Starting phenix.real_space_refine on Thu Sep 18 13:50:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zkh_60196/09_2025/8zkh_60196_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zkh_60196/09_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_60196/09_2025/8zkh_60196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zkh_60196/09_2025/8zkh_60196.map" model { file = "/net/cci-nas-00/data/ceres_data/8zkh_60196/09_2025/8zkh_60196_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zkh_60196/09_2025/8zkh_60196_trim.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 21, 'PHE:plan': 10, 'TYR:plan': 8, 'GLU:plan': 10, 'TRP:plan': 10, 'HIS:plan': 11, 'ASP:plan': 14, 'ASN:plan1': 7, 'GLN:plan1': 6} 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: 4.34, per 1000 atoms: 0.25 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: 1.62 Conformation dependent library (CDL) restraints added in 775.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.54 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: 2.50 Time building geometry restraints manager: 2.13 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: 0.940 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.480 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.150 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.012 0.000 ARG A3719 TYR 0.024 0.001 TYR A3088 PHE 0.011 0.001 PHE D 574 TRP 0.015 0.001 TRP A4056 HIS 0.003 0.000 HIS B 379 Details of bonding type rmsd covalent geometry : bond 0.00369 (17532) covalent geometry : angle 0.69654 (23841) SS BOND : bond 0.31819 ( 4) SS BOND : angle 20.72410 ( 8) hydrogen bonds : bond 0.14390 ( 960) hydrogen bonds : angle 5.88954 ( 2787) link_NAG-ASN : bond 0.15746 ( 8) link_NAG-ASN : angle 6.56411 ( 24) *********************** 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 : 0.635 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: 0.5650 time to fit residues: 240.9446 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 : 0.864 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 531 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.174452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.119244 restraints weight = 22090.280| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.32 r_work: 0.3455 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17544 Z= 0.131 Angle : 0.596 10.409 23873 Z= 0.300 Chirality : 0.040 0.330 2756 Planarity : 0.004 0.064 2972 Dihedral : 9.605 176.884 2613 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.58 % Favored : 93.38 % Rotamer: Outliers : 3.58 % Allowed : 17.03 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.19), residues: 2159 helix: 1.85 (0.15), residues: 1150 sheet: -0.22 (0.42), residues: 182 loop : -2.44 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3246 TYR 0.016 0.001 TYR D 248 PHE 0.010 0.001 PHE D 576 TRP 0.009 0.001 TRP A3939 HIS 0.006 0.001 HIS A4081 Details of bonding type rmsd covalent geometry : bond 0.00262 (17532) covalent geometry : angle 0.59138 (23841) SS BOND : bond 0.00393 ( 4) SS BOND : angle 2.09233 ( 8) hydrogen bonds : bond 0.04703 ( 960) hydrogen bonds : angle 4.13371 ( 2787) link_NAG-ASN : bond 0.00293 ( 8) link_NAG-ASN : angle 2.10095 ( 24) *********************** 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 319 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 258 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 3096 HIS cc_start: 0.6430 (t-90) cc_final: 0.6181 (t70) REVERT: A 3275 PHE cc_start: 0.4145 (OUTLIER) cc_final: 0.2196 (t80) REVERT: A 3321 ASP cc_start: 0.5617 (p0) cc_final: 0.5256 (p0) REVERT: A 3936 TRP cc_start: 0.6970 (OUTLIER) cc_final: 0.6647 (m-90) REVERT: A 4042 GLN cc_start: 0.8206 (pt0) cc_final: 0.8004 (mt0) REVERT: A 4074 LEU cc_start: 0.4856 (OUTLIER) cc_final: 0.4619 (mt) REVERT: A 4086 LEU cc_start: 0.8545 (mp) cc_final: 0.8275 (mm) REVERT: B 527 TYR cc_start: 0.6920 (t80) cc_final: 0.6585 (t80) REVERT: B 531 ASN cc_start: 0.6532 (m-40) cc_final: 0.5964 (m-40) REVERT: B 590 MET cc_start: 0.8247 (mmp) cc_final: 0.7944 (mmm) REVERT: B 648 GLU cc_start: 0.7712 (tp30) cc_final: 0.7364 (pt0) REVERT: C 294 LYS cc_start: 0.7433 (mppt) cc_final: 0.6981 (mptp) REVERT: C 477 GLU cc_start: 0.4980 (tm-30) cc_final: 0.4202 (mt-10) REVERT: C 577 ILE cc_start: 0.8746 (pt) cc_final: 0.8533 (pp) REVERT: C 592 ARG cc_start: 0.8193 (ttm170) cc_final: 0.7902 (ttt180) REVERT: C 622 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7887 (mt0) REVERT: C 643 ASP cc_start: 0.8223 (t0) cc_final: 0.7958 (t0) REVERT: C 686 GLU cc_start: 0.8347 (pp20) cc_final: 0.8137 (pp20) REVERT: D 232 ILE cc_start: 0.7546 (tp) cc_final: 0.7209 (mm) REVERT: D 244 SER cc_start: 0.7335 (t) cc_final: 0.7059 (m) REVERT: D 380 TRP cc_start: 0.6840 (t-100) cc_final: 0.6184 (t60) REVERT: D 394 ASP cc_start: 0.7286 (p0) cc_final: 0.6954 (m-30) REVERT: D 524 ILE cc_start: 0.7098 (mt) cc_final: 0.6872 (mt) REVERT: D 536 LEU cc_start: 0.8333 (tp) cc_final: 0.8058 (pt) REVERT: D 590 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7012 (tpt) outliers start: 61 outliers final: 17 residues processed: 293 average time/residue: 0.5005 time to fit residues: 