb=" CA VAL A 661 " pdb=" CG1 VAL A 661 " pdb=" CG2 VAL A 661 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.34e+00 ... (remaining 1764 not shown) Planarity restraints: 2130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 483 " -0.016 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C GLY B 483 " 0.058 2.00e-02 2.50e+03 pdb=" O GLY B 483 " -0.022 2.00e-02 2.50e+03 pdb=" N ALA B 484 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 483 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C GLY A 483 " 0.058 2.00e-02 2.50e+03 pdb=" O GLY A 483 " -0.022 2.00e-02 2.50e+03 pdb=" N ALA A 484 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 483 " -0.016 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C GLY C 483 " 0.057 2.00e-02 2.50e+03 pdb=" O GLY C 483 " -0.022 2.00e-02 2.50e+03 pdb=" N ALA C 484 " -0.019 2.00e-02 2.50e+03 ... (remaining 2127 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 192 2.61 - 3.18: 10258 3.18 - 3.75: 17520 3.75 - 4.33: 25883 4.33 - 4.90: 44207 Nonbonded interactions: 98060 Sorted by model distance: nonbonded pdb=" O SER A 509 " pdb=" CG1 ILE A 510 " model vdw 2.035 3.440 nonbonded pdb=" O SER C 509 " pdb=" CG1 ILE C 510 " model vdw 2.035 3.440 nonbonded pdb=" O SER B 509 " pdb=" CG1 ILE B 510 " model vdw 2.036 3.440 nonbonded pdb=" OG1 THR C 278 " pdb=" O LEU C 282 " model vdw 2.222 2.440 nonbonded pdb=" OG1 THR A 278 " pdb=" O LEU A 282 " model vdw 2.222 2.440 ... (remaining 98055 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.140 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.005 0.052 11763 Z= 0.308 Angle : 0.760 11.198 15951 Z= 0.453 Chirality : 0.063 0.466 1767 Planarity : 0.006 0.058 2130 Dihedral : 13.221 84.141 4182 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.59 % Allowed : 8.43 % Favored : 90.98 % Rotamer: Outliers : 0.97 % Allowed : 0.32 % Favored : 98.71 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.21), residues: 1530 helix: -0.25 (0.48), residues: 105 sheet: -0.65 (0.25), residues: 546 loop : -2.26 (0.18), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 496 HIS 0.009 0.003 HIS B 476 PHE 0.013 0.001 PHE A 521 TYR 0.012 0.001 TYR C 458 ARG 0.003 0.000 ARG B 619 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 1.240 Fit side-chains REVERT: A 670 CYS cc_start: 0.8277 (t) cc_final: 0.8021 (t) REVERT: A 736 ASP cc_start: 0.7251 (t0) cc_final: 0.7034 (t0) REVERT: B 600 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7555 (mt-10) REVERT: B 670 CYS cc_start: 0.8251 (t) cc_final: 0.8039 (t) outliers start: 12 outliers final: 6 residues processed: 126 average time/residue: 0.1667 time to fit residues: 34.2586 Evaluate side-chains 90 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 508 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 chunk 72 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN A 471 ASN B 385 ASN B 471 ASN B 636 ASN C 385 ASN C 471 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 11763 Z= 0.546 Angle : 0.744 7.473 15951 Z= 0.407 Chirality : 0.054 0.299 1767 Planarity : 0.006 0.072 2130 Dihedral : 6.127 39.144 1689 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.59 % Allowed : 10.20 % Favored : 89.22 % Rotamer: Outliers : 1.70 % Allowed : 9.47 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.21), residues: 1530 helix: -0.99 (0.46), residues: 105 sheet: -1.14 (0.25), residues: 507 loop : -2.27 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 502 HIS 0.008 0.002 HIS B 476 PHE 0.020 0.002 PHE A 447 TYR 0.017 0.002 TYR B 587 ARG 0.004 0.001 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 1.312 Fit side-chains REVERT: A 385 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8373 (m110) REVERT: A 479 MET cc_start: 0.8111 (ttt) cc_final: 0.7911 (ttt) REVERT: A 670 CYS cc_start: 0.8118 (t) cc_final: 0.7806 (t) REVERT: B 479 MET cc_start: 0.8194 (ttt) cc_final: 0.7960 (ttt) REVERT: C 385 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8198 (m110) REVERT: C 479 MET cc_start: 0.7940 (ttt) cc_final: 0.7710 (ttt) REVERT: C 498 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: C 770 ARG cc_start: 0.7883 (ttt-90) cc_final: 0.7658 (tmt170) outliers start: 21 outliers final: 12 residues processed: 92 average time/residue: 0.2025 time to fit residues: 29.0668 Evaluate side-chains 85 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 385 