Starting phenix.real_space_refine on Tue Apr 16 06:30:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkm_36373/04_2024/8jkm_36373.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkm_36373/04_2024/8jkm_36373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkm_36373/04_2024/8jkm_36373.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkm_36373/04_2024/8jkm_36373.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkm_36373/04_2024/8jkm_36373.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkm_36373/04_2024/8jkm_36373.pdb" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.020 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: 5 Type Number sf(0) Gaussians S 96 5.16 5 C 12316 2.51 5 N 3140 2.21 5 O 3368 1.98 5 H 19252 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 684": "OE1" <-> "OE2" Residue "B GLU 684": "OE1" <-> "OE2" Residue "C GLU 684": "OE1" <-> "OE2" Residue "D GLU 684": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 38172 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 9543 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 19, 'TRANS': 566} Chain breaks: 4 Chain: "B" Number of atoms: 9543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 9543 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 19, 'TRANS': 566} Chain breaks: 4 Chain: "C" Number of atoms: 9543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 9543 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 19, 'TRANS': 566} Chain breaks: 4 Chain: "D" Number of atoms: 9543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 9543 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 19, 'TRANS': 566} Chain breaks: 4 Time building chain proxies: 18.65, per 1000 atoms: 0.49 Number of scatterers: 38172 At special positions: 0 Unit cell: (142.29, 142.29, 119.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 O 3368 8.00 N 3140 7.00 C 12316 6.00 H 19252 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 33.75 Conformation dependent library (CDL) restraints added in 4.4 seconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 68.3% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.938A pdb=" N LEU A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 176 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.693A pdb=" N LYS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 215 through 221 removed outlier: 4.199A pdb=" N ARG A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 228 removed outlier: 4.014A pdb=" N ASN A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 Processing helix chain 'A' and resid 250 through 261 removed outlier: 4.138A pdb=" N VAL A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 275 through 279 removed outlier: 4.101A pdb=" N GLY A 279 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 322 through 331 removed outlier: 3.827A pdb=" N HIS A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 357 Processing helix chain 'A' and resid 372 through 380 Processing helix chain 'A' and resid 382 through 391 removed outlier: 4.278A pdb=" N HIS A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 452 through 466 Processing helix chain 'A' and resid 466 through 491 Processing helix chain 'A' and resid 504 through 531 Processing helix chain 'A' and resid 550 through 569 Processing helix chain 'A' and resid 575 through 594 removed outlier: 3.767A pdb=" N LEU A 590 " --> pdb=" O TRP A 586 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A 591 " --> pdb=" O MET A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 599 removed outlier: 4.381A pdb=" N LEU A 598 " --> pdb=" O GLY A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 636 removed outlier: 3.870A pdb=" N LEU A 610 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE A 611 " --> pdb=" O GLN A 607 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LYS A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 631 " --> pdb=" O GLY A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 680 removed outlier: 4.420A pdb=" N LEU A 670 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 726 Processing helix chain 'A' and resid 727 through 730 Processing helix chain 'A' and resid 731 through 748 removed outlier: 3.552A pdb=" N PHE A 748 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.938A pdb=" N LEU B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 176 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.693A pdb=" N LYS B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 215 through 221 removed outlier: 4.199A pdb=" N ARG B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 removed outlier: 4.014A pdb=" N ASN B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 248 Processing helix chain 'B' and resid 250 through 261 removed outlier: 4.138A pdb=" N VAL B 254 " --> pdb=" O CYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 275 through 279 removed outlier: 4.101A pdb=" N GLY B 279 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 322 through 331 removed outlier: 3.827A pdb=" N HIS B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 357 Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'B' and resid 382 through 391 removed outlier: 4.278A pdb=" N HIS B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG B 391 " --> pdb=" O GLN B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 445 through 450 Processing helix chain 'B' and resid 452 through 466 Processing helix chain 'B' and resid 466 through 491 Processing helix chain 'B' and resid 504 through 531 Processing helix chain 'B' and resid 550 through 569 Processing helix chain 'B' and resid 575 through 594 removed outlier: 3.767A pdb=" N LEU B 590 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR B 591 " --> pdb=" O MET B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 599 removed outlier: 4.381A pdb=" N LEU B 598 " --> pdb=" O GLY B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 636 removed outlier: 3.869A pdb=" N LEU B 610 " --> pdb=" O ILE B 606 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE B 611 " --> pdb=" O GLN B 607 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LYS B 612 " --> pdb=" O LYS B 608 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA B 631 " --> pdb=" O GLY B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 680 removed outlier: 4.421A pdb=" N LEU B 670 " --> pdb=" O PHE B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 726 Processing helix chain 'B' and resid 727 through 730 Processing helix chain 'B' and resid 731 through 748 removed outlier: 3.552A pdb=" N PHE B 748 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 161 removed outlier: 3.938A pdb=" N LEU C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 176 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.693A pdb=" N LYS C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 215 through 221 removed outlier: 4.199A pdb=" N ARG C 219 " --> pdb=" O ASP C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 228 removed outlier: 4.014A pdb=" N ASN C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 248 Processing helix chain 'C' and resid 250 through 261 removed outlier: 4.138A pdb=" N VAL C 254 " --> pdb=" O CYS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 275 through 279 removed outlier: 4.101A pdb=" N GLY C 279 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 297 through 307 Processing helix chain 'C' and resid 322 through 331 removed outlier: 3.827A pdb=" N HIS C 326 " --> pdb=" O ASN C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 357 Processing helix chain 'C' and resid 372 through 380 Processing helix chain 'C' and resid 382 through 391 removed outlier: 4.278A pdb=" N HIS C 388 " --> pdb=" O GLY C 384 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 400 Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 445 through 450 Processing helix chain 'C' and resid 452 through 466 Processing helix chain 'C' and resid 466 through 491 Processing helix chain 'C' and resid 504 through 531 Processing helix chain 'C' and resid 550 through 569 Processing helix chain 'C' and resid 575 through 594 removed outlier: 3.767A pdb=" N LEU C 590 " --> pdb=" O TRP C 586 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR C 591 " --> pdb=" O MET C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 599 removed outlier: 4.381A pdb=" N LEU C 598 " --> pdb=" O GLY C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 636 removed outlier: 3.870A pdb=" N LEU C 610 " --> pdb=" O ILE C 606 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE C 611 " --> pdb=" O GLN C 607 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LYS C 612 " --> pdb=" O LYS C 608 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA C 631 " --> pdb=" O GLY C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 680 removed outlier: 4.420A pdb=" N LEU C 670 " --> pdb=" O PHE C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 726 Processing helix chain 'C' and resid 727 through 730 Processing helix chain 'C' and resid 731 through 748 removed outlier: 3.551A pdb=" N PHE C 748 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 161 removed outlier: 3.938A pdb=" N LEU D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 176 Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.693A pdb=" N LYS D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 215 Processing helix chain 'D' and resid 215 through 221 removed outlier: 4.199A pdb=" N ARG D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 228 removed outlier: 4.015A pdb=" N ASN D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 248 Processing helix chain 'D' and resid 250 through 261 removed outlier: 4.138A pdb=" N VAL D 254 " --> pdb=" O CYS D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 275 through 279 removed outlier: 4.101A pdb=" N GLY D 279 " --> pdb=" O LYS D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 297 through 307 Processing helix chain 'D' and resid 322 through 331 removed outlier: 3.827A pdb=" N HIS D 326 " --> pdb=" O ASN D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 357 Processing helix chain 'D' and resid 372 through 380 Processing helix chain 'D' and