167.8608 Evaluate side-chains 236 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3275 PHE Chi-restraints excluded: chain A residue 3288 ILE Chi-restraints excluded: chain A residue 3559 HIS Chi-restraints excluded: chain A residue 3563 LEU Chi-restraints excluded: chain A residue 3718 THR Chi-restraints excluded: chain A residue 3936 TRP 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 377 SER Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 377 SER 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 228 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 153 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 4 optimal weight: 0.0170 chunk 42 optimal weight: 2.9990 chunk 85 optimal weight: 0.0470 chunk 180 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3261 HIS A3559 HIS A4042 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.170828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.114706 restraints weight = 22198.336| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.32 r_work: 0.3390 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17544 Z= 0.144 Angle : 0.598 13.705 23873 Z= 0.304 Chirality : 0.042 0.365 2756 Planarity : 0.004 0.061 2972 Dihedral : 8.361 149.854 2604 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.44 % Favored : 93.52 % Rotamer: Outliers : 4.70 % Allowed : 17.32 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.19), residues: 2159 helix: 1.87 (0.15), residues: 1165 sheet: -0.35 (0.41), residues: 178 loop : -2.50 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3246 TYR 0.017 0.002 TYR D 486 PHE 0.022 0.001 PHE D 506 TRP 0.010 0.001 TRP A3939 HIS 0.011 0.001 HIS A3559 Details of bonding type rmsd covalent geometry : bond 0.00318 (17532) covalent geometry : angle 0.59159 (23841) SS BOND : bond 0.00663 ( 4) SS BOND : angle 2.32199 ( 8) hydrogen bonds : bond 0.05463 ( 960) hydrogen bonds : angle 4.07182 ( 2787) link_NAG-ASN : bond 0.00269 ( 8) link_NAG-ASN : angle 2.53474 ( 24) *********************** 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 317 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 237 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 3096 HIS cc_start: 0.6492 (t-90) cc_final: 0.6237 (t70) REVERT: A 3275 PHE cc_start: 0.4464 (OUTLIER) cc_final: 0.2507 (t80) REVERT: A 3321 ASP cc_start: 0.5438 (p0) cc_final: 0.5173 (p0) REVERT: A 3331 VAL cc_start: 0.7690 (m) cc_final: 0.7481 (m) REVERT: A 3334 TYR cc_start: 0.6049 (OUTLIER) cc_final: 0.5596 (m-80) REVERT: A 3671 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7619 (tp) REVERT: A 3719 ARG cc_start: 0.6007 (mmm160) cc_final: 0.5773 (mmm160) REVERT: A 3936 TRP cc_start: 0.6973 (OUTLIER) cc_final: 0.6670 (m-90) REVERT: A 4074 LEU cc_start: 0.4611 (OUTLIER) cc_final: 0.4348 (mt) REVERT: B 527 TYR cc_start: 0.7043 (t80) cc_final: 0.6712 (t80) REVERT: B 531 ASN cc_start: 0.6787 (m-40) cc_final: 0.6323 (m-40) REVERT: B 590 MET cc_start: 0.8272 (mmp) cc_final: 0.7954 (mmm) REVERT: B 648 GLU cc_start: 0.7807 (tp30) cc_final: 0.7447 (pt0) REVERT: C 228 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8486 (mt) REVERT: C 251 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8375 (ttt90) REVERT: C 294 LYS cc_start: 0.7529 (mppt) cc_final: 0.7122 (mptp) REVERT: C 477 GLU cc_start: 0.5122 (OUTLIER) cc_final: 0.4353 (tm-30) REVERT: C 581 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7055 (ptp90) REVERT: C 585 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: C 592 ARG cc_start: 0.8466 (ttm170) cc_final: 0.8165 (ttt180) REVERT: C 622 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8181 (mt0) REVERT: C 643 ASP cc_start: 0.8208 (t0) cc_final: 0.7896 (t0) REVERT: C 650 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: D 232 ILE cc_start: 0.7527 (tp) cc_final: 0.7206 (mm) REVERT: D 239 TYR cc_start: 0.7507 (t80) cc_final: 0.7079 (t80) REVERT: D 255 GLN cc_start: 0.7699 (tt0) cc_final: 0.7349 (mm110) REVERT: D 380 TRP cc_start: 0.7011 (t-100) cc_final: 0.6273 (t60) REVERT: D 536 LEU cc_start: 0.8297 (tp) cc_final: 0.8028 (pt) REVERT: D 584 SER cc_start: 0.8367 (m) cc_final: 0.8128 (p) REVERT: D 590 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7018 (tpt) outliers start: 80 outliers final: 31 residues processed: 280 average time/residue: 0.4828 time to fit residues: 154.6294 Evaluate side-chains 252 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3252 GLU Chi-restraints excluded: chain A residue 3262 ILE Chi-restraints excluded: chain A residue 3275 PHE 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 3573 SER Chi-restraints excluded: chain A residue 3586 VAL Chi-restraints excluded: chain A residue 3671 LEU Chi-restraints excluded: chain A residue 3675 LEU 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 4043 LEU 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 C residue 228 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 513 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 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 313 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 69 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 181 optimal weight: 30.0000 