Starting phenix.real_space_refine on Sun Jun 15 10:53:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zkh_60196/06_2025/8zkh_60196_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zkh_60196/06_2025/8zkh_60196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zkh_60196/06_2025/8zkh_60196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zkh_60196/06_2025/8zkh_60196.map" model { file = "/net/cci-nas-00/data/ceres_data/8zkh_60196/06_2025/8zkh_60196_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zkh_60196/06_2025/8zkh_60196_trim.cif" } resolution = 2.3 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= 0.009 sd= 0.104 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 1 5.49 5 S 77 5.16 5 C 11194 2.51 5 N 2820 2.21 5 O 3030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17124 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 5347 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 198} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 4 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 794 Unresolved non-hydrogen angles: 1040 Unresolved non-hydrogen dihedrals: 694 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 14, 'TYR:plan': 8, 'ASN:plan1': 7, 'TRP:plan': 10, 'HIS:plan': 11, 'PHE:plan': 10, 'GLU:plan': 10, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 493 Chain: "B" Number of atoms: 3896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3896 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 10, 'TRANS': 461} Chain breaks: 1 Chain: "C" Number of atoms: 3891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3891 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 10, 'TRANS': 460} Chain breaks: 1 Chain: "D" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3811 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 10, 'TRANS': 451} Chain breaks: 1 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.54, per 1000 atoms: 0.62 Number of scatterers: 17124 At special positions: 0 Unit cell: (127.179, 157.615, 126.092, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 77 16.00 P 1 15.00 O 3030 8.00 N 2820 7.00 C 11194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4066 " - pdb=" SG CYS A4087 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.65 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 344 " distance=2.16 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG B1003 " - " ASN B 362 " " NAG B1004 " - " ASN B 328 " " NAG C1002 " - " ASN C 375 " " NAG C1003 " - " ASN C 362 " " NAG C1004 " - " ASN C 328 " " NAG D1001 " - " ASN D 375 " " NAG D1002 " - " ASN D 362 " " NAG D1003 " - " ASN D 328 " Time building additional restraints: 4.78 Conformation dependent library (CDL) restraints added in 2.6 seconds 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4132 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 5 sheets defined 58.3% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 3074 through 3104 removed outlier: 4.016A pdb=" N MET A3078 " --> pdb=" O ASN A3074 " (cutoff:3.500A) Processing helix chain 'A' and resid 3244 through 3248 removed outlier: 3.526A pdb=" N LEU A3248 " --> pdb=" O PHE A3245 " (cutoff:3.500A) Processing helix chain 'A' and resid 3250 through 3255 Processing helix chain 'A' and resid 3262 through 3266 removed outlier: 3.975A pdb=" N SER A3265 " --> pdb=" O ILE A3262 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE A3266 " --> pdb=" O TRP A3263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3262 through 3266' Processing helix chain 'A' and resid 3278 through 3301 Processing helix chain 'A' and resid 3323 through 3332 removed outlier: 3.535A pdb=" N LEU A3327 " --> pdb=" O VAL A3323 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A3328 " --> pdb=" O ALA A3324 " (cutoff:3.500A) Processing helix chain 'A' and resid 3333 through 3342 removed outlier: 3.746A pdb=" N ILE A3340 " --> pdb=" O VAL A3336 " (cutoff:3.500A) Processing helix chain 'A' and resid 3558 through 3574 removed outlier: 4.573A pdb=" N LEU A3564 " --> pdb=" O GLY A3560 " (cutoff:3.500A) Processing helix chain 'A' and resid 3581 through 3602 removed outlier: 3.666A pdb=" N ALA A3587 " --> pdb=" O GLY A3583 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A3589 " --> pdb=" O SER A3585 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A3590 " --> pdb=" O VAL A3586 " (cutoff:3.500A) Processing helix chain 'A' and resid 3603 through 3608 Processing helix chain 'A' and resid 3656 through 3689 Processing helix chain 'A' and resid 3691 through 3709 Processing helix chain 'A' and resid 3710 through 3716 removed outlier: 3.648A pdb=" N ALA A3716 " --> pdb=" O ARG A3712 " (cutoff:3.500A) Processing helix chain 'A' and resid 3722 through 3730 Processing helix chain 'A' and resid 3730 through 3737 Processing helix chain 'A' and resid 3828 through 3841 Processing helix chain 'A' and resid 3892 through 3896 removed outlier: 3.979A pdb=" N GLY A3896 " --> pdb=" O LEU A3893 " (cutoff:3.500A) Processing helix chain 'A' and resid 3898 through 3926 Processing helix chain 'A' and resid 3933 through 3969 removed outlier: 3.946A pdb=" N LEU A3940 " --> pdb=" O TRP A3936 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A3949 " --> pdb=" O THR A3945 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG A3952 " --> pdb=" O THR A3948 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY A3969 " --> pdb=" O ARG A3965 " (cutoff:3.500A) Processing helix chain 'A' and resid 3977 through 4005 removed outlier: 3.823A pdb=" N SER A3985 " --> pdb=" O ALA A3981 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A4003 " --> pdb=" O LEU A3999 " (cutoff:3.500A) Processing helix chain 'A' and resid 4006 through 4012 removed outlier: 4.574A pdb=" N ARG A4010 " --> pdb=" O ARG A4007 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLN A4011 " --> pdb=" O PHE A4008 " (cutoff:3.500A) Processing helix chain 'A' and resid 4013 through 4049 removed outlier: 3.743A pdb=" N LYS A4017 " --> pdb=" O SER A4013 " (cutoff:3.500A) Proline residue: A4024 - end of helix Processing helix chain 'A' and resid 4081 through 4096 removed outlier: 3.991A pdb=" N LEU A4085 " --> pdb=" O HIS A4081 " (cutoff:3.500A) Processing helix chain 'A' and resid 4100 through 4114 removed outlier: 3.830A pdb=" N TRP A4108 " --> pdb=" O VAL A4104 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 242 Processing helix chain 'B' and resid 245 through 259 removed outlier: 3.996A pdb=" N TYR B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 removed outlier: 3.686A pdb=" N LEU B 273 " --> pdb=" O PHE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 285 Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 334 through 338 removed outlier: 3.510A pdb=" N ARG B 338 " --> pdb=" O GLN B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 367 removed outlier: 3.709A pdb=" N ILE B 367 " --> pdb=" O THR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 467 through 497 removed outlier: 4.419A pdb=" N ILE B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 530 removed outlier: 3.667A pdb=" N LEU B 510 " --> pdb=" O PHE B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 541 removed outlier: 3.564A pdb=" N LEU B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 572 removed outlier: 3.554A pdb=" N ALA B 552 " --> pdb=" O PHE B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 576 Processing helix chain 'B' and resid 580 through 620 removed outlier: 3.623A pdb=" N SER B 584 " --> pdb=" O ASN B 580 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 585 " --> pdb=" O ARG B 581 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LYS B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 599 " --> pdb=" O LYS B 595 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 642 removed outlier: 3.522A pdb=" N LEU B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 651 removed outlier: 4.000A pdb=" N ILE B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 671 through 697 removed outlier: 3.850A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 241 Processing helix chain 'C' and resid 246 through 259 removed outlier: 3.642A pdb=" N THR C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 removed outlier: 3.683A pdb=" N LEU C 273 " --> pdb=" O