resid 382 through 391 removed outlier: 4.278A pdb=" N HIS D 388 " --> pdb=" O GLY D 384 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG D 391 " --> pdb=" O GLN D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 400 Processing helix chain 'D' and resid 432 through 439 Processing helix chain 'D' and resid 445 through 450 Processing helix chain 'D' and resid 452 through 466 Processing helix chain 'D' and resid 466 through 491 Processing helix chain 'D' and resid 504 through 531 Processing helix chain 'D' and resid 550 through 569 Processing helix chain 'D' and resid 575 through 594 removed outlier: 3.767A pdb=" N LEU D 590 " --> pdb=" O TRP D 586 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR D 591 " --> pdb=" O MET D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 599 removed outlier: 4.381A pdb=" N LEU D 598 " --> pdb=" O GLY D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 636 removed outlier: 3.870A pdb=" N LEU D 610 " --> pdb=" O ILE D 606 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE D 611 " --> pdb=" O GLN D 607 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LYS D 612 " --> pdb=" O LYS D 608 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 631 " --> pdb=" O GLY D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 680 removed outlier: 4.420A pdb=" N LEU D 670 " --> pdb=" O PHE D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 726 Processing helix chain 'D' and resid 727 through 730 Processing helix chain 'D' and resid 731 through 748 removed outlier: 3.552A pdb=" N PHE D 748 " --> pdb=" O ILE D 744 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 410 removed outlier: 3.665A pdb=" N ASP A 408 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N SER A 416 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ALA A 410 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL A 414 " --> pdb=" O ALA A 410 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 405 through 410 removed outlier: 3.666A pdb=" N ASP B 408 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N SER B 416 " --> pdb=" O ASP B 408 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ALA B 410 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B 414 " --> pdb=" O ALA B 410 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 405 through 410 removed outlier: 3.665A pdb=" N ASP C 408 " --> pdb=" O SER C 416 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N SER C 416 " --> pdb=" O ASP C 408 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ALA C 410 " --> pdb=" O VAL C 414 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C 414 " --> pdb=" O ALA C 410 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 405 through 410 removed outlier: 3.665A pdb=" N ASP D 408 " --> pdb=" O SER D 416 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N SER D 416 " --> pdb=" O ASP D 408 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ALA D 410 " --> pdb=" O VAL D 414 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL D 414 " --> pdb=" O ALA D 410 " (cutoff:3.500A) 1088 hydrogen bonds defined for protein. 3144 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: 15.16 Time building geometry restraints manager: 34.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 19220 1.03 - 1.23: 32 1.23 - 1.42: 8116 1.42 - 1.61: 11056 1.61 - 1.81: 160 Bond restraints: 38584 Sorted by residual: bond pdb=" C GLN D 492 " pdb=" N PRO D 493 " ideal model delta sigma weight residual 1.330 1.345 -0.015 1.19e-02 7.06e+03 1.50e+00 bond pdb=" C GLN A 492 " pdb=" N PRO A 493 " ideal model delta sigma weight residual 1.330 1.345 -0.015 1.19e-02 7.06e+03 1.50e+00 bond pdb=" C GLN C 492 " pdb=" N PRO C 493 " ideal model delta sigma weight residual 1.330 1.345 -0.015 1.19e-02 7.06e+03 1.50e+00 bond pdb=" C GLN B 492 " pdb=" N PRO B 493 " ideal model delta sigma weight residual 1.330 1.345 -0.015 1.19e-02 7.06e+03 1.50e+00 bond pdb=" CB MET B 680 " pdb=" CG MET B 680 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.27e+00 ... (remaining 38579 not shown) Histogram of bond angle deviations from ideal: 74.56 - 86.45: 28 86.45 - 98.34: 4 98.34 - 110.23: 36691 110.23 - 122.13: 27561 122.13 - 134.02: 5416 Bond angle restraints: 69700 Sorted by residual: angle pdb=" CB ASN D 637 " pdb=" CA ASN D 637 " pdb=" HA ASN D 637 " ideal model delta sigma weight residual 109.00 74.56 34.44 3.00e+00 1.11e-01 1.32e+02 angle pdb=" CB ASN C 637 " pdb=" CA ASN C 637 " pdb=" HA ASN C 637 " ideal model delta sigma weight residual 109.00 74.56 34.44 3.00e+00 1.11e-01 1.32e+02 angle pdb=" CB ASN B 637 " pdb=" CA ASN B 637 " pdb=" HA ASN B 637 " ideal model delta sigma weight residual 109.00 74.56 34.44 3.00e+00 1.11e-01 1.32e+02 angle pdb=" CB ASN A 637 " pdb=" CA ASN A 637 " pdb=" HA ASN A 637 " ideal model delta sigma weight residual 109.00 74.56 34.44 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C ASN D 637 " pdb=" CA ASN D 637 " pdb=" HA ASN D 637 " ideal model delta sigma weight residual 109.00 75.32 33.68 3.00e+00 1.11e-01 1.26e+02 ... (remaining 69695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 