chunk 141 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3559 HIS B 430 ASN B 434 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 = 0.4145 r_free = 0.4145 target = 0.166735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.110063 restraints weight = 22009.168| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.30 r_work: 0.3328 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17544 Z= 0.220 Angle : 0.673 11.607 23873 Z= 0.344 Chirality : 0.045 0.414 2756 Planarity : 0.005 0.060 2972 Dihedral : 8.195 141.319 2604 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 5.28 % Allowed : 17.79 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.18), residues: 2159 helix: 1.70 (0.15), residues: 1156 sheet: -0.58 (0.39), residues: 178 loop : -2.43 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 306 TYR 0.023 0.002 TYR D 486 PHE 0.018 0.002 PHE B 568 TRP 0.016 0.002 TRP D 293 HIS 0.011 0.002 HIS A3559 Details of bonding type rmsd covalent geometry : bond 0.00530 (17532) covalent geometry : angle 0.66461 (23841) SS BOND : bond 0.00414 ( 4) SS BOND : angle 3.07620 ( 8) hydrogen bonds : bond 0.06764 ( 960) hydrogen bonds : angle 4.28270 ( 2787) link_NAG-ASN : bond 0.00319 ( 8) link_NAG-ASN : angle 3.00588 ( 24) *********************** 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 316 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 226 time to evaluate : 0.762 Fit side-chains REVERT: A 3089 MET cc_start: 0.7813 (mtt) cc_final: 0.7368 (tpp) REVERT: A 3096 HIS cc_start: 0.6684 (t-90) cc_final: 0.6433 (t70) REVERT: A 3321 ASP cc_start: 0.5663 (p0) cc_final: 0.5421 (p0) REVERT: A 3671 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7648 (tp) REVERT: A 3721 GLU cc_start: 0.6265 (pm20) cc_final: 0.5759 (tp30) REVERT: A 4006 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.7962 (tt) REVERT: B 500 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6692 (mt) REVERT: B 502 TYR cc_start: 0.7439 (t80) cc_final: 0.7188 (t80) REVERT: B 531 ASN cc_start: 0.6862 (m-40) cc_final: 0.6418 (m-40) REVERT: B 590 MET cc_start: 0.8277 (mmp) cc_final: 0.7410 (mtt) REVERT: B 648 GLU cc_start: 0.7916 (tp30) cc_final: 0.7607 (pt0) REVERT: B 656 LEU cc_start: 0.7911 (tp) cc_final: 0.7668 (tt) REVERT: C 274 SER cc_start: 0.8760 (OUTLIER) cc_final: 0.8544 (m) REVERT: C 294 LYS cc_start: 0.7519 (mppt) cc_final: 0.7173 (mptp) REVERT: C 477 GLU cc_start: 0.5296 (OUTLIER) cc_final: 0.4890 (tm-30) REVERT: C 581 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7088 (ptp90) REVERT: C 592 ARG cc_start: 0.8514 (ttm170) cc_final: 0.8161 (mtp180) REVERT: C 622 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8374 (mt0) REVERT: C 643 ASP cc_start: 0.8308 (t0) cc_final: 0.8057 (t0) REVERT: C 650 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: D 232 ILE cc_start: 0.7642 (tp) cc_final: 0.7372 (mm) REVERT: D 239 TYR cc_start: 0.7880 (t80) cc_final: 0.7495 (t80) REVERT: D 255 GLN cc_start: 0.7773 (tt0) cc_final: 0.7502 (mm110) REVERT: D 380 TRP cc_start: 0.7254 (t-100) cc_final: 0.6547 (t60) REVERT: D 536 LEU cc_start: 0.8184 (tp) cc_final: 0.7941 (pt) REVERT: D 590 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7062 (tpt) outliers start: 90 outliers final: 44 residues processed: 287 average time/residue: 0.5209 time to fit residues: 170.9393 Evaluate side-chains 266 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 213 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 3262 ILE Chi-restraints excluded: chain A residue 3275 PHE 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 3586 VAL Chi-restraints excluded: chain A residue 3597 LEU Chi-restraints excluded: chain A residue 3671 LEU Chi-restraints excluded: chain A residue 3883 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 4006 LEU Chi-restraints excluded: chain A residue 4025 GLU Chi-restraints excluded: chain A residue 4043 LEU 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 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 B residue 500 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 383 ILE 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 513 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 624 ASP Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 650 GLU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain D residue 221 LEU 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 425 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 186 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 46 optimal weight: 20.0000 chunk 23 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 120 optimal weight: 0.0970 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3559 HIS A3695 HIS A3982 GLN A4081 HIS ** C 434 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.170781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.114662 restraints weight = 21995.099| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.30 r_work: 0.3393 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17544 Z= 0.119 Angle : 0.559 10.364 23873 Z= 0.284 Chirality : 0.040 0.361 2756 Planarity : 0.003 0.057 2972 Dihedral : 7.241 134.557 2604 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.76 % Allowed : 20.