PHE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 285 Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 334 through 338 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.975A pdb=" N GLU C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 367 removed outlier: 3.730A pdb=" N TRP C 366 " --> pdb=" O GLY C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 375 Processing helix chain 'C' and resid 398 through 412 removed outlier: 3.632A pdb=" N ALA C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 497 removed outlier: 4.160A pdb=" N ILE C 497 " --> pdb=" O LEU C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 531 removed outlier: 3.542A pdb=" N SER C 530 " --> pdb=" O ILE C 526 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 541 removed outlier: 3.941A pdb=" N GLU C 540 " --> pdb=" O LEU C 536 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 541 " --> pdb=" O GLN C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 572 Processing helix chain 'C' and resid 573 through 576 Processing helix chain 'C' and resid 580 through 593 Processing helix chain 'C' and resid 593 through 620 removed outlier: 3.819A pdb=" N PHE C 598 " --> pdb=" O ALA C 594 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 642 removed outlier: 3.691A pdb=" N ILE C 640 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU C 641 " --> pdb=" O PHE C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 653 Processing helix chain 'C' and resid 656 through 671 removed outlier: 3.727A pdb=" N TYR C 660 " --> pdb=" O LEU C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 697 removed outlier: 3.734A pdb=" N GLU C 697 " --> pdb=" O GLN C 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 243 removed outlier: 3.632A pdb=" N SER D 243 " --> pdb=" O TYR D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 259 removed outlier: 3.729A pdb=" N LEU D 256 " --> pdb=" O MET D 252 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 257 " --> pdb=" O MET D 253 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP D 259 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 removed outlier: 3.627A pdb=" N LEU D 273 " --> pdb=" O PHE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 283 Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 370 through 375 removed outlier: 3.729A pdb=" N LEU D 374 " --> pdb=" O SER D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 412 removed outlier: 3.840A pdb=" N ALA D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 498 Processing helix chain 'D' and resid 505 through 532 removed outlier: 4.284A pdb=" N CYS D 509 " --> pdb=" O SER D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 539 removed outlier: 4.657A pdb=" N LEU D 536 " --> pdb=" O GLU D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 572 removed outlier: 3.806A pdb=" N ALA D 552 " --> pdb=" O PHE D 548 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 564 " --> pdb=" O ASN D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 576 removed outlier: 3.618A pdb=" N PHE D 576 " --> pdb=" O LEU D 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 573 through 576' Processing helix chain 'D' and resid 580 through 593 removed outlier: 3.626A pdb=" N CYS D 593 " --> pdb=" O THR D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 620 removed outlier: 3.505A pdb=" N ILE D 602 " --> pdb=" O PHE D 598 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET D 603 " --> pdb=" O GLY D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 641 Processing helix chain 'D' and resid 646 through 653 Processing helix chain 'D' and resid 657 through 670 Processing helix chain 'D' and resid 671 through 696 removed outlier: 3.581A pdb=" N MET D 675 " --> pdb=" O ILE D 671 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3852 through 3853 removed outlier: 3.500A pdb=" N LEU A3863 " --> pdb=" O SER A3858 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3852 through 3853 Processing sheet with id=AA3, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.641A pdb=" N ARG B 320 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE B 424 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG B 322 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR B 422 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU B 324 " --> pdb=" O ARG B 420 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 391 through 394 removed outlier: 6.538A pdb=" N ARG C 320 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE C 424 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG C 322 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR C 422 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU C 324 " --> pdb=" O ARG C 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 391 through 394 removed outlier: 6.614A pdb=" N ARG D 320 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE D 424 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG D 322 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR D 422 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU D 324 " --> pdb=" O ARG D 420 " (cutoff:3.500A) 962 hydrogen bonds defined for protein. 2787 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: 5.37 Time building geometry restraints manager: 5.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2656 1.31 - 1.43: 5122 1.43 - 1.56: 9635 1.56 - 1.69: 4 1.69 - 1.81: 115 Bond restraints: 17532 Sorted by residual: bond pdb=" C1 NAG C1003 " pdb=" O5 NAG C1003 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C1 NAG D1002 " pdb=" O5 NAG D1002 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C1 PGW A4401 " pdb=" O01 PGW A4401 " ideal model delta sigma weight residual 1.332 1.399 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C19 PGW A4401 " pdb=" O03 PGW A4401 " ideal model delta sigma weight residual 1.332 1.396 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C LEU D 573 " pdb=" O LEU D 573 " ideal model delta sigma weight residual 1.236 1.196 0.040 1.29e-02 6.01e+03 9.41e+00 ... (remaining 17527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 23711 3.75 - 7.51: 109 7.51 - 11.26: 18 11.26 - 15.02: 2 15.02 - 18.77: 1 Bond angle restraints: 23841 Sorted by residual: angle pdb=" N ARG A3753 " pdb=" CA ARG A3753 " pdb=" C ARG A3753 " ideal model delta sigma weight residual 114.31 104.69 9.62 1.29e+00 6.01e-01 5.56e+01 angle pdb=" N GLN A3751 " pdb=" CA GLN A3751 " pdb=" C GLN A3751 " ideal model delta sigma weight residual 108.74 118.93 -10.19 1.38e+00 5.25e-01 5.45e+01 angle pdb=" N TRP D 570 " pdb=" CA TRP D 570 " pdb=" C TRP D 570 " ideal model delta sigma weight residual 113.88 105.24 8.64 1.23e+00 6.61e-01 4.94e+01 angle pdb=" N PHE D 576 " pdb=" CA PHE D 576 " pdb=" C PHE D 576 " ideal model delta sigma weight residual 113.55 104.84 8.71 1.26e+00 6.30e-01 4.78e+01 angle pdb=" C TYR A3334 " pdb=" N PRO A3335 " pdb=" CA PRO A3335 " ideal model delta sigma weight residual 119.05 126.31 -7.26 1.11e+00 8.12e-01 4.28e+01 ... (remaining 23836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.69: 9936 32.69 - 65.38: 318 65.38 - 98.06: 27 98.06 - 130.75: 7 130.75 - 163.44: 3 Dihedral angle restraints: 10291 sinusoidal: 3904 harmonic: 6387 Sorted by residual: dihedral pdb=" CB CYS C 331 " pdb=" SG CYS C 331 " pdb=" SG CYS C 344 " pdb=" CB CYS C 344 " ideal model delta sinusoidal sigma weight residual 93.00 169.41 -76.41 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS B 331 " pdb=" SG CYS B 331 " pdb=" SG CYS B 344 " pdb=" CB CYS B 344 " ideal model delta sinusoidal sigma weight residual 93.00 134.62 -41.62 1 1.00e+01 1.00e-02 2.42e+01 dihedral pdb=" C15 PGW A4401 " pdb=" C26 PGW A4401 " pdb=" C27 PGW A4401 " pdb=" C25 PGW A4401 " ideal model delta sinusoidal sigma weight residual 185.14 21.70 163.44 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 10288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.713: 2755 0.713 - 1.427: 0 1.427 - 2.140: 0 2.140 - 2.854: 0 2.854 - 3.567: 1 Chirality restraints: 2756 Sorted by residual: chirality pdb=" C1 NAG D1001 " pdb=" ND2 ASN D 375 " pdb=" C2 NAG D1001 " pdb=" O5 NAG D1001 " both_signs ideal model delta sigma weight residual False -2.40 1.17 -3.57 2.00e-01 2.50e+01 3.18e+02 chirality pdb=" CA VAL A3332 " pdb=" N VAL