16127 16.57 - 33.14: 1449 33.14 - 49.71: 296 49.71 - 66.29: 164 66.29 - 82.86: 32 Dihedral angle restraints: 18068 sinusoidal: 9720 harmonic: 8348 Sorted by residual: dihedral pdb=" C ASN B 637 " pdb=" N ASN B 637 " pdb=" CA ASN B 637 " pdb=" CB ASN B 637 " ideal model delta harmonic sigma weight residual -122.60 -133.22 10.62 0 2.50e+00 1.60e-01 1.81e+01 dihedral pdb=" C ASN D 637 " pdb=" N ASN D 637 " pdb=" CA ASN D 637 " pdb=" CB ASN D 637 " ideal model delta harmonic sigma weight residual -122.60 -133.19 10.59 0 2.50e+00 1.60e-01 1.79e+01 dihedral pdb=" C ASN A 637 " pdb=" N ASN A 637 " pdb=" CA ASN A 637 " pdb=" CB ASN A 637 " ideal model delta harmonic sigma weight residual -122.60 -133.18 10.58 0 2.50e+00 1.60e-01 1.79e+01 ... (remaining 18065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2939 0.085 - 0.169: 81 0.169 - 0.254: 0 0.254 - 0.339: 0 0.339 - 0.423: 4 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CA ASN D 637 " pdb=" N ASN D 637 " pdb=" C ASN D 637 " pdb=" CB ASN D 637 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA ASN B 637 " pdb=" N ASN B 637 " pdb=" C ASN B 637 " pdb=" CB ASN B 637 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA ASN A 637 " pdb=" N ASN A 637 " pdb=" C ASN A 637 " pdb=" CB ASN A 637 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 3021 not shown) Planarity restraints: 5500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 497 " -0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO C 498 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 498 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 498 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 497 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO D 498 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 498 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 498 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 497 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO A 498 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 498 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 498 " 0.039 5.00e-02 4.00e+02 ... (remaining 5497 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 1528 2.14 - 2.76: 74459 2.76 - 3.37: 112258 3.37 - 3.99: 133973 3.99 - 4.60: 211479 Nonbonded interactions: 533697 Sorted by model distance: nonbonded pdb=" O LEU C 676 " pdb=" H GLY C 681 " model vdw 1.526 1.850 nonbonded pdb=" O LEU A 676 " pdb=" H GLY A 681 " model vdw 1.526 1.850 nonbonded pdb=" O LEU D 676 " pdb=" H GLY D 681 " model vdw 1.526 1.850 nonbonded pdb=" O LEU B 676 " pdb=" H GLY B 681 " model vdw 1.526 1.850 nonbonded pdb=" OG SER B 416 " pdb="HH11 ARG B 779 " model vdw 1.578 1.850 ... (remaining 533692 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.810 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: 0.590 Extract box with map and model: 5.860 Check model and map are aligned: 0.610 Set scattering table: 0.390 Process input model: 126.730 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19332 Z= 0.180 Angle : 0.608 5.991 26180 Z= 0.339 Chirality : 0.039 0.423 3024 Planarity : 0.004 0.072 3248 Dihedral : 13.651 82.858 7044 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.38 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.19), residues: 2304 helix: 0.70 (0.14), residues: 1364 sheet: -1.63 (0.66), residues: 56 loop : -1.57 (0.24), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 586 HIS 0.007 0.001 HIS A 731 PHE 0.016 0.001 PHE C 669 TYR 0.020 0.002 TYR D 303 ARG 0.005 0.000 ARG C 661 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 601 time to evaluate : 3.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.1080 (tpt) cc_final: -0.0010 (tpt) REVERT: A 425 ASP cc_start: 0.7265 (m-30) cc_final: 0.6688 (m-30) REVERT: B 223 MET cc_start: 0.1100 (tpt) cc_final: 0.0004 (tpt) REVERT: C 223 MET cc_start: 0.1074 (tpt) cc_final: -0.0025 (tpt) REVERT: C 425 ASP cc_start: 0.7240 (m-30) cc_final: 0.6661 (m-30) REVERT: D 223 MET cc_start: 0.1098 (tpt) cc_final: -0.0004 (tpt) REVERT: D 425 ASP cc_start: 0.7270 (m-30) cc_final: 0.6701 (m-30) outliers start: 0 outliers final: 0 residues processed: 601 average time/residue: 0.8485 time to fit residues: 749.9437 Evaluate side-chains 408 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 3.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.9980 chunk 175 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN B 239 GLN C 239 GLN D 239 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19332 Z= 0.296 Angle : 0.659 10.394 26180 Z= 0.357 Chirality : 0.041 0.458 3024 Planarity : 0.005 0.051 3248 Dihedral : 4.825 20.558 2576 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.99 % Favored : 91.84 % Rotamer: Outliers : 2.55 % Allowed : 11.18 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.18), residues: 2304 helix: 0.27 (0.13), residues: 1404 sheet: -2.45 (0.59), residues: 56 loop : -1.87 (0.24), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 586 HIS 0.008 0.002 HIS D 243 PHE 0.028 0.002 PHE C 172 TYR 0.019 0.002 TYR C 235 ARG 0.006 0.001 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 400 time to evaluate : 3.