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.19), residues: 2159 helix: 1.94 (0.15), residues: 1166 sheet: -0.44 (0.40), residues: 178 loop : -2.39 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 528 TYR 0.022 0.001 TYR D 486 PHE 0.013 0.001 PHE D 506 TRP 0.016 0.001 TRP A3939 HIS 0.008 0.001 HIS A3559 Details of bonding type rmsd covalent geometry : bond 0.00249 (17532) covalent geometry : angle 0.55145 (23841) SS BOND : bond 0.00468 ( 4) SS BOND : angle 1.94226 ( 8) hydrogen bonds : bond 0.04736 ( 960) hydrogen bonds : angle 3.93556 ( 2787) link_NAG-ASN : bond 0.00178 ( 8) link_NAG-ASN : angle 2.70081 ( 24) *********************** 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 286 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 222 time to evaluate : 0.699 Fit side-chains REVERT: A 3089 MET cc_start: 0.7772 (mtt) cc_final: 0.7378 (tpt) REVERT: A 3096 HIS cc_start: 0.6536 (t-90) cc_final: 0.6274 (t70) REVERT: A 3321 ASP cc_start: 0.5533 (p0) cc_final: 0.5275 (p0) REVERT: A 3721 GLU cc_start: 0.6122 (pm20) cc_final: 0.5761 (tp30) REVERT: A 4010 ARG cc_start: 0.7633 (tpt170) cc_final: 0.7370 (mpp-170) REVERT: B 306 ARG cc_start: 0.8179 (mtm180) cc_final: 0.7961 (mtm180) REVERT: B 500 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6647 (mt) REVERT: B 502 TYR cc_start: 0.7521 (t80) cc_final: 0.7318 (t80) REVERT: B 531 ASN cc_start: 0.6754 (m-40) cc_final: 0.6290 (m-40) REVERT: B 590 MET cc_start: 0.8224 (mmp) cc_final: 0.7930 (mmm) REVERT: B 595 LYS cc_start: 0.7825 (tppt) cc_final: 0.7609 (tppt) REVERT: B 648 GLU cc_start: 0.8127 (tp30) cc_final: 0.7785 (pt0) REVERT: C 274 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8542 (m) REVERT: C 294 LYS cc_start: 0.7369 (mppt) cc_final: 0.7017 (mptp) REVERT: C 477 GLU cc_start: 0.5200 (tm-30) cc_final: 0.4292 (mt-10) REVERT: C 585 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7529 (tp40) REVERT: C 592 ARG cc_start: 0.8515 (ttm170) cc_final: 0.8174 (mtp180) REVERT: C 622 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8218 (mt0) REVERT: C 643 ASP cc_start: 0.7946 (t0) cc_final: 0.7493 (t0) REVERT: C 650 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: D 232 ILE cc_start: 0.7582 (tp) cc_final: 0.7282 (mm) REVERT: D 239 TYR cc_start: 0.7779 (t80) cc_final: 0.7386 (t80) REVERT: D 253 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6856 (ttt) REVERT: D 255 GLN cc_start: 0.7768 (tt0) cc_final: 0.7513 (mm110) REVERT: D 313 ASN cc_start: 0.7053 (OUTLIER) cc_final: 0.6715 (OUTLIER) REVERT: D 380 TRP cc_start: 0.7087 (t-100) cc_final: 0.6395 (t60) REVERT: D 483 PHE cc_start: 0.7050 (m-80) cc_final: 0.6741 (m-80) REVERT: D 490 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6007 (mt-10) REVERT: D 536 LEU cc_start: 0.8175 (tp) cc_final: 0.7928 (pt) outliers start: 64 outliers final: 34 residues processed: 262 average time/residue: 0.5479 time to fit residues: 162.8660 Evaluate side-chains 252 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 211 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 3262 ILE Chi-restraints excluded: chain A residue 3266 ILE Chi-restraints excluded: chain A residue 3275 PHE 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 3597 LEU Chi-restraints excluded: chain A residue 3883 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 4043 LEU 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 361 ARG Chi-restraints excluded: chain B residue 377 SER 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 274 SER Chi-restraints excluded: chain C residue 383 ILE 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 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 C residue 685 SER Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 313 ASN Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 490 GLU 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 166 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 30.0000 chunk 82 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 204 optimal weight: 0.0070 chunk 3 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 11 optimal weight: 0.0980 overall best weight: 1.4202 ------------------------------------------------------------------------------- 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 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.169477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113457 restraints weight = 21925.727| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.27 r_work: 0.3373 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17544 Z= 0.138 Angle : 0.584 13.391 23873 Z= 0.295 Chirality : 0.040 0.339 2756 Planarity : 0.004 0.054 2972 Dihedral : 7.151 134.324 2604 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.99 % Allowed : 20.73 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.19), residues: 2159 helix: 1.96 (0.15), residues: 1166 sheet: -0.46 (0.39), residues: 180 loop : -2.34 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 528 TYR 0.021 0.001 TYR D 486 PHE 0.013 0.001 PHE D 506 TRP 0.013 0.001 TRP A3298 HIS 0.009 0.001 HIS A3559 Details of bonding type rmsd covalent geometry : bond 0.00308 (17532) covalent geometry : angle 0.57642 (23841) SS BOND : bond 0.00376 ( 4) SS BOND : angle 2.51895 ( 8) hydrogen bonds : bond 0.05170 ( 960) hydrogen bonds : angle 3.95973 ( 2787) link_NAG-ASN : bond 0.00168 ( 8) link_NAG-ASN : angle 2.59978 ( 24) *********************** 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 283 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 215 time to evaluate : 0.609 Fit side-chains REVERT: A 3089 MET cc_start: 0.7763 (mtt) cc_final: 0.7345 (tpt) REVERT: A 3096 HIS cc_start: 0.6545 (t-90) cc_final: 0.6286 (t70) REVERT: A 3321 ASP cc_start: 0.5555 (p0) cc_final: 0.5312 (p0) REVERT: A 4010 ARG cc_start: 0.7616 (tpt170) cc_final: 0.7349 (mpp-170) REVERT: B 500 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6682 (mt) REVERT: B 531 ASN cc_start: 0.6828 (m-40) cc_final: 0.6386 (m-40) REVERT: B 590 MET cc_start: 0.8213 (mmp) cc_final: 0.7917 (mmm) REVERT: B 595 LYS cc_start: 0.7892 (tppt) cc_final: 0.7689 (tppt) REVERT: B 648 GLU cc_start: 0.8209 (tp30) cc_final: 0.7825 (pt0) REVERT: C 274 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.8502 (m) REVERT: C 294 LYS cc_start: 0.7374 (mppt) cc_final: 0.6987 (mptp) REVERT: C 477 GLU cc_start: 0.5164 (tm-30) cc_final: 0.4712 (tm-30) REVERT: C 491 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7640 (tp30) REVERT: C 528 ARG cc_start: 0.6607 (ptt90) cc_final: 0.6394 (ptt180) REVERT: C 585 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7548 (tp40) REVERT: C 592 ARG cc_start: 0.8532 (ttm170) cc_final: 0.8192 (mtp180) REVERT: C 622 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8235 (mt0) REVERT: C 643 ASP cc_start: 0.7979 (t0) cc_final: 0.7531 (t0) REVERT: C 650 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: D 232 ILE cc_start: 0.7582 (tp) cc_final: 0.7309 (mm) REVERT: D 239 TYR cc_start: 0.7848 (t80) cc_final: 0.7446 (t80) REVERT: D 253 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6848 (ttt) REVERT: D 255 GLN cc_start: 0.7770 (tt0) cc_final: 0.7484 (mm110) REVERT: D 380 TRP cc_start: 0.7160 (t-100) cc_final: 0.6441 (t60) REVERT: D 490 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6158 (mt-10) REVERT: D 536 LEU cc_start: 0.8246 (tp) cc_final: 0.8042 (pt) REVERT: D 590 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.6856 (tpt) outliers start: 68 outliers final: 47 residues processed: 258 average time/residue: 0.5571 time to fit residues: 163.6880 Evaluate side-chains 264 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 208 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 3262 ILE Chi-restraints excluded: chain A residue 3266 ILE Chi-restraints excluded: chain A residue 3275 PHE 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 3331 VAL 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 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 4043 LEU 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 221 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 377 SER 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 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 491 GLU Chi-restraints excluded: chain C residue 513 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 C residue 673 LEU Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 490 GLU 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 25 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 209 optimal weight: 0.9990 chunk 137 optimal weight: 0.1980 chunk 142 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 6 optimal weight: 30.0000 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3559 HIS A4081 HIS B 550 HIS ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 559 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.171815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.116329 restraints weight = 22010.756| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.29 r_work: 0.3413 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4040 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= 0.109 Angle : 0.550 12.446 23873 Z= 0.277 Chirality : 0.039 0.308 2756 Planarity : 0.003 0.051 2972 Dihedral : 6.748 128.796 2604 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.41 % Allowed : 21.37 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.19), residues: 2159 helix: 2.12 (0.15), residues: 1166 sheet: -0.32 (0.40), residues: 178 loop : -2.30 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 528 TYR 0.021 0.001 TYR C 486 PHE 0.012 0.001 PHE D 506 TRP 0.017 0.001 TRP A3298 HIS 0.010 0.001 HIS A3559 Details of bonding type rmsd covalent geometry : bond 0.00220 (17532) covalent geometry : angle 0.54413 (23841) SS BOND : bond 0.00221 ( 4) SS BOND : angle 1.76831 ( 8) hydrogen bonds : bond 0.04330 ( 960) hydrogen bonds : angle 3.81828 ( 2787) link_NAG-ASN : bond 0.00151 ( 8) link_NAG-ASN : angle 2.28787 ( 24) *********************** 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: 58 poor density : 223 time to evaluate : 0.732 Fit side-chains REVERT: A 3089 MET cc_start: 0.7825 (mtt) cc_final: 0.7400 (tpt) REVERT: A 3096 HIS cc_start: 0.6579 (t-90) cc_final: 0.6311 (t70) REVERT: A 3321 ASP cc_start: 0.5613 (p0) cc_final: 0.5405 (p0) REVERT: A 3334 TYR cc_start: 0.6359 (OUTLIER) cc_final: 0.5697 (m-80) REVERT: B 306 ARG cc_start: 0.7985 (mtm180) cc_final: 0.7704 (mtm180) REVERT: B 500 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6484 (mt) REVERT: B 531 ASN cc_start: 0.6843 (m-40) cc_final: 0.6423 (m-40) REVERT: B 590 MET cc_start: 0.8198 (mmp) cc_final: 0.7915 (mmm) REVERT: B 648 GLU cc_start: 0.8269 (tp30) cc_final: 0.7917 (pt0) REVERT: C 274 SER cc_start: 0.8699 (p) cc_final: 0.8466 (m) REVERT: C 294 LYS cc_start: 0.7322 (mppt) cc_final: 0.6940 (mptp) REVERT: C 477 GLU cc_start: 0.5127 (tm-30) cc_final: 0.4231 (mt-10) REVERT: C 585 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: C 592 ARG cc_start: 0.8500 (ttm170) cc_final: 0.8174 (mtp180) REVERT: C 643 ASP cc_start: 0.7923 (t0) cc_final: 0.7401 (t0) REVERT: C 650 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: D 232 ILE cc_start: 0.7564 (tp) cc_final: 0.7263 (mm) REVERT: D 239 TYR cc_start: 0.7783 (t80) cc_final: 0.7378 (t80) REVERT: D 253 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6786 (ttt) REVERT: D 255 GLN cc_start: 0.7766 (tt0) cc_final: 0.7499 (mm110) REVERT: D 380 TRP cc_start: 0.7072 (t-100) cc_final: 0.6365 (t60) REVERT: D 536 LEU cc_start: 0.8321 (tp) cc_final: 0.8070 (pt) outliers start: 58 outliers final: 35 residues processed: 261 average time/residue: 0.5375 time to fit residues: 160.4099 Evaluate side-chains 246 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 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 3978 ASP Chi-restraints excluded: chain A residue 4025 GLU Chi-restraints excluded: chain A residue 4043 LEU 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 377 SER 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 B residue 534 VAL 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 585 GLN Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 650 GLU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 425 ASP 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 118 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 187 optimal weight: 9.9990 chunk 189 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 88 optimal weight: 0.4980 chunk 101 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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** B 430 ASN ** 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 = 0.4183 r_free = 0.4183 target = 0.170776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.115500 restraints weight = 21938.006| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.24 r_work: 0.3399 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17544 Z= 0.119 Angle : 0.564 12.051 23873 Z= 0.284 Chirality : 0.039 0.297 2756 Planarity : 0.004 0.068 2972 Dihedral : 6.701 126.088 2604 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.05 % Allowed : 22.20 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.19), residues: 2159 helix: 2.14 (0.15), residues: 1166 sheet: -0.28 (0.39), residues: 178 loop : -2.29 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A3924 TYR 0.021 0.001 TYR C 486 PHE 0.011 0.001 PHE D 506 TRP 0.019 0.001 TRP A3298 HIS 0.010 0.001 HIS A3559 Details of bonding type rmsd covalent geometry : bond 0.00257 (17532) covalent geometry : angle 0.55950 (23841) SS BOND : bond 0.00262 ( 4) SS BOND : angle 1.72187 ( 8) hydrogen bonds : bond 0.04606 ( 960) hydrogen bonds : angle 3.83852 ( 2787) link_NAG-ASN : bond 0.00145 ( 8) link_NAG-ASN : angle 2.21843 ( 24) *********************** 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 264 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 212 time to evaluate : 0.688 Fit side-chains REVERT: A 3089 MET cc_start: 0.7812 (mtt) cc_final: 0.7391 (tpt) REVERT: A 3096 HIS cc_start: 0.6575 (t-90) cc_final: 0.6298 (t70) REVERT: A 3321 ASP cc_start: 0.5491 (p0) cc_final: 0.5284 (p0) REVERT: A 3719 ARG cc_start: 0.5784 (mmm160) cc_final: 0.5491 (mmm160) REVERT: A 3721 GLU cc_start: 0.6439 (pm20) cc_final: 0.6176 (tp30) REVERT: B 306 ARG cc_start: 0.8019 (mtm180) cc_final: 0.7706 (mtm180) REVERT: B 500 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6483 (mt) REVERT: B 531 ASN cc_start: 0.6815 (m-40) cc_final: 0.6394 (m-40) REVERT: B 590 MET cc_start: 0.8219 (mmp) cc_final: 0.7936 (mmm) REVERT: B 648 GLU cc_start: 0.8230 (tp30) cc_final: 0.7845 (pt0) REVERT: C 274 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8466 (m) REVERT: C 294 LYS cc_start: 0.7317 (mppt) cc_final: 0.6929 (mptp) REVERT: C 477 GLU cc_start: 0.5059 (tm-30) cc_final: 0.4167 (mt-10) REVERT: C 585 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: C 592 ARG cc_start: 0.8511 (ttm170) cc_final: 0.8190 (mtp180) REVERT: C 643 ASP cc_start: 0.7952 (t0) cc_final: 0.7409 (t0) REVERT: C 650 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: D 232 ILE cc_start: 0.7492 (tp) cc_final: 0.7219 (mm) REVERT: D 239 TYR cc_start: 0.7803 (t80) cc_final: 0.7372 (t80) REVERT: D 253 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6688 (ttt) REVERT: D 255 GLN cc_start: 0.7765 (tt0) cc_final: 0.7563 (mm110) REVERT: D 380 TRP cc_start: 0.7126 (t-100) cc_final: 0.6456 (t60) REVERT: D 477 GLU cc_start: 0.5561 (tt0) cc_final: 