A3332 " pdb=" C VAL A3332 " pdb=" CB VAL A3332 " both_signs ideal model delta sigma weight residual False 2.44 2.09 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA ASN D 578 " pdb=" N ASN D 578 " pdb=" C ASN D 578 " pdb=" CB ASN D 578 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 2753 not shown) Planarity restraints: 2980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D1001 " -0.353 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG D1001 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG D1001 " -0.145 2.00e-02 2.50e+03 pdb=" N2 NAG D1001 " 0.538 2.00e-02 2.50e+03 pdb=" O7 NAG D1001 " -0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 375 " -0.126 2.00e-02 2.50e+03 1.92e-01 4.61e+02 pdb=" CG ASN D 375 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN D 375 " -0.077 2.00e-02 2.50e+03 pdb=" ND2 ASN D 375 " 0.351 2.00e-02 2.50e+03 pdb=" C1 NAG D1001 " -0.193 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 260 " 0.064 5.00e-02 4.00e+02 9.52e-02 1.45e+01 pdb=" N PRO D 261 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO D 261 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 261 " 0.051 5.00e-02 4.00e+02 ... (remaining 2977 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 2 1.93 - 2.67: 252 2.67 - 3.41: 23849 3.41 - 4.16: 37106 4.16 - 4.90: 70398 Nonbonded interactions: 131607 Sorted by model distance: nonbonded pdb=" NE2 GLN A4042 " pdb=" NE1 TRP D 570 " model vdw 1.186 3.200 nonbonded pdb=" NE2 GLN A4042 " pdb=" CD1 TRP D 570 " model vdw 1.838 3.340 nonbonded pdb=" O GLY A3326 " pdb=" OG SER A3330 " model vdw 2.020 3.040 nonbonded pdb=" O ARG A3750 " pdb=" O VAL A3850 " model vdw 2.093 3.040 nonbonded pdb=" OG1 THR D 265 " pdb=" OE1 GLU D 266 " model vdw 2.239 3.040 ... (remaining 131602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 219 through 293 or resid 311 through 697 or resid 1002 thr \ ough 1003)) selection = (chain 'C' and (resid 219 through 293 or resid 311 through 697 or resid 1002 thr \ ough 1003)) selection = (chain 'D' and (resid 219 through 697 or resid 1002 through 1003)) } 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: 0.570 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: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 40.900 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 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:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 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 : 0.007 0.624 17544 Z= 0.351 Angle : 0.820 46.112 23873 Z= 0.425 Chirality : 0.080 3.567 2756 Planarity : 0.007 0.303 2972 Dihedral : 16.074 163.441 6147 Min Nonbonded Distance : 1.186 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.13 % Favored : 92.64 % Rotamer: Outliers : 0.88 % Allowed : 12.74 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.19), residues: 2159 helix: 1.51 (0.16), residues: 1123 sheet: -0.16 (0.42), residues: 182 loop : -2.53 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A4056 HIS 0.003 0.000 HIS B 379 PHE 0.011 0.001 PHE D 574 TYR 0.024 0.001 TYR A3088 ARG 0.012 0.000 ARG A3719 Details of bonding type rmsd link_NAG-ASN : bond 0.15746 ( 8) link_NAG-ASN : angle 6.56411 ( 24) hydrogen bonds : bond 0.14390 ( 960) hydrogen bonds : angle 5.88954 ( 2787) SS BOND : bond 0.31819 ( 4) SS BOND : angle 20.72410 ( 8) covalent geometry : bond 0.00369 (17532) covalent geometry : angle 0.69654 (23841) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 367 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3096 HIS cc_start: 0.6580 (t-90) cc_final: 0.6367 (t70) REVERT: A 3321 ASP cc_start: 0.5478 (p0) cc_final: 0.5102 (p0) REVERT: A 4086 LEU cc_start: 0.8345 (mp) cc_final: 0.8060 (mm) REVERT: B 494 GLU cc_start: 0.6739 (mt-10) cc_final: 0.6485 (mp0) REVERT: B 502 TYR cc_start: 0.7263 (t80) cc_final: 0.6964 (t80) REVERT: B 590 MET cc_start: 0.7469 (mmp) cc_final: 0.7188 (mmm) REVERT: C 294 LYS cc_start: 0.7233 (mppt) cc_final: 0.6923 (mptp) REVERT: C 477 GLU cc_start: 0.4511 (tm-30) cc_final: 0.4196 (mt-10) REVERT: D 232 ILE cc_start: 0.7530 (tp) cc_final: 0.7199 (mm) REVERT: D 244 SER cc_start: 0.7607 (t) cc_final: 0.7314 (m) REVERT: D 252 MET cc_start: 0.6249 (mtp) cc_final: 0.5965 (mpt) REVERT: D 313 ASN cc_start: 0.7444 (OUTLIER) cc_final: 0.7140 (p0) REVERT: D 380 TRP cc_start: 0.6416 (t-100) cc_final: 0.6040 (t60) REVERT: D 524 ILE cc_start: 0.7266 (mt) cc_final: 0.7052 (mt) REVERT: D 536 LEU cc_start: 0.8284 (tp) cc_final: 0.8048 (pt) outliers start: 15 outliers final: 5 residues processed: 379 average time/residue: 1.1027 time to fit residues: 473.4702 Evaluate side-chains 245 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 239 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3336 VAL Chi-restraints excluded: chain A residue 4025 GLU Chi-restraints excluded: chain A residue 4052 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 313 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 10.0000 chunk 164 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3559 HIS ** A4042 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 ASN ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.172723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.117021 restraints weight = 22108.068| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.31 r_work: 0.3425 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17544 Z= 0.140 Angle : 0.620 10.635 23873 Z= 0.311 Chirality : 0.042 0.342 2756 Planarity : 0.004 0.063 2972 Dihedral : 9.588 177.554 2613 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.81 % Favored : 93.14 % Rotamer: Outliers : 3.82 % Allowed : 16.68 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.19), residues: 2159 helix: 1.75 (0.15), residues: 1156 sheet: -0.35 (0.42), residues: 184 loop : -2.50 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A4056 HIS 0.005 0.001 HIS A4081 PHE 0.012 0.001 PHE B 423 TYR 0.016 0.002 TYR C 486 ARG 0.008 0.001 ARG A3246 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 8) link_NAG-ASN : angle 2.27425 ( 24) hydrogen bonds : bond 0.05078 ( 960) hydrogen bonds : angle 4.16210 ( 2787) SS BOND : bond 0.00660 ( 4) SS BOND : angle 2.47885 ( 8) covalent geometry : bond 0.00306 (17532) covalent geometry : angle 0.61414 (23841) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 256 time to evaluate : 1.788 Fit side-chains revert: symmetry clash REVERT: A 3096 HIS cc_start: 0.6453 (t-90) cc_final: 0.6199 (t70) REVERT: A 3275 PHE cc_start: 0.4144 (OUTLIER) cc_final: 0.2283 (t80) REVERT: A 3321 ASP cc_start: 0.5496 (p0) cc_final: 0.5187 (p0) REVERT: A 3936 TRP cc_start: 0.6967 (OUTLIER) cc_final: 0.6650 (m-90) REVERT: A 4042 GLN cc_start: 0.8202 (pt0) cc_final: 0.7920 (mt0) REVERT: A 4074 LEU cc_start: 0.4879 (OUTLIER) cc_final: 0.4617 (mt) REVERT: A 4086 LEU cc_start: 0.8648 (mp) cc_final: 0.8371 (mm) REVERT: B 527 TYR cc_start: 0.6998 (t80) cc_final: 0.6617 (t80) REVERT: B 531 ASN cc_start: 0.6542 (m110) cc_final: 0.6010 (m-40) REVERT: B 590 MET cc_start: 0.8320 (mmp) cc_final: 0.8002 (mmm) REVERT: B 648 GLU cc_start: 0.7754 (tp30) cc_final: 0.7387 (pt0) REVERT: C 228 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8445 (mp) REVERT: C 294 LYS cc_start: 0.7484 (mppt) cc_final: 0.7044 (mptp) REVERT: C 341 ILE cc_start: 0.8325 (mt) cc_final: 0.8096 (mm) REVERT: C 477 GLU cc_start: 0.5018 (tm-30) cc_final: 0.4226 (mt-10) REVERT: C 592 ARG cc_start: 0.8333 (ttm170) cc_final: 0.8003 (ttt180) REVERT: C 622 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8076 (mt0) REVERT: C 643 ASP cc_start: 0.8229 (t0) cc_final: 0.7958 (t0) REVERT: D 232 ILE cc_start: 0.7562 (tp) cc_final: 0.7209 (mm) REVERT: D 244 SER cc_start: 0.7072 (t) cc_final: 0.6807 (m) REVERT: D 380 TRP cc_start: 0.6972 (t-100) cc_final: 0.6315 (t60) REVERT: D 394 ASP cc_start: 0.7288 (p0) cc_final: 0.7062 (m-30) REVERT: D 524 ILE cc_start: 0.7107 (mt) cc_final: 0.6891 (mt) REVERT: D 536 LEU cc_start: 0.8269 (tp) cc_final: 0.8012 (pt) REVERT: D 590 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7025 (tpt) outliers start: 65 outliers final: 19 residues processed: 295 average time/residue: 1.0449 time to fit residues: 352.4906 Evaluate side-chains 241 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3275 