ASN Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 680 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN A 471 ASN C 385 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11763 Z= 0.242 Angle : 0.583 6.847 15951 Z= 0.316 Chirality : 0.048 0.221 1767 Planarity : 0.005 0.070 2130 Dihedral : 5.443 28.353 1689 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.54 % Favored : 90.07 % Rotamer: Outliers : 2.59 % Allowed : 10.44 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.20), residues: 1530 helix: -1.13 (0.43), residues: 108 sheet: -0.57 (0.25), residues: 489 loop : -2.45 (0.18), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 502 HIS 0.004 0.001 HIS C 476 PHE 0.010 0.001 PHE A 447 TYR 0.021 0.001 TYR B 362 ARG 0.002 0.000 ARG A 772 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 80 time to evaluate : 1.202 Fit side-chains REVERT: A 670 CYS cc_start: 0.8146 (t) cc_final: 0.7858 (t) REVERT: B 479 MET cc_start: 0.8052 (ttt) cc_final: 0.7841 (ttt) REVERT: C 600 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7779 (mt-10) outliers start: 32 outliers final: 17 residues processed: 106 average time/residue: 0.1693 time to fit residues: 29.4803 Evaluate side-chains 83 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 670 CYS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 680 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 39 optimal weight: 20.0000 chunk 123 optimal weight: 0.0570 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN A 471 ASN B 471 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 ASN C 473 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11763 Z= 0.255 Angle : 0.575 8.015 15951 Z= 0.309 Chirality : 0.048 0.291 1767 Planarity : 0.005 0.064 2130 Dihedral : 5.263 24.656 1689 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.52 % Favored : 89.22 % Rotamer: Outliers : 2.27 % Allowed : 11.08 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.20), residues: 1530 helix: -1.10 (0.44), residues: 108 sheet: -0.55 (0.25), residues: 486 loop : -2.46 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 502 HIS 0.004 0.001 HIS A 476 PHE 0.010 0.001 PHE A 447 TYR 0.017 0.001 TYR B 362 ARG 0.002 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 82 time to evaluate : 1.283 Fit side-chains REVERT: A 670 CYS cc_start: 0.8125 (t) cc_final: 0.7846 (t) REVERT: B 479 MET cc_start: 0.8155 (ttt) cc_final: 0.7951 (ttt) REVERT: C 498 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: C 725 VAL cc_start: 0.8912 (m) cc_final: 0.8706 (m) outliers start: 28 outliers final: 22 residues processed: 101 average time/residue: 0.1632 time to fit residues: 27.6047 Evaluate side-chains 94 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 71 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 670 CYS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 680 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 ASN B 471 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11763 Z= 0.236 Angle : 0.555 6.558 15951 Z= 0.300 Chirality : 0.047 0.231 1767 Planarity : 0.005 0.064 2130 Dihedral : 5.121 23.993 1687 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.13 % Favored : 89.67 % Rotamer: Outliers : 2.99 % Allowed : 12.30 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.20), residues: 1530 helix: -1.08 (0.44), residues: 108 sheet: -0.54 (0.25), residues: 483 loop : -2.43 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 502 HIS 0.003 0.001 HIS C 476 PHE 0.009 0.001 PHE A 447 TYR 0.012 0.001 TYR B 587 ARG 0.001 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 81 time to evaluate : 1.410 Fit side-chains REVERT: A 670 CYS cc_start: 0.8079 (t) cc_final: 0.7807 (t) REVERT: A 725 VAL cc_start: 0.8923 (m) cc_final: 0.8704 (m) REVERT: C 498 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: C 564 MET cc_start: 0.8318 (mtt) cc_final: 0.8027 (mtt) REVERT: C 725 VAL cc_start: 0.8903 (m) cc_final: 0.8695 (m) outliers start: 37 outliers final: 26 residues processed: 112 average time/residue: 0.1707 time to fit residues: 32.0096 Evaluate side-chains 103 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 76 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 670 CYS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 680 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 0.0770 chunk 29 optimal weight: 0.0770 chunk 86 