0.4980 (tp30) REVERT: D 490 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6466 (mm-30) REVERT: D 536 LEU cc_start: 0.8332 (tp) cc_final: 0.8021 (pt) outliers start: 52 outliers final: 38 residues processed: 248 average time/residue: 0.5418 time to fit residues: 153.4427 Evaluate side-chains 249 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 3262 ILE Chi-restraints excluded: chain A residue 3266 ILE Chi-restraints excluded: chain A residue 3275 PHE 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 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 4043 LEU 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 377 SER 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 B residue 534 VAL Chi-restraints excluded: chain C residue 221 LEU 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 513 VAL Chi-restraints excluded: chain C residue 585 GLN Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 650 GLU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 253 MET 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 425 ASP Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 689 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 50 optimal weight: 20.0000 chunk 177 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 200 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 88 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.169075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.113438 restraints weight = 21901.404| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.24 r_work: 0.3370 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4200 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= 0.147 Angle : 0.597 11.853 23873 Z= 0.304 Chirality : 0.041 0.291 2756 Planarity : 0.004 0.050 2972 Dihedral : 6.939 129.900 2604 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.41 % Allowed : 22.08 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.19), residues: 2159 helix: 2.09 (0.15), residues: 1166 sheet: -0.36 (0.39), residues: 178 loop : -2.27 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A3924 TYR 0.021 0.002 TYR C 486 PHE 0.013 0.001 PHE C 600 TRP 0.023 0.001 TRP A3298 HIS 0.010 0.001 HIS A3559 Details of bonding type rmsd covalent geometry : bond 0.00336 (17532) covalent geometry : angle 0.59206 (23841) SS BOND : bond 0.00331 ( 4) SS BOND : angle 2.05043 ( 8) hydrogen bonds : bond 0.05238 ( 960) hydrogen bonds : angle 3.93816 ( 2787) link_NAG-ASN : bond 0.00179 ( 8) link_NAG-ASN : angle 2.26833 ( 24) *********************** 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 267 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 209 time to evaluate : 0.513 Fit side-chains REVERT: A 3089 MET cc_start: 0.7766 (mtt) cc_final: 0.7352 (tpt) REVERT: A 3096 HIS cc_start: 0.6619 (t-90) cc_final: 0.6348 (t70) REVERT: A 3321 ASP cc_start: 0.5516 (p0) cc_final: 0.5292 (p0) REVERT: A 3719 ARG cc_start: 0.5775 (mmm160) cc_final: 0.5557 (mmm160) REVERT: A 3721 GLU cc_start: 0.6441 (pm20) cc_final: 0.6221 (tp30) REVERT: B 500 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6512 (mt) REVERT: B 531 ASN cc_start: 0.6823 (m-40) cc_final: 0.6397 (m-40) REVERT: B 590 MET cc_start: 0.8222 (mmp) cc_final: 0.7926 (mmm) REVERT: B 648 GLU cc_start: 0.8264 (tp30) cc_final: 0.7876 (pt0) REVERT: C 274 SER cc_start: 0.8694 (OUTLIER) cc_final: 0.8469 (m) REVERT: C 294 LYS cc_start: 0.7339 (mppt) cc_final: 0.6990 (mptp) REVERT: C 477 GLU cc_start: 0.5158 (tm-30) cc_final: 0.4335 (tm-30) REVERT: C 585 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7501 (tp40) REVERT: C 592 ARG cc_start: 0.8509 (ttm170) cc_final: 0.8185 (mtp180) REVERT: C 643 ASP cc_start: 0.7952 (t0) cc_final: 0.7542 (t0) REVERT: C 650 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: D 232 ILE cc_start: 0.7550 (tp) cc_final: 0.7284 (mm) REVERT: D 239 TYR cc_start: 0.7858 (t80) cc_final: 0.7416 (t80) REVERT: D 253 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6788 (ttt) REVERT: D 255 GLN cc_start: 0.7801 (tt0) cc_final: 0.7537 (mm110) REVERT: D 380 TRP cc_start: 0.7169 (t-100) cc_final: 0.6479 (t60) REVERT: D 477 GLU cc_start: 0.5594 (tt0) cc_final: 0.4984 (tp30) REVERT: D 536 LEU cc_start: 0.8318 (tp) cc_final: 0.8024 (pt) REVERT: D 590 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.6699 (tpt) outliers start: 58 outliers final: 39 residues processed: 249 average time/residue: 0.4831 time to fit residues: 138.3934 Evaluate side-chains 252 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 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 3597 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 4043 LEU 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 377 SER 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 B residue 534 VAL Chi-restraints excluded: chain C residue 221 LEU 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 513 VAL Chi-restraints excluded: chain C residue 585 GLN Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 650 GLU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 253 MET 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 425 ASP Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 590 