PHE Chi-restraints excluded: chain A residue 3276 THR Chi-restraints excluded: chain A residue 3288 ILE Chi-restraints excluded: chain A residue 3563 LEU Chi-restraints excluded: chain A residue 3922 TRP Chi-restraints excluded: chain A residue 3936 TRP Chi-restraints excluded: chain A residue 3978 ASP Chi-restraints excluded: chain A residue 4052 VAL Chi-restraints excluded: chain A residue 4074 LEU Chi-restraints excluded: chain A residue 4093 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 622 GLN Chi-restraints excluded: chain C residue 689 SER Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 590 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 199 optimal weight: 9.9990 chunk 147 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3261 HIS A3695 HIS A4042 GLN B 531 ASN ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.171899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.116112 restraints weight = 21998.053| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.31 r_work: 0.3412 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17544 Z= 0.129 Angle : 0.575 15.619 23873 Z= 0.289 Chirality : 0.040 0.359 2756 Planarity : 0.004 0.060 2972 Dihedral : 8.243 162.572 2604 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.35 % Favored : 93.61 % Rotamer: Outliers : 4.46 % Allowed : 17.62 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 2159 helix: 1.94 (0.15), residues: 1159 sheet: -0.36 (0.41), residues: 182 loop : -2.45 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A3939 HIS 0.004 0.001 HIS B 379 PHE 0.023 0.001 PHE D 506 TYR 0.017 0.001 TYR D 486 ARG 0.008 0.000 ARG A3719 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 8) link_NAG-ASN : angle 2.56161 ( 24) hydrogen bonds : bond 0.04934 ( 960) hydrogen bonds : angle 3.98780 ( 2787) SS BOND : bond 0.00653 ( 4) SS BOND : angle 1.89378 ( 8) covalent geometry : bond 0.00273 (17532) covalent geometry : angle 0.56897 (23841) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 237 time to evaluate : 1.824 Fit side-chains revert: symmetry clash REVERT: A 3096 HIS cc_start: 0.6488 (t-90) cc_final: 0.6200 (t70) REVERT: A 3275 PHE cc_start: 0.4312 (OUTLIER) cc_final: 0.2393 (t80) REVERT: A 3321 ASP cc_start: 0.5507 (p0) cc_final: 0.5218 (p0) REVERT: A 3331 VAL cc_start: 0.7672 (m) cc_final: 0.7463 (m) REVERT: A 3334 TYR cc_start: 0.6088 (OUTLIER) cc_final: 0.5596 (m-80) REVERT: A 3563 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6558 (tp) REVERT: A 3936 TRP cc_start: 0.6958 (OUTLIER) cc_final: 0.6657 (m-90) REVERT: A 4074 LEU cc_start: 0.4838 (OUTLIER) cc_final: 0.4598 (mt) REVERT: B 527 TYR cc_start: 0.6954 (t80) cc_final: 0.6638 (t80) REVERT: B 531 ASN cc_start: 0.6678 (m-40) cc_final: 0.6205 (m-40) REVERT: B 590 MET cc_start: 0.8221 (mmp) cc_final: 0.7902 (mmm) REVERT: B 648 GLU cc_start: 0.7800 (tp30) cc_final: 0.7410 (pt0) REVERT: C 251 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8366 (ttt90) REVERT: C 294 LYS cc_start: 0.7517 (mppt) cc_final: 0.7121 (mptp) REVERT: C 477 GLU cc_start: 0.5022 (OUTLIER) cc_final: 0.4133 (mt-10) REVERT: C 528 ARG cc_start: 0.6935 (ptt90) cc_final: 0.6733 (ptt90) REVERT: C 585 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7727 (tt0) REVERT: C 592 ARG cc_start: 0.8405 (ttm170) cc_final: 0.8119 (ttt180) REVERT: C 622 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8147 (mt0) REVERT: C 643 ASP cc_start: 0.8169 (t0) cc_final: 0.7825 (t0) REVERT: C 650 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: D 232 ILE cc_start: 0.7511 (tp) cc_final: 0.7186 (mm) REVERT: D 239 TYR cc_start: 0.7462 (t80) cc_final: 0.7029 (t80) REVERT: D 253 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6870 (ttt) REVERT: D 255 GLN cc_start: 0.7683 (tt0) cc_final: 0.7345 (mm110) REVERT: D 380 TRP cc_start: 0.7026 (t-100) cc_final: 0.6292 (t60) REVERT: D 524 ILE cc_start: 0.7172 (mt) cc_final: 0.6951 (mt) REVERT: D 536 LEU cc_start: 0.8238 (tp) cc_final: 0.7983 (pt) REVERT: D 584 SER cc_start: 0.8339 (m) cc_final: 0.8126 (p) REVERT: D 590 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.6970 (tpt) REVERT: D 631 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8131 (mt-10) outliers start: 76 outliers final: 28 residues processed: 281 average time/residue: 1.0129 time to fit residues: 327.1394 Evaluate side-chains 260 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 220 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3252 GLU Chi-restraints excluded: chain A residue 3275 PHE Chi-restraints excluded: chain A residue 3276 THR Chi-restraints excluded: chain A residue 3278 ILE Chi-restraints excluded: chain A residue 3288 ILE Chi-restraints excluded: chain A residue 3332 VAL Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3563 LEU Chi-restraints excluded: chain A residue 3586 VAL Chi-restraints excluded: chain A residue 3597 LEU Chi-restraints excluded: chain A residue 3893 LEU Chi-restraints excluded: chain A residue 3898 SER Chi-restraints excluded: chain A residue 3922 TRP Chi-restraints excluded: chain A residue 3936 TRP Chi-restraints excluded: chain A residue 4006 LEU Chi-restraints excluded: chain A residue 4052 VAL Chi-restraints excluded: chain A residue 4056 TRP Chi-restraints excluded: chain A residue 4074 LEU Chi-restraints excluded: chain A residue 4083 SER Chi-restraints excluded: chain A residue 4093 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 585 GLN Chi-restraints excluded: chain C residue 622 GLN Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 650 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 590 MET Chi-restraints excluded: chain D residue 689 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 117 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 181 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 42 optimal weight: 40.0000 chunk 123 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3559 HIS B 550 HIS ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 ASN ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.172511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.116264 restraints weight = 21970.231| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.32 r_work: 0.3416 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17544 Z= 0.117 Angle : 0.551 12.271 23873 Z= 0.277 Chirality : 0.040 0.380 2756 Planarity : 0.003 0.058 2972 Dihedral : 7.463 133.251 2604 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.39 % Favored : 93.56 % Rotamer: Outliers : 4.40 % Allowed : 18.91 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 2159 helix: 2.08 (0.15), residues: 1160 sheet: -0.40 (0.41), residues: 182 loop : -2.40 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A3939 HIS 0.006 0.001 HIS A3559 PHE 0.016 0.001 PHE D 506 TYR 0.023 0.001 TYR D 486 ARG 0.010 0.000 ARG A3719 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 8) link_NAG-ASN : angle 2.36341 ( 24) hydrogen bonds : bond 0.04577 ( 960) hydrogen bonds : angle 3.87494 ( 2787) SS BOND : bond 0.00385 ( 4) SS BOND : angle 2.00087 ( 8) covalent geometry : bond 0.00246 (17532) covalent geometry : angle 0.54529 (23841) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 229 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3096 HIS cc_start: 0.6450 (t-90) cc_final: 0.6157 (t70) REVERT: A 3275 PHE cc_start: 0.4304 (OUTLIER) cc_final: 0.2361 (t80) REVERT: A 3321 ASP cc_start: 0.5462 (p0) cc_final: 0.5226 (p0) REVERT: A 4074 LEU cc_start: 0.4820 (OUTLIER) cc_final: 0.4591 (mt) REVERT: B 500 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6529 (mt) REVERT: B 527 TYR cc_start: 0.7048 (t80) cc_final: 0.6735 (t80) REVERT: B 531 ASN cc_start: 0.6753 (m-40) cc_final: 0.6316 (m-40) REVERT: B 590 MET cc_start: 0.8232 (mmp) cc_final: 0.7912 (mmm) REVERT: B 648 GLU cc_start: 0.7995 (tp30) cc_final: 0.7623 (pt0) REVERT: C 251 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8388 (ttt90) REVERT: C 294 LYS cc_start: 0.7422 (mppt) cc_final: 0.7064 (mptp) REVERT: C 477 GLU cc_start: 0.5014 (tm-30) cc_final: 0.4164 (mt-10) REVERT: C 581 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.7022 (ptp90) REVERT: C 592 ARG cc_start: 0.8430 (ttm170) cc_final: 0.8160 (ttm170) REVERT: C 622 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8118 (mt0) REVERT: C 643 ASP cc_start: 0.7984 (t0) cc_final: 0.7578 (t0) REVERT: C 650 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: D 232 ILE cc_start: 0.7463 (tp) cc_final: 0.7140 (mm) REVERT: D 239 TYR cc_start: 0.7572 (t80) cc_final: 0.7104 (t80) REVERT: D 253 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6812 (ttt) REVERT: D 255 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7411 (mm110) REVERT: D 380 TRP cc_start: 0.7065 (t-100) cc_final: 0.6395 (t60) REVERT: D 524 ILE cc_start: 0.7261 (mt) cc_final: 0.7058 (mt) REVERT: D 536 LEU cc_start: 0.8132 (tp) cc_final: 0.7827 (pt) REVERT: D 584 SER cc_start: 0.8356 (m) cc_final: 0.8143 (p) REVERT: D 590 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.6888 (tpt) REVERT: D 631 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8110 (mt-10) outliers start: 75 outliers final: 38 residues processed: 275 average time/residue: 1.0634 time to fit residues: 334.5355 Evaluate side-chains 263 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 215 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3249 LEU Chi-restraints excluded: chain A residue 3252 GLU Chi-restraints excluded: chain A residue 3275 PHE Chi-restraints excluded: chain A residue 3276 THR Chi-restraints excluded: chain A residue 3278 ILE Chi-restraints excluded: chain A residue 3288 ILE Chi-restraints excluded: chain A residue 3586 VAL Chi-restraints excluded: chain A residue 3597 LEU Chi-restraints excluded: chain A residue 3893 LEU Chi-restraints excluded: chain A residue 3898 SER Chi-restraints excluded: chain A residue 3916 VAL Chi-restraints excluded: chain A residue 3922 TRP Chi-restraints excluded: chain A residue 3978 ASP Chi-restraints excluded: chain A residue 4025 GLU Chi-restraints excluded: chain A residue 4051 CYS Chi-restraints excluded: chain A residue 4052 VAL Chi-restraints excluded: chain A residue 4056 TRP Chi-restraints excluded: chain A residue 4069 THR Chi-restraints excluded: chain A residue 4074 LEU Chi-restraints excluded: chain A residue 4083 SER Chi-restraints excluded: chain A residue 4093 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 581 ARG Chi-restraints excluded: chain C residue 622 GLN Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 650 GLU Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 590 MET Chi-restraints excluded: chain D residue 689 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 9 optimal weight: 30.0000 chunk 196 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3559 HIS A4081 HIS ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.170079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.113593 restraints weight = 22131.786| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.30 r_work: 0.3375 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17544 Z= 0.146 Angle : 0.580 10.655 23873 Z= 0.294 Chirality : 0.041 0.380 2756 Planarity : 0.004 0.054 2972 Dihedral : 7.343 131.399 2604 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.87 % Allowed : 19.32 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.19), residues: 2159 helix: 1.98 (0.15), residues: 1165 sheet: -0.42 (0.40), residues: 180 loop : -2.37 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A3939 HIS 0.009 0.001 HIS A3559 PHE 0.015 0.001 PHE D 506 TYR 0.022 0.002 TYR D 486 ARG 0.010 0.000 ARG A3719 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 8) link_NAG-ASN : angle 2.61988 ( 24) hydrogen bonds : bond 0.05315 ( 960) hydrogen bonds : angle 3.96308 ( 2787) SS BOND : bond 0.00226 ( 4) SS BOND : angle 2.09636 ( 8) covalent geometry : bond 0.00334 (17532) covalent geometry : angle 0.57302 (23841) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 216 time to evaluate : 1.757 Fit side-chains REVERT: A 3089 MET cc_start: 0.7783 (mtt) cc_final: 0.7245 (tpt) REVERT: A 3096 HIS cc_start: 0.6519 (t-90) cc_final: 0.6255 (t70) REVERT: A 3275 PHE cc_start: 0.4453 (OUTLIER) cc_final: 0.2437 (t80) REVERT: A 3321 ASP cc_start: 0.5598 (p0) cc_final: 0.5385 (p0) REVERT: A 3334 TYR cc_start: 0.6309 (OUTLIER) cc_final: 0.5819 (m-80) REVERT: A 3708 GLU cc_start: 0.6699 (mt-10) cc_final: 0.6322 (mt-10) REVERT: A 3721 GLU cc_start: 0.6322 (pm20) cc_final: 0.5904 (tp30) REVERT: A 4074 LEU cc_start: 0.4708 (OUTLIER) cc_final: 0.4418 (mt) REVERT: B 500 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6464 (mt) REVERT: B 527 TYR cc_start: 0.7167 (t80) cc_final: 0.6836 (t80) REVERT: B 531 ASN cc_start: 0.6738 (m-40) cc_final: 0.6303 (m-40) REVERT: B 590 MET cc_start: 0.8297 (mmp) cc_final: 0.8008 (mmm) REVERT: B 648 GLU cc_start: 0.8099 (tp30) cc_final: 0.7742 (pt0) REVERT: C 251 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8376 (ttt180) REVERT: C 274 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8447 (m) REVERT: C 294 LYS cc_start: 0.7399 (mppt) cc_final: 0.7007 (mptp) REVERT: C 477 GLU cc_start: 0.5173 (OUTLIER) cc_final: 0.4502 (tm-30) REVERT: C 581 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6901 (ptp90) REVERT: C 592 ARG cc_start: 0.8532 (ttm170) cc_final: 0.8220 (mtp180) REVERT: C 622 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8213 (mt0) REVERT: C 643 ASP cc_start: 0.8175 (t0) cc_final: 0.7778 (t0) REVERT: C 650 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7918 (tt0) REVERT: D 232 ILE cc_start: 0.7546 (tp) cc_final: 0.7237 (mm) REVERT: D 239 TYR cc_start: 0.7629 (t80) cc_final: 0.7188 (t80) REVERT: D 253 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6884 (ttt) REVERT: D 255 GLN cc_start: 0.7749 (tt0) cc_final: 0.7467 (mm110) REVERT: D 380 TRP cc_start: 0.7103 (t-100) cc_final: 0.6436 (t60) REVERT: D 490 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6165 (mt-10) REVERT: D 536 LEU cc_start: 0.8159 (tp) cc_final: 0.7850 (pt) REVERT: D 584 SER cc_start: 0.8423 (m) cc_final: 0.8210 (p) REVERT: D 590 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.6853 (tpt) outliers start: 83 outliers final: 38 residues processed: 269 average time/residue: 1.1025 time to fit residues: 340.7676 Evaluate side-chains 259 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 208 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3091 MET Chi-restraints excluded: chain A residue 3249 LEU Chi-restraints excluded: chain A residue 3252 GLU Chi-restraints excluded: chain A residue 3275 PHE Chi-restraints excluded: chain A residue 3276 THR Chi-restraints excluded: chain A residue 3278 ILE Chi-restraints excluded: chain A residue 3288 ILE Chi-restraints excluded: chain A residue 3297 VAL Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3586 VAL Chi-restraints excluded: chain A residue 3597 LEU Chi-restraints excluded: chain A residue 3675 LEU Chi-restraints excluded: chain A residue 3893 LEU Chi-restraints excluded: chain A residue 3916 VAL Chi-restraints excluded: chain A residue 3922 TRP Chi-restraints excluded: chain A residue 3978 ASP Chi-restraints excluded: chain A residue 4025 GLU Chi-restraints excluded: chain A residue 4051 CYS Chi-restraints excluded: chain A residue 4052 VAL Chi-restraints excluded: chain A residue 4069 THR Chi-restraints excluded: chain A residue 4074 LEU Chi-restraints excluded: chain A residue 4083 SER Chi-restraints excluded: chain A residue 4093 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 581 ARG Chi-restraints excluded: chain C residue 622 GLN Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 650 GLU Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 590 MET Chi-restraints excluded: chain D residue 689 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 141 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 160 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 152 optimal weight: 4.9990 chunk 166 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3559 HIS A4081 HIS ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.170577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114346 restraints weight = 21987.464| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.29 r_work: 0.3389 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17544 Z= 0.128 Angle : 0.565 13.043 23873 Z= 0.284 Chirality : 0.040 0.349 2756 Planarity : 0.003 0.051 2972 Dihedral : 7.083 130.270 2604 