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.2029 (tpt) cc_final: 0.1261 (tpt) REVERT: A 425 ASP cc_start: 0.7222 (m-30) cc_final: 0.6701 (m-30) REVERT: A 578 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7012 (tmm) REVERT: A 625 MET cc_start: 0.7649 (mtp) cc_final: 0.7083 (mtp) REVERT: B 223 MET cc_start: 0.1968 (tpt) cc_final: 0.1212 (tpt) REVERT: B 425 ASP cc_start: 0.7250 (m-30) cc_final: 0.6696 (m-30) REVERT: B 553 TYR cc_start: 0.7538 (t80) cc_final: 0.7314 (t80) REVERT: B 578 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.6945 (tmm) REVERT: B 625 MET cc_start: 0.7545 (mtp) cc_final: 0.6858 (mtp) REVERT: C 223 MET cc_start: 0.2059 (tpt) cc_final: 0.1285 (tpt) REVERT: C 425 ASP cc_start: 0.7232 (m-30) cc_final: 0.6708 (m-30) REVERT: C 578 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6969 (tmm) REVERT: C 625 MET cc_start: 0.7534 (mtp) cc_final: 0.6866 (mtp) REVERT: D 223 MET cc_start: 0.2039 (tpt) cc_final: 0.1268 (tpt) REVERT: D 425 ASP cc_start: 0.7223 (m-30) cc_final: 0.6708 (m-30) REVERT: D 553 TYR cc_start: 0.7718 (t80) cc_final: 0.7202 (t80) REVERT: D 578 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.6972 (tmm) REVERT: D 625 MET cc_start: 0.7563 (mtp) cc_final: 0.6891 (mtp) outliers start: 53 outliers final: 39 residues processed: 433 average time/residue: 0.7146 time to fit residues: 486.9333 Evaluate side-chains 411 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 368 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain A residue 777 CYS Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 672 ASP Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 760 GLU Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 672 ASP Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 747 SER Chi-restraints excluded: chain D residue 777 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 58 optimal weight: 30.0000 chunk 211 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19332 Z= 0.306 Angle : 0.659 10.286 26180 Z= 0.355 Chirality : 0.041 0.461 3024 Planarity : 0.005 0.044 3248 Dihedral : 4.857 19.615 2576 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.03 % Favored : 91.80 % Rotamer: Outliers : 2.84 % Allowed : 13.82 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2304 helix: -0.04 (0.13), residues: 1436 sheet: -2.76 (0.55), residues: 56 loop : -2.28 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 586 HIS 0.006 0.002 HIS C 731 PHE 0.018 0.002 PHE D 284 TYR 0.017 0.002 TYR C 303 ARG 0.004 0.001 ARG B 510 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 411 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.2382 (tpt) cc_final: 0.1575 (tpt) REVERT: A 372 SER cc_start: 0.8057 (t) cc_final: 0.7820 (p) REVERT: A 425 ASP cc_start: 0.6921 (m-30) cc_final: 0.6701 (m-30) REVERT: A 453 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7703 (tp30) REVERT: A 578 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.6919 (tmm) REVERT: A 718 MET cc_start: 0.6472 (ttt) cc_final: 0.6203 (ttp) REVERT: B 223 MET cc_start: 0.2672 (tpt) cc_final: 0.1875 (tpt) REVERT: B 372 SER cc_start: 0.8067 (t) cc_final: 0.7831 (p) REVERT: B 425 ASP cc_start: 0.6917 (m-30) cc_final: 0.6709 (m-30) REVERT: B 453 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7714 (tp30) REVERT: B 578 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.6935 (tmm) REVERT: B 622 LEU cc_start: 0.7991 (tp) cc_final: 0.7453 (pp) REVERT: B 625 MET cc_start: 0.7532 (mtp) cc_final: 0.6942 (mtp) REVERT: C 223 MET cc_start: 0.2593 (tpt) cc_final: 0.1786 (tpt) REVERT: C 372 SER cc_start: 0.8058 (t) cc_final: 0.7827 (p) REVERT: C 425 ASP cc_start: 0.6931 (m-30) cc_final: 0.6721 (m-30) REVERT: C 453 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7726 (tp30) REVERT: C 578 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.6943 (tmm) REVERT: C 622 LEU cc_start: 0.8011 (tp) cc_final: 0.7448 (pp) REVERT: C 625 MET cc_start: 0.7475 (mtp) cc_final: 0.6873 (mtp) REVERT: C 718 MET cc_start: 0.6498 (ttt) cc_final: 0.6231 (ttp) REVERT: D 223 MET cc_start: 0.2357 (tpt) cc_final: 0.1551 (tpt) REVERT: D 372 SER cc_start: 0.8076 (t) cc_final: 0.7840 (p) REVERT: D 453 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7710 (tp30) REVERT: D 578 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7328 (ttp) REVERT: D 622 LEU cc_start: 0.8037 (tp) cc_final: 0.7497 (pp) REVERT: D 625 MET cc_start: 0.7516 (mtp) cc_final: 0.6944 (mtp) outliers start: 59 outliers final: 44 residues processed: 443 average time/residue: 0.6806 time to fit residues: 466.4304 Evaluate side-chains 431 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 383 time to evaluate : 3.