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 ASN B 471 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11763 Z= 0.214 Angle : 0.541 7.159 15951 Z= 0.292 Chirality : 0.046 0.193 1767 Planarity : 0.005 0.061 2130 Dihedral : 5.049 23.576 1686 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.54 % Favored : 90.26 % Rotamer: Outliers : 3.16 % Allowed : 12.78 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.20), residues: 1530 helix: -0.99 (0.44), residues: 108 sheet: -0.51 (0.24), residues: 495 loop : -2.40 (0.18), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 502 HIS 0.003 0.001 HIS A 476 PHE 0.009 0.001 PHE A 447 TYR 0.012 0.001 TYR B 587 ARG 0.001 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 87 time to evaluate : 1.442 Fit side-chains REVERT: A 670 CYS cc_start: 0.7981 (t) cc_final: 0.7721 (t) REVERT: A 725 VAL cc_start: 0.8940 (m) cc_final: 0.8717 (m) REVERT: C 498 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: C 725 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8678 (m) outliers start: 39 outliers final: 28 residues processed: 119 average time/residue: 0.1619 time to fit residues: 32.5940 Evaluate side-chains 110 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 80 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 670 CYS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 725 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN A 471 ASN B 471 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11763 Z= 0.183 Angle : 0.532 6.330 15951 Z= 0.288 Chirality : 0.046 0.221 1767 Planarity : 0.004 0.060 2130 Dihedral : 4.908 22.558 1686 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.67 % Favored : 90.13 % Rotamer: Outliers : 2.67 % Allowed : 13.03 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.21), residues: 1530 helix: -0.84 (0.45), residues: 108 sheet: -0.45 (0.24), residues: 495 loop : -2.35 (0.18), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 502 HIS 0.003 0.001 HIS C 465 PHE 0.012 0.001 PHE C 387 TYR 0.011 0.001 TYR B 587 ARG 0.001 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 89 time to evaluate : 1.341 Fit side-chains REVERT: A 670 CYS cc_start: 0.7971 (t) cc_final: 0.7697 (t) REVERT: A 725 VAL cc_start: 0.8928 (m) cc_final: 0.8696 (m) REVERT: C 498 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: C 600 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7709 (mt-10) REVERT: C 725 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8657 (m) outliers start: 33 outliers final: 28 residues processed: 114 average time/residue: 0.1670 time to fit residues: 32.0202 Evaluate side-chains 114 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 84 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 670 CYS Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 725 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 44 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN A 471 ASN B 471 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11763 Z= 0.177 Angle : 0.525 6.128 15951 Z= 0.284 Chirality : 0.046 0.197 1767 Planarity : 0.004 0.058 2130 Dihedral : 4.845 21.946 1686 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.41 % Favored : 90.39 % Rotamer: Outliers : 2.83 % Allowed : 13.59 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.21), residues: 1530 helix: -0.76 (0.46), residues: 108 sheet: -0.48 (0.24), residues: 495 loop : -2.32 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 502 HIS 0.003 0.001 HIS A 476 PHE 0.014 0.001 PHE C 387 TYR 0.011 0.001 TYR C 587 ARG 0.001 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 88 time to evaluate : 1.342 Fit side-chains REVERT: A 725 VAL cc_start: 0.8916 (m) cc_final: 0.8676 (m) REVERT: B 471 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.8072 (m-40) REVERT: C 498 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: C 600 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7712 (mt-10) REVERT: C 725 VAL cc_start: 0.8863 (OUTLIER) cc_final: 0.8644 (m) outliers start: 35 outliers final: 28 residues processed: 114 average time/residue: 0.1697 time to fit residues: 32.0997 Evaluate side-chains 118 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 87 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 670 CYS Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 725 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 2.9990 chunk 137 optimal weight: 