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 69 optimal weight: 0.9990 chunk 139 optimal weight: 0.0020 chunk 166 optimal weight: 0.0970 chunk 31 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 198 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 10 optimal weight: 30.0000 chunk 89 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 = 0.4201 r_free = 0.4201 target = 0.172586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.117782 restraints weight = 21955.830| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.25 r_work: 0.3430 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17544 Z= 0.107 Angle : 0.560 11.725 23873 Z= 0.282 Chirality : 0.039 0.274 2756 Planarity : 0.003 0.050 2972 Dihedral : 6.545 123.168 2604 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.29 % Allowed : 23.31 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.19), residues: 2159 helix: 2.23 (0.15), residues: 1165 sheet: -0.29 (0.39), residues: 178 loop : -2.26 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A3924 TYR 0.022 0.001 TYR C 486 PHE 0.011 0.001 PHE D 506 TRP 0.020 0.001 TRP A3298 HIS 0.011 0.001 HIS A3559 Details of bonding type rmsd covalent geometry : bond 0.00215 (17532) covalent geometry : angle 0.55459 (23841) SS BOND : bond 0.00186 ( 4) SS BOND : angle 2.99398 ( 8) hydrogen bonds : bond 0.04088 ( 960) hydrogen bonds : angle 3.76165 ( 2787) link_NAG-ASN : bond 0.00173 ( 8) link_NAG-ASN : angle 1.95510 ( 24) ********************** 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 248 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 0.718 Fit side-chains REVERT: A 3089 MET cc_start: 0.7799 (mtt) cc_final: 0.7391 (tpt) REVERT: A 3096 HIS cc_start: 0.6517 (t-90) cc_final: 0.6235 (t70) REVERT: A 3097 LYS cc_start: 0.6952 (ttmm) cc_final: 0.6702 (ttmp) REVERT: A 3321 ASP cc_start: 0.5644 (p0) cc_final: 0.5437 (p0) REVERT: A 3721 GLU cc_start: 0.6483 (pm20) cc_final: 0.6238 (tp30) REVERT: B 500 LEU cc_start: 0.6637 (OUTLIER) cc_final: 0.6405 (mt) REVERT: B 531 ASN cc_start: 0.6716 (m-40) cc_final: 0.6288 (m110) REVERT: B 590 MET cc_start: 0.8199 (mmp) cc_final: 0.7920 (mmm) REVERT: B 648 GLU cc_start: 0.8248 (tp30) cc_final: 0.7895 (pt0) REVERT: C 294 LYS cc_start: 0.7328 (mppt) cc_final: 0.6923 (mptp) REVERT: C 477 GLU cc_start: 0.5095 (tm-30) cc_final: 0.4247 (mt-10) REVERT: C 585 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7468 (tt0) REVERT: C 592 ARG cc_start: 0.8509 (ttm170) cc_final: 0.8186 (mtp180) REVERT: C 643 ASP cc_start: 0.7920 (t0) cc_final: 0.7409 (t0) REVERT: C 650 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: D 232 ILE cc_start: 0.7480 (tp) cc_final: 0.7203 (mm) REVERT: D 239 TYR cc_start: 0.7803 (t80) cc_final: 0.7337 (t80) REVERT: D 255 GLN cc_start: 0.7823 (tt0) cc_final: 0.7592 (mm110) REVERT: D 380 TRP cc_start: 0.7084 (t-100) cc_final: 0.6362 (t60) REVERT: D 536 LEU cc_start: 0.8307 (tp) cc_final: 0.8036 (pt) outliers start: 39 outliers final: 27 residues processed: 236 average time/residue: 0.5339 time to fit residues: 144.2905 Evaluate side-chains 235 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3091 MET Chi-restraints excluded: chain A residue 3275 PHE 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 3893 LEU Chi-restraints excluded: chain A residue 3978 ASP Chi-restraints excluded: chain A residue 4043 LEU 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 377 SER 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 B residue 534 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 585 GLN 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 275 SER Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 522 ILE 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 27 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 47 optimal weight: 50.0000 chunk 191 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 155 optimal weight: 0.4980 chunk 126 optimal weight: 0.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.167693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.111730 restraints weight = 22019.865| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.25 r_work: 0.3346 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17544 Z= 0.188 Angle : 0.643 11.487 23873 Z= 0.328 Chirality : 0.042 0.279 2756 Planarity : 0.004 0.049 2972 Dihedral : 7.196 131.568 2604 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.58 % Allowed : 23.02 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.19), residues: 2159 helix: 2.03 (0.15), residues: 1166 sheet: -0.41 (0.39), residues: 178 loop : -2.27 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 528 TYR 0.022 0.002 TYR B 502 PHE 0.017 0.002 PHE C 646 TRP 0.024 0.001 TRP A3298 HIS 0.011 0.001 HIS A3559 Details of bonding type rmsd covalent geometry : bond 0.00448 (17532) covalent geometry : angle 0.63306 (23841) SS BOND : bond 0.00781 ( 4) SS BOND : angle 4.72244 ( 8) hydrogen bonds : bond 0.05884 ( 960) hydrogen bonds : angle 4.05270 ( 2787) link_NAG-ASN : bond 0.00238 ( 8) link_NAG-ASN : angle 2.27129 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10892.74 seconds wall clock time: 184 minutes 58.91 seconds (11098.91 seconds total)