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 777 CYS Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 777 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 7.9990 chunk 158 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 211 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19332 Z= 0.330 Angle : 0.689 11.320 26180 Z= 0.367 Chirality : 0.041 0.466 3024 Planarity : 0.005 0.045 3248 Dihedral : 5.065 20.509 2576 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.81 % Favored : 90.02 % Rotamer: Outliers : 3.95 % Allowed : 16.52 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.17), residues: 2304 helix: -0.26 (0.13), residues: 1440 sheet: -2.93 (0.54), residues: 56 loop : -2.43 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 737 HIS 0.005 0.001 HIS B 731 PHE 0.016 0.002 PHE D 751 TYR 0.022 0.002 TYR A 346 ARG 0.005 0.001 ARG D 503 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 403 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7772 (tp30) REVERT: A 578 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7074 (tmm) REVERT: A 625 MET cc_start: 0.7748 (mtp) cc_final: 0.7369 (mtp) REVERT: B 453 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7802 (tp30) REVERT: B 578 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7058 (tmm) REVERT: B 622 LEU cc_start: 0.8146 (tp) cc_final: 0.7549 (pp) REVERT: B 625 MET cc_start: 0.7610 (mtp) cc_final: 0.7030 (mtp) REVERT: C 453 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7779 (tp30) REVERT: C 578 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7072 (tmm) REVERT: C 625 MET cc_start: 0.7670 (mtp) cc_final: 0.7021 (mtp) REVERT: D 453 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7777 (tp30) REVERT: D 482 MET cc_start: 0.7840 (tpp) cc_final: 0.7311 (tpp) REVERT: D 578 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7081 (tmm) REVERT: D 622 LEU cc_start: 0.8156 (tp) cc_final: 0.7564 (pp) REVERT: D 625 MET cc_start: 0.7604 (mtp) cc_final: 0.7037 (mtp) outliers start: 82 outliers final: 70 residues processed: 463 average time/residue: 0.6775 time to fit residues: 486.8157 Evaluate side-chains 446 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 372 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain A residue 777 CYS Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 760 GLU Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 591 TYR Chi-restraints excluded: chain D residue 626 ILE Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 777 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 3 optimal weight: 30.0000 chunk 166 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 191 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN B 317 GLN C 317 GLN D 317 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19332 Z= 0.244 Angle : 0.626 10.972 26180 Z= 0.331 Chirality : 0.040 0.462 3024 Planarity : 0.004 0.042 3248 Dihedral : 4.829 18.525 2576 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.20 % Favored : 91.62 % Rotamer: Outliers : 4.72 % Allowed : 18.59 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.17), residues: 2304 helix: 0.10 (0.13), residues: 1440 sheet: -3.02 (0.56), residues: 56 loop : -2.36 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 733 HIS 0.005 0.001 HIS C 731 PHE 0.015 0.001 PHE C 524 TYR 0.022 0.002 TYR A 346 ARG 0.004 0.000 ARG B 503 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 384 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7702 (tp30) REVERT: A 622 LEU cc_start: 0.8414 (tp) cc_final: 0.8029 (tp) REVERT: A 625 MET cc_start: 0.7767 (mtp) cc_final: 0.7444 (mtp) REVERT: B 453 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7710 (tp30) REVERT: B 625 MET cc_start: 0.7672 (mtp) cc_final: 0.7069 (mtp) REVERT: C 453 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7716 (tp30) REVERT: C 625 MET cc_start: 0.7688 (mtp) cc_final: 0.7053 (mtp) REVERT: D 453 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7690 (tp30) REVERT: D 578 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7051 (tmm) REVERT: D 625 MET cc_start: 0.7660 (mtp) cc_final: 0.7057 (mtp) outliers start: 98 outliers final: 91 residues processed: 447 average time/residue: 0.7642 time to fit residues: 523.9951 Evaluate side-chains 461 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 369 time to evaluate : 3.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 553 TYR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 777 CYS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 553 TYR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 388 HIS Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 591 TYR Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 747 SER Chi-restraints excluded: chain D residue 777 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 131 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.6031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19332 Z= 0.208 Angle : 0.597 11.081 26180 Z= 0.314 Chirality : 0.039 0.462 3024 Planarity : 0.004 0.042 3248 Dihedral : 4.626 18.078 2576 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.07 % Favored : 91.75 % Rotamer: Outliers : 4.19 % Allowed : 20.23 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.17), residues: 2304 helix: 0.52 (0.13), residues: 1420 sheet: -2.93 (0.56), residues: 56 loop : -2.18 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 733 HIS 0.006 0.001 