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.52 % Allowed : 19.85 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 2159 helix: 2.02 (0.15), residues: 1166 sheet: -0.40 (0.39), residues: 180 loop : -2.35 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A3939 HIS 0.009 0.001 HIS A3559 PHE 0.013 0.001 PHE D 506 TYR 0.021 0.001 TYR D 486 ARG 0.007 0.000 ARG C 528 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 8) link_NAG-ASN : angle 2.53675 ( 24) hydrogen bonds : bond 0.04901 ( 960) hydrogen bonds : angle 3.89660 ( 2787) SS BOND : bond 0.00246 ( 4) SS BOND : angle 2.06843 ( 8) covalent geometry : bond 0.00281 (17532) covalent geometry : angle 0.55860 (23841) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 218 time to evaluate : 1.782 Fit side-chains REVERT: A 3089 MET cc_start: 0.7804 (mtt) cc_final: 0.7280 (tpt) REVERT: A 3096 HIS cc_start: 0.6449 (t-90) cc_final: 0.6168 (t70) REVERT: A 3275 PHE cc_start: 0.4496 (OUTLIER) cc_final: 0.2454 (t80) REVERT: A 3321 ASP cc_start: 0.5618 (p0) cc_final: 0.5412 (p0) REVERT: A 3708 GLU cc_start: 0.6746 (mt-10) cc_final: 0.6358 (mt-10) REVERT: A 3721 GLU cc_start: 0.6193 (pm20) cc_final: 0.5810 (tp30) REVERT: A 4074 LEU cc_start: 0.4754 (OUTLIER) cc_final: 0.4533 (mt) REVERT: B 306 ARG cc_start: 0.8255 (mtm180) cc_final: 0.7959 (mtm180) REVERT: B 500 LEU cc_start: 0.6791 (OUTLIER) cc_final: 0.6490 (mt) REVERT: B 527 TYR cc_start: 0.7156 (t80) cc_final: 0.6824 (t80) REVERT: B 531 ASN cc_start: 0.6774 (m-40) cc_final: 0.6350 (m-40) REVERT: B 590 MET cc_start: 0.8212 (mmp) cc_final: 0.7921 (mmm) REVERT: B 648 GLU cc_start: 0.8143 (tp30) cc_final: 0.7792 (pt0) REVERT: C 251 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8375 (ttt180) REVERT: C 294 LYS cc_start: 0.7404 (mppt) cc_final: 0.6984 (mptp) REVERT: C 477 GLU cc_start: 0.5152 (tm-30) cc_final: 0.4310 (tm-30) REVERT: C 581 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6891 (ptp90) REVERT: C 592 ARG cc_start: 0.8521 (ttm170) cc_final: 0.8189 (mtp180) REVERT: C 622 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: C 643 ASP cc_start: 0.7953 (t0) cc_final: 0.7504 (t0) REVERT: C 650 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7928 (tt0) REVERT: D 232 ILE cc_start: 0.7547 (tp) cc_final: 0.7228 (mm) REVERT: D 239 TYR cc_start: 0.7646 (t80) cc_final: 0.7119 (t80) REVERT: D 253 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6930 (ttt) REVERT: D 255 GLN cc_start: 0.7744 (tt0) cc_final: 0.7483 (mm110) REVERT: D 380 TRP cc_start: 0.7064 (t-100) cc_final: 0.6412 (t60) REVERT: D 490 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6211 (mt-10) REVERT: D 536 LEU cc_start: 0.8219 (tp) cc_final: 0.7962 (pt) REVERT: D 584 SER cc_start: 0.8434 (m) cc_final: 0.8227 (p) REVERT: D 590 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.6883 (tpt) outliers start: 77 outliers final: 46 residues processed: 269 average time/residue: 1.0557 time to fit residues: 324.2418 Evaluate side-chains 263 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 207 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3249 LEU Chi-restraints excluded: chain A residue 3252 GLU Chi-restraints excluded: chain A residue 3266 ILE Chi-restraints excluded: chain A residue 3275 PHE Chi-restraints excluded: chain A residue 3276 THR Chi-restraints excluded: chain A residue 3278 ILE Chi-restraints excluded: chain A residue 3288 ILE Chi-restraints excluded: chain A residue 3297 VAL Chi-restraints excluded: chain A residue 3563 LEU Chi-restraints excluded: chain A residue 3586 VAL Chi-restraints excluded: chain A residue 3590 LEU Chi-restraints excluded: chain A residue 3597 LEU Chi-restraints excluded: chain A residue 3675 LEU Chi-restraints excluded: chain A residue 3883 LEU Chi-restraints excluded: chain A residue 3893 LEU Chi-restraints excluded: chain A residue 3898 SER Chi-restraints excluded: chain A residue 3916 VAL Chi-restraints excluded: chain A residue 3922 TRP Chi-restraints excluded: chain A residue 3978 ASP Chi-restraints excluded: chain A residue 4025 GLU Chi-restraints excluded: chain A residue 4051 CYS Chi-restraints excluded: chain A residue 4052 VAL Chi-restraints excluded: chain A residue 4074 LEU Chi-restraints excluded: chain A residue 4083 SER Chi-restraints excluded: chain A residue 4093 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 581 ARG Chi-restraints excluded: chain C residue 622 GLN Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 650 GLU Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 590 MET Chi-restraints excluded: chain D residue 689 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 149 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 214 optimal weight: 0.0270 chunk 67 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3559 HIS ** A4081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN D 559 ASN D 580 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.171887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.116187 restraints weight = 21990.893| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.27 r_work: 0.3412 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17544 Z= 0.112 Angle : 0.551 12.289 23873 Z= 0.278 Chirality : 0.039 0.318 2756 Planarity : 0.003 0.060 2972 Dihedral : 6.761 125.974 2604 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.46 % Allowed : 21.43 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.19), residues: 2159 helix: 2.13 (0.15), residues: 1164 sheet: -0.30 (0.40), residues: 178 loop : -2.33 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A3298 HIS 0.009 0.001 HIS A3559 PHE 0.012 0.001 PHE D 506 TYR 0.021 0.001 TYR D 486 ARG 0.012 0.000 ARG A3924 Details of bonding type rmsd link_NAG-ASN : bond 0.00142 ( 8) link_NAG-ASN : angle 2.30652 ( 24) hydrogen bonds : bond 0.04412 ( 960) hydrogen bonds : angle 3.80172 ( 2787) SS BOND : bond 0.00275 ( 4) SS BOND : angle 2.33681 ( 8) covalent geometry : bond 0.00233 (17532) covalent geometry : angle 0.54439 (23841) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 222 time to evaluate : 1.806 Fit side-chains REVERT: A 3089 MET cc_start: 0.7850 (mtt) cc_final: 0.7334 (tpt) REVERT: A 3096 HIS cc_start: 0.6508 (t-90) cc_final: 0.6250 (t70) REVERT: A 3334 TYR cc_start: 0.6141 (OUTLIER) cc_final: 0.5477 (m-80) REVERT: A 3708 GLU cc_start: 0.6693 (mt-10) cc_final: 0.6274 (mt-10) REVERT: A 3721 GLU cc_start: 0.6197 (pm20) cc_final: 0.5821 (tp30) REVERT: A 4010 ARG cc_start: 0.7597 (tpt170) cc_final: 0.7331 (mpp-170) REVERT: B 306 ARG cc_start: 0.8217 (mtm180) cc_final: 0.7938 (mtm180) REVERT: B 495 ILE cc_start: 0.6780 (OUTLIER) cc_final: 0.6551 (tt) REVERT: B 500 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6468 (mt) REVERT: B 527 TYR cc_start: 0.7127 (t80) cc_final: 0.6783 (t80) REVERT: B 531 ASN cc_start: 0.6790 (m-40) cc_final: 0.6367 (m-40) REVERT: B 590 MET cc_start: 0.8172 (mmp) cc_final: 0.7854 (mmm) REVERT: B 648 GLU cc_start: 0.8193 (tp30) cc_final: 0.7833 (pt0) REVERT: C 251 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8341 (ttt180) REVERT: C 294 LYS cc_start: 0.7387 (mppt) cc_final: 0.6977 (mptp) REVERT: C 477 GLU cc_start: 0.5071 (OUTLIER) cc_final: 0.4199 (mt-10) REVERT: C 581 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6947 (ptp90) REVERT: C 585 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7979 (tt0) REVERT: C 592 ARG cc_start: 0.8504 (ttm170) cc_final: 0.8178 (mtp180) REVERT: C 622 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8123 (mt0) REVERT: C 643 ASP cc_start: 0.7938 (t0) cc_final: 0.7427 (t0) REVERT: C 650 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7915 (tt0) REVERT: D 232 ILE cc_start: 0.7520 (tp) cc_final: 0.7208 (mm) REVERT: D 239 TYR cc_start: 0.7611 (t80) cc_final: 0.7037 (t80) REVERT: D 255 GLN cc_start: 0.7745 (tt0) cc_final: 0.7488 (mm110) REVERT: D 380 TRP cc_start: 0.7061 (t-100) cc_final: 0.6405 (t60) REVERT: D 536 LEU cc_start: 0.8154 (tp) cc_final: 0.7874 (pt) REVERT: D 584 SER cc_start: 0.8440 (m) cc_final: 0.8238 (p) outliers start: 59 outliers final: 37 residues processed: 260 average time/residue: 1.3177 time to fit residues: 388.3853 Evaluate side-chains 260 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3091 MET Chi-restraints excluded: chain A residue 3249 LEU