0.0000 chunk 141 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 42 optimal weight: 0.0870 chunk 124 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN A 471 ASN B 471 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11763 Z= 0.139 Angle : 0.513 6.185 15951 Z= 0.275 Chirality : 0.045 0.182 1767 Planarity : 0.004 0.058 2130 Dihedral : 4.672 20.512 1686 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.22 % Favored : 90.59 % Rotamer: Outliers : 2.27 % Allowed : 14.08 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.21), residues: 1530 helix: -0.69 (0.47), residues: 108 sheet: -0.43 (0.25), residues: 492 loop : -2.28 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 502 HIS 0.003 0.001 HIS B 465 PHE 0.013 0.001 PHE C 387 TYR 0.010 0.001 TYR A 587 ARG 0.003 0.000 ARG C 437 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 101 time to evaluate : 1.357 Fit side-chains REVERT: A 725 VAL cc_start: 0.8897 (m) cc_final: 0.8656 (m) REVERT: A 769 TYR cc_start: 0.6909 (m-80) cc_final: 0.6637 (m-80) REVERT: C 318 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8422 (p0) REVERT: C 600 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7632 (mt-10) REVERT: C 725 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8641 (m) outliers start: 28 outliers final: 22 residues processed: 124 average time/residue: 0.1600 time to fit residues: 33.0192 Evaluate side-chains 114 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 471 ASN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 318 ASN Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 725 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 101 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 140 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 12 optimal weight: 0.4980 chunk 93 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN A 471 ASN ** A 695 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 11763 Z= 0.257 Angle : 0.813 59.190 15951 Z= 0.475 Chirality : 0.047 0.307 1767 Planarity : 0.005 0.102 2130 Dihedral : 4.736 30.969 1686 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.22 % Favored : 90.59 % Rotamer: Outliers : 1.86 % Allowed : 14.32 % Favored : 83.82 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.21), residues: 1530 helix: -0.68 (0.47), residues: 108 sheet: -0.42 (0.25), residues: 492 loop : -2.28 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 502 HIS 0.003 0.001 HIS A 476 PHE 0.011 0.001 PHE C 387 TYR 0.010 0.001 TYR A 587 ARG 0.004 0.000 ARG C 437 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 1.389 Fit side-chains REVERT: A 725 VAL cc_start: 0.8902 (m) cc_final: 0.8658 (m) REVERT: B 471 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8170 (m-40) REVERT: C 600 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7638 (mt-10) REVERT: C 725 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8650 (m) outliers start: 23 outliers final: 19 residues processed: 110 average time/residue: 0.1633 time to fit residues: 30.2423 Evaluate side-chains 110 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 725 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 5.9990 chunk 37 optimal weight: 0.0980 chunk 111 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 121 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 106 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN ** A 695 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.126886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.104367 restraints weight = 14630.160| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.45 r_work: 0.3283 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 11763 Z= 0.257 Angle : 0.813 59.190 15951 Z= 0.475 Chirality : 0.047 0.307 1767 Planarity : 0.005 0.102 2130 Dihedral : 4.736 30.969 1686 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.22 % Favored : 90.59 % Rotamer: Outliers : 1.78 % Allowed : 14.32 % Favored : 83.90 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.21), residues: 1530 helix: -0.68 (0.47), residues: 108 sheet: -0.42 (0.25), residues: 492 loop : -2.28 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 502 HIS 0.003 0.001 HIS A 476 PHE 0.011 0.001 PHE C 387 TYR 0.010 0.001 TYR A 587 ARG 0.004 0.000 ARG C 437 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2234.28 seconds wall clock time: 41 minutes 5.91 seconds (2465.91 seconds total)