HIS C 243 PHE 0.018 0.001 PHE B 524 TYR 0.021 0.002 TYR A 346 ARG 0.003 0.000 ARG D 503 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 401 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 LYS cc_start: 0.7664 (mmtm) cc_final: 0.7108 (mttm) REVERT: A 453 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7664 (tp30) REVERT: A 622 LEU cc_start: 0.8403 (tp) cc_final: 0.8022 (tp) REVERT: A 625 MET cc_start: 0.7790 (mtp) cc_final: 0.7472 (mtp) REVERT: B 442 LYS cc_start: 0.7693 (mmtm) cc_final: 0.7127 (mttm) REVERT: B 453 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7678 (tp30) REVERT: B 622 LEU cc_start: 0.8262 (tp) cc_final: 0.7734 (tp) REVERT: B 625 MET cc_start: 0.7757 (mtp) cc_final: 0.7125 (mtp) REVERT: C 442 LYS cc_start: 0.7671 (mmtm) cc_final: 0.7114 (mttm) REVERT: C 453 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7667 (tp30) REVERT: C 622 LEU cc_start: 0.8279 (tp) cc_final: 0.7751 (tp) REVERT: C 625 MET cc_start: 0.7760 (mtp) cc_final: 0.7120 (mtp) REVERT: D 442 LYS cc_start: 0.7672 (mmtm) cc_final: 0.7130 (mttm) REVERT: D 578 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.6997 (tmm) REVERT: D 622 LEU cc_start: 0.8274 (tp) cc_final: 0.7747 (tp) REVERT: D 625 MET cc_start: 0.7764 (mtp) cc_final: 0.7141 (mtp) outliers start: 87 outliers final: 79 residues processed: 458 average time/residue: 0.7903 time to fit residues: 541.6609 Evaluate side-chains 468 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 388 time to evaluate : 3.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 553 TYR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 777 CYS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 553 TYR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 388 HIS Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 457 GLU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 777 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 223 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.6329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19332 Z= 0.213 Angle : 0.599 11.312 26180 Z= 0.315 Chirality : 0.039 0.466 3024 Planarity : 0.004 0.041 3248 Dihedral : 4.589 17.826 2576 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.94 % Favored : 91.88 % Rotamer: Outliers : 5.39 % Allowed : 19.12 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.17), residues: 2304 helix: 0.63 (0.13), residues: 1420 sheet: -2.96 (0.57), residues: 56 loop : -2.14 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 733 HIS 0.009 0.002 HIS B 243 PHE 0.020 0.001 PHE A 624 TYR 0.018 0.002 TYR B 628 ARG 0.003 0.000 ARG D 746 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 383 time to evaluate : 3.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 LYS cc_start: 0.7701 (mmtm) cc_final: 0.7181 (mttm) REVERT: A 453 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7697 (tp30) REVERT: A 622 LEU cc_start: 0.8404 (tp) cc_final: 0.8039 (tp) REVERT: A 625 MET cc_start: 0.7786 (mtp) cc_final: 0.7440 (mtp) REVERT: B 442 LYS cc_start: 0.7698 (mmtm) cc_final: 0.7149 (mttm) REVERT: B 453 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7669 (tp30) REVERT: B 622 LEU cc_start: 0.8277 (tp) cc_final: 0.7722 (tp) REVERT: B 625 MET cc_start: 0.7748 (mtp) cc_final: 0.7159 (mtp) REVERT: C 442 LYS cc_start: 0.7704 (mmtm) cc_final: 0.7185 (mttm) REVERT: C 453 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7727 (tp30) REVERT: C 622 LEU cc_start: 0.8257 (tp) cc_final: 0.7760 (tp) REVERT: C 625 MET cc_start: 0.7756 (mtp) cc_final: 0.7131 (mtp) REVERT: D 442 LYS cc_start: 0.7707 (mmtm) cc_final: 0.7206 (mttm) REVERT: D 578 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.6994 (tmm) REVERT: D 622 LEU cc_start: 0.8296 (tp) cc_final: 0.7748 (tp) REVERT: D 625 MET cc_start: 0.7753 (mtp) cc_final: 0.7135 (mtp) outliers start: 112 outliers final: 102 residues processed: 458 average time/residue: 0.7929 time to fit residues: 547.0102 Evaluate side-chains 487 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 384 time to evaluate : 3.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 553 TYR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 777 CYS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 553 TYR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 388 HIS Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 777 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 152 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 175 optimal weight: 10.0000 chunk 203 optimal weight: 0.3980 chunk 214 optimal weight: 6.