Chi-restraints excluded: chain A residue 3252 GLU Chi-restraints excluded: chain A residue 3266 ILE Chi-restraints excluded: chain A residue 3275 PHE Chi-restraints excluded: chain A residue 3276 THR Chi-restraints excluded: chain A residue 3278 ILE Chi-restraints excluded: chain A residue 3288 ILE Chi-restraints excluded: chain A residue 3297 VAL Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3563 LEU Chi-restraints excluded: chain A residue 3586 VAL Chi-restraints excluded: chain A residue 3590 LEU Chi-restraints excluded: chain A residue 3883 LEU Chi-restraints excluded: chain A residue 3893 LEU Chi-restraints excluded: chain A residue 3922 TRP Chi-restraints excluded: chain A residue 3978 ASP Chi-restraints excluded: chain A residue 4025 GLU Chi-restraints excluded: chain A residue 4051 CYS Chi-restraints excluded: chain A residue 4052 VAL Chi-restraints excluded: chain A residue 4083 SER Chi-restraints excluded: chain A residue 4093 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 581 ARG Chi-restraints excluded: chain C residue 622 GLN Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 650 GLU Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 689 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 202 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 136 optimal weight: 0.0170 chunk 43 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3559 HIS A4081 HIS ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.172850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.117259 restraints weight = 22013.792| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.29 r_work: 0.3429 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17544 Z= 0.105 Angle : 0.543 11.789 23873 Z= 0.271 Chirality : 0.039 0.298 2756 Planarity : 0.003 0.049 2972 Dihedral : 6.494 119.741 2604 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.88 % Allowed : 21.96 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 2159 helix: 2.21 (0.15), residues: 1164 sheet: -0.25 (0.40), residues: 178 loop : -2.30 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A3298 HIS 0.010 0.001 HIS A3559 PHE 0.011 0.001 PHE D 506 TYR 0.021 0.001 TYR C 486 ARG 0.010 0.000 ARG A3924 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 8) link_NAG-ASN : angle 2.10252 ( 24) hydrogen bonds : bond 0.04144 ( 960) hydrogen bonds : angle 3.74588 ( 2787) SS BOND : bond 0.00282 ( 4) SS BOND : angle 1.92157 ( 8) covalent geometry : bond 0.00214 (17532) covalent geometry : angle 0.53775 (23841) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 227 time to evaluate : 1.741 Fit side-chains REVERT: A 3089 MET cc_start: 0.7813 (mtt) cc_final: 0.7338 (tpt) REVERT: A 3096 HIS cc_start: 0.6504 (t-90) cc_final: 0.6209 (t70) REVERT: A 3708 GLU cc_start: 0.6683 (mt-10) cc_final: 0.6297 (mt-10) REVERT: A 3721 GLU cc_start: 0.6230 (pm20) cc_final: 0.5849 (tp30) REVERT: A 4010 ARG cc_start: 0.7596 (tpt170) cc_final: 0.7301 (mpp-170) REVERT: B 306 ARG cc_start: 0.8221 (mtm180) cc_final: 0.7898 (mtm180) REVERT: B 495 ILE cc_start: 0.6854 (OUTLIER) cc_final: 0.6395 (mt) REVERT: B 500 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6425 (mt) REVERT: B 527 TYR cc_start: 0.7093 (t80) cc_final: 0.6767 (t80) REVERT: B 531 ASN cc_start: 0.6770 (m-40) cc_final: 0.6344 (m-40) REVERT: B 590 MET cc_start: 0.8182 (mmp) cc_final: 0.7871 (mmm) REVERT: B 648 GLU cc_start: 0.8202 (tp30) cc_final: 0.7856 (pt0) REVERT: C 294 LYS cc_start: 0.7339 (mppt) cc_final: 0.6923 (mptp) REVERT: C 477 GLU cc_start: 0.5038 (OUTLIER) cc_final: 0.4189 (mt-10) REVERT: C 581 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.7083 (ptp90) REVERT: C 592 ARG cc_start: 0.8493 (ttm170) cc_final: 0.8166 (mtp180) REVERT: C 622 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8100 (mt0) REVERT: C 643 ASP cc_start: 0.7944 (t0) cc_final: 0.7436 (t0) REVERT: C 650 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: D 232 ILE cc_start: 0.7519 (tp) cc_final: 0.7211 (mm) REVERT: D 239 TYR cc_start: 0.7548 (t80) cc_final: 0.6991 (t80) REVERT: D 242 MET cc_start: 0.6820 (tpp) cc_final: 0.6619 (tpp) REVERT: D 255 GLN cc_start: 0.7709 (tt0) cc_final: 0.7488 (mm110) REVERT: D 380 TRP cc_start: 0.7071 (t-100) cc_final: 0.6410 (t60) REVERT: D 490 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6573 (mm-30) REVERT: D 536 LEU cc_start: 0.8236 (tp) cc_final: 0.7886 (pt) outliers start: 49 outliers final: 31 residues processed: 257 average time/residue: 1.0602 time to fit residues: 311.6786 Evaluate side-chains 248 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3091 MET Chi-restraints excluded: chain A residue 3266 ILE Chi-restraints excluded: chain A residue 3275 PHE Chi-restraints excluded: chain A residue 3276 THR Chi-restraints excluded: chain A residue 3288 ILE Chi-restraints excluded: chain A residue 3297 VAL Chi-restraints excluded: chain A residue 3563 LEU Chi-restraints excluded: chain A residue 3568 VAL Chi-restraints excluded: chain A residue 3590 LEU Chi-restraints excluded: chain A residue 3675 LEU Chi-restraints excluded: chain A residue 3893 LEU Chi-restraints excluded: chain A residue 3922 TRP Chi-restraints excluded: chain A residue 3978 ASP Chi-restraints excluded: chain A residue 4025 GLU Chi-restraints excluded: chain A residue 4051 CYS Chi-restraints excluded: chain A residue 4052 VAL Chi-restraints excluded: chain A residue 4083 SER Chi-restraints excluded: chain A residue 4093 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 581 ARG Chi-restraints excluded: chain C residue 622 GLN Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 650 GLU Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 522 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 54 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 162 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 47 optimal weight: 30.0000 chunk 139 optimal weight: 5.9990 chunk 177 optimal weight: 0.7980 chunk 187 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 199 optimal weight: 7.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3559 HIS A4005 GLN ** A4081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 ASN D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.167432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.111362 restraints weight = 21987.254| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.25 r_work: 0.3342 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17544 Z= 0.201 Angle : 0.643 11.363 23873 Z= 0.330 Chirality : 0.043 0.309 2756 Planarity : 0.004 0.054 2972 Dihedral : 7.212 130.603 2604 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.64 % Allowed : 21.90 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.19), residues: 2159 helix: 1.97 (0.15), residues: 1164 sheet: -0.42 (0.39), residues: 178 loop : -2.32 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A3298 HIS 0.010 0.001 HIS A3559 PHE 0.018 0.002 PHE C 646 TYR 0.020 0.002 TYR C 486 ARG 0.013 0.001 ARG A3719 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 8) link_NAG-ASN : angle 2.42882 ( 24) hydrogen bonds : bond 0.06143 ( 960) hydrogen bonds : angle 4.07296 ( 2787) SS BOND : bond 0.00469 ( 4) SS BOND : angle 2.97221 ( 8) covalent geometry : bond 0.00489 (17532) covalent geometry : angle 0.63651 (23841) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 216 time to evaluate : 1.951 Fit side-chains REVERT: A 3089 MET cc_start: 0.7793 (mtt) cc_final: 0.7367 (tpp) REVERT: A 3096 HIS cc_start: 0.6648 (t-90) cc_final: 0.6392 (t70) REVERT: A 3708 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6488 (mt-10) REVERT: B 306 ARG cc_start: 0.8460 (mtm180) cc_final: 0.8215 (mtm180) REVERT: B 500 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6503 (mt) REVERT: B 531 ASN cc_start: 0.6950 (m-40) cc_final: 0.6562 (m110) REVERT: B 590 MET cc_start: 0.8250 (mmp) cc_final: 0.7419 (mtt) REVERT: B 648 GLU cc_start: 0.8184 (tp30) cc_final: 0.7822 (pt0) REVERT: C 274 SER cc_start: 0.8754 (p) cc_final: 0.8540 (m) REVERT: C 294 LYS cc_start: 0.7404 (mppt) cc_final: 0.7036 (mptp) REVERT: C 581 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6949 (ptp90) REVERT: C 585 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7910 (tt0) REVERT: C 592 ARG cc_start: 0.8524 (ttm170) cc_final: 0.8191 (mtp180) REVERT: C 622 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8336 (mt0) REVERT: C 643 ASP cc_start: 0.8174 (t0) cc_final: 0.7779 (t0) REVERT: C 650 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: D 232 ILE cc_start: 0.7595 (tp) cc_final: 0.7314 (mm) REVERT: D 239 TYR cc_start: 0.7882 (t80) cc_final: 0.7403 (t80) REVERT: D 242 MET cc_start: 0.7099 (tpp) cc_final: 0.6753 (ttm) REVERT: D 255 GLN cc_start: 0.7727 (tt0) cc_final: 0.7477 (mm110) REVERT: D 380 TRP cc_start: 0.7200 (t-100) cc_final: 0.6534 (t60) REVERT: D 536 LEU cc_start: 0.8244 (tp) cc_final: 0.7876 (pt) REVERT: D 576 PHE cc_start: 0.8821 (m-80) cc_final: 0.8620 (m-80) REVERT: D 590 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.6958 (tpt) outliers start: 62 outliers final: 37 residues processed: 256 average time/residue: 1.0466 time to fit residues: 306.3474 Evaluate side-chains 255 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 212 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3091 MET Chi-restraints excluded: chain A residue 3249 LEU Chi-restraints excluded: chain A residue 3275 PHE Chi-restraints excluded: chain A residue 3276 THR Chi-restraints excluded: chain A residue 3278 ILE Chi-restraints excluded: chain A residue 3288 ILE Chi-restraints excluded: chain A residue 3563 LEU Chi-restraints excluded: chain A residue 3568 VAL Chi-restraints excluded: chain A residue 3586 VAL Chi-restraints excluded: chain A residue 3590 LEU Chi-restraints excluded: chain A residue 3883 LEU Chi-restraints excluded: chain A residue 3893 LEU Chi-restraints excluded: chain A residue 3898 SER Chi-restraints excluded: chain A residue 3916 VAL Chi-restraints excluded: chain A residue 3978 ASP Chi-restraints excluded: chain A residue 4025 GLU Chi-restraints excluded: chain A residue 4051 CYS Chi-restraints excluded: chain A residue 4052 VAL Chi-restraints excluded: chain A residue 4083 SER Chi-restraints excluded: chain A residue 4093 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 581 ARG Chi-restraints excluded: chain C residue 585 GLN Chi-restraints excluded: chain C residue 622 GLN Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 650 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 590 MET Chi-restraints excluded: chain D residue 689 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 30.0000 chunk 19 optimal weight: 5.9990 chunk 168 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3559 HIS A3982 GLN A4081 HIS ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.170319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.115027 restraints weight = 21951.116| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.25 r_work: 0.3392 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17544 Z= 0.125 Angle : 0.582 11.318 23873 Z= 0.294 Chirality : 0.040 0.290 2756 Planarity : 0.004 0.058 2972 Dihedral : 6.826 128.762 2604 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.70 % Allowed : 22.84 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.19), residues: 2159 helix: 2.09 (0.15), residues: 1166 sheet: -0.37 (0.39), residues: 178 loop : -2.28 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A3298 HIS 0.010 0.001 HIS A3559 PHE 0.011 0.001 PHE D 506 TYR 0.021 0.001 TYR C 486 ARG 0.014 0.000 ARG A3719 Details of bonding type rmsd link_NAG-ASN : bond 0.00155 ( 8) link_NAG-ASN : angle 2.15794 ( 24) hydrogen bonds : bond 0.04773 ( 960) hydrogen bonds : angle 3.86492 ( 2787) SS BOND : bond 0.00294 ( 4) SS BOND : angle 2.10025 ( 8) covalent geometry : bond 0.00272 (17532) covalent geometry : angle 0.57738 (23841) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 220 time to evaluate : 1.787 Fit side-chains REVERT: A 3089 MET cc_start: 0.7813 (mtt) cc_final: 0.7397 (tpp) REVERT: A 3096 HIS cc_start: 0.6532 (t-90) cc_final: 0.6223 (t70) REVERT: A 4010 ARG cc_start: 0.7641 (tpt170) cc_final: 0.7293 (mpp-170) REVERT: B 500 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6424 (mt) REVERT: B 531 ASN cc_start: 0.6822 (m-40) cc_final: 0.6399 (m-40) REVERT: B 590 MET cc_start: 0.8180 (mmp) cc_final: 0.7392 (mtt) REVERT: B 648 GLU cc_start: 0.8176 (tp30) cc_final: 0.7828 (pt0) REVERT: C 294 LYS cc_start: 0.7380 (mppt) cc_final: 0.6978 (mptp) REVERT: C 477 GLU cc_start: 0.4832 (tm-30) cc_final: 0.4151 (mt-10) REVERT: C 581 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6993 (ptp90) REVERT: C 585 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: C 592 ARG cc_start: 0.8539 (ttm170) cc_final: 0.8199 (mtp180) REVERT: C 622 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8201 (mt0) REVERT: C 643 ASP cc_start: 0.7957 (t0) cc_final: 0.7425 (t0) REVERT: C 650 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: D 232 ILE cc_start: 0.7578 (tp) cc_final: 0.7281 (mm) REVERT: D 239 TYR cc_start: 0.7791 (t80) cc_final: 0.7312 (t80) REVERT: D 380 TRP cc_start: 0.7091 (t-100) cc_final: 0.6410 (t60) REVERT: D 536 LEU cc_start: 0.8262 (tp) cc_final: 0.7944 (pt) REVERT: D 576 PHE cc_start: 0.8810 (m-80) cc_final: 0.8585 (m-80) REVERT: D 590 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.6832 (tpt) outliers start: 46 outliers final: 36 residues processed: 251 average time/residue: 1.3352 time to fit residues: 383.1538 Evaluate side-chains 256 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 214 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3091 MET Chi-restraints excluded: chain A residue 3262 ILE Chi-restraints excluded: chain A residue 3266 ILE Chi-restraints excluded: chain A residue 3275 PHE Chi-restraints excluded: chain A residue 3276 THR Chi-restraints excluded: chain A residue 3288 ILE Chi-restraints excluded: chain A residue 3563 LEU Chi-restraints excluded: chain A residue 3568 VAL Chi-restraints excluded: chain A residue 3586 VAL Chi-restraints excluded: chain A residue 3590 LEU Chi-restraints excluded: chain A residue 3883 LEU Chi-restraints excluded: chain A residue 3893 LEU Chi-restraints excluded: chain A residue 3978 ASP Chi-restraints excluded: chain A residue 4025 GLU Chi-restraints excluded: chain A residue 4051 CYS Chi-restraints excluded: chain A residue 4052 VAL Chi-restraints excluded: chain A residue 4083 SER Chi-restraints excluded: chain A residue 4093 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 559 ASN Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 581 ARG Chi-restraints excluded: chain C residue 585 GLN Chi-restraints excluded: chain C residue 622 GLN Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 650 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 590 MET Chi-restraints excluded: chain D residue 689 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 69 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 203 optimal weight: 0.9990 chunk 199 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 136 optimal weight: 0.0570 chunk 42 optimal weight: 20.0000 chunk 109 optimal weight: 0.8980 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3559 HIS A4081 HIS ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.171833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.116735 restraints weight = 22001.251| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.26 r_work: 0.3418 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 17544 Z= 0.113 Angle : 0.554 11.192 23873 Z= 0.282 Chirality : 0.039 0.275 2756 Planarity : 0.004 0.073 2972 Dihedral : 6.522 123.078 2604 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.52 % Allowed : 22.67 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.19), residues: 2159 helix: 2.19 (0.15), residues: 1167 sheet: -0.30 (0.39), residues: 178 loop : -2.25 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A3298 HIS 0.010 0.001 HIS A3559 PHE 0.011 0.001 PHE D 506 TYR 0.025 0.001 TYR B 502 ARG 0.015 0.000 ARG A3719 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 8) link_NAG-ASN : angle 1.96632 ( 24) hydrogen bonds : bond 0.04284 ( 960) hydrogen bonds : angle 3.76779 ( 2787) SS BOND : bond 0.00225 ( 4) SS BOND : angle 1.70221 ( 8) covalent geometry : bond 0.00237 (17532) covalent geometry : angle 0.55022 (23841) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25558.86 seconds wall clock time: 447 minutes 52.58 seconds (26872.58 seconds total)