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.6501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19332 Z= 0.186 Angle : 0.588 11.229 26180 Z= 0.306 Chirality : 0.038 0.464 3024 Planarity : 0.004 0.042 3248 Dihedral : 4.402 17.512 2576 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.77 % Favored : 93.06 % Rotamer: Outliers : 4.53 % Allowed : 20.42 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 2304 helix: 0.83 (0.13), residues: 1424 sheet: -2.94 (0.58), residues: 56 loop : -2.03 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 733 HIS 0.009 0.001 HIS D 243 PHE 0.020 0.001 PHE D 624 TYR 0.016 0.001 TYR A 628 ARG 0.003 0.000 ARG D 503 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 381 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.2499 (mmt) cc_final: 0.1936 (tpt) REVERT: A 442 LYS cc_start: 0.7676 (mmtm) cc_final: 0.7279 (mttm) REVERT: A 622 LEU cc_start: 0.8370 (tp) cc_final: 0.8022 (tp) REVERT: A 625 MET cc_start: 0.7816 (mtp) cc_final: 0.7494 (mtp) REVERT: A 718 MET cc_start: 0.6847 (ttt) cc_final: 0.6534 (ttp) REVERT: B 223 MET cc_start: 0.2500 (mmt) cc_final: 0.1934 (tpt) REVERT: B 442 LYS cc_start: 0.7703 (mmtm) cc_final: 0.7267 (mttm) REVERT: B 453 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7752 (tp30) REVERT: B 482 MET cc_start: 0.7539 (tpt) cc_final: 0.6830 (tpp) REVERT: B 622 LEU cc_start: 0.8232 (tp) cc_final: 0.7720 (tp) REVERT: B 625 MET cc_start: 0.7799 (mtp) cc_final: 0.7195 (mtp) REVERT: C 223 MET cc_start: 0.2491 (mmt) cc_final: 0.1929 (tpt) REVERT: C 442 LYS cc_start: 0.7686 (mmtm) cc_final: 0.7288 (mttm) REVERT: C 482 MET cc_start: 0.7555 (tpt) cc_final: 0.6816 (tpp) REVERT: C 622 LEU cc_start: 0.8235 (tp) cc_final: 0.7736 (tp) REVERT: C 625 MET cc_start: 0.7831 (mtp) cc_final: 0.7214 (mtp) REVERT: D 223 MET cc_start: 0.2504 (mmt) cc_final: 0.1939 (tpt) REVERT: D 442 LYS cc_start: 0.7644 (mmtm) cc_final: 0.7237 (mttm) REVERT: D 578 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.6956 (tmm) REVERT: D 622 LEU cc_start: 0.8230 (tp) cc_final: 0.7724 (tp) REVERT: D 625 MET cc_start: 0.7826 (mtp) cc_final: 0.7216 (mtp) outliers start: 94 outliers final: 83 residues processed: 437 average time/residue: 0.7873 time to fit residues: 515.5924 Evaluate side-chains 457 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 373 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 553 TYR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 777 CYS Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 591 TYR Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 553 TYR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 591 TYR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 388 HIS Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 777 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 4.9990 chunk 208 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 125 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN B 317 GLN C 317 GLN D 317 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.6575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19332 Z= 0.155 Angle : 0.573 11.069 26180 Z= 0.296 Chirality : 0.038 0.461 3024 Planarity : 0.004 0.040 3248 Dihedral : 4.157 17.390 2576 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.95 % Favored : 93.97 % Rotamer: Outliers : 3.90 % Allowed : 22.11 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.18), residues: 2304 helix: 1.12 (0.13), residues: 1420 sheet: -2.87 (0.59), residues: 56 loop : -2.02 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 733 HIS 0.011 0.001 HIS C 243 PHE 0.017 0.001 PHE C 524 TYR 0.016 0.001 TYR A 628 ARG 0.002 0.000 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 392 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.2559 (mmt) cc_final: 0.1982 (tpt) REVERT: A 442 LYS cc_start: 0.7743 (mmtm) cc_final: 0.7258 (mttm) REVERT: A 622 LEU cc_start: 0.8361 (tp) cc_final: 0.7991 (tp) REVERT: A 625 MET cc_start: 0.7858 (mtp) cc_final: 0.7472 (mtp) REVERT: A 718 MET cc_start: 0.6632 (ttt) cc_final: 0.6346 (ttp) REVERT: A 742 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8983 (mm) REVERT: B 223 MET cc_start: 0.2542 (mmt) cc_final: 0.1960 (tpt) REVERT: B 442 LYS cc_start: 0.7756 (mmtm) cc_final: 0.7243 (mttm) REVERT: B 482 MET cc_start: 0.7615 (tpt) cc_final: 0.6892 (tpp) REVERT: B 622 LEU cc_start: 0.8175 (tp) cc_final: 0.7702 (tp) REVERT: B 625 MET cc_start: 0.7653 (mtp) cc_final: 0.7050 (mtp) REVERT: B 742 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8980 (mm) REVERT: C 223 MET cc_start: 0.2542 (mmt) cc_final: 0.1960 (tpt) REVERT: C 442 LYS cc_start: 0.7751 (mmtm) cc_final: 0.7265 (mttm) REVERT: C 622 LEU cc_start: 0.8219 (tp) cc_final: 0.7767 (tp) REVERT: C 625 MET cc_start: 0.7601 (mtp) cc_final: 0.7012 (mtp) REVERT: C 742 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8970 (mm) REVERT: D 223 MET cc_start: 0.2551 (mmt) cc_final: 0.1966 (tpt) REVERT: D 442 LYS cc_start: 0.7710 (mmtm) cc_final: 0.7229 (mttm) REVERT: D 622 LEU cc_start: 0.8192 (tp) cc_final: 0.7721 (tp) REVERT: D 625 MET cc_start: 0.7662 (mtp) cc_final: 0.7078 (mtp) outliers start: 81 outliers final: 71 residues processed: 437 average time/residue: 0.7487 time to fit residues: 485.5843 Evaluate side-chains 450 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 376 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 553 TYR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 777 CYS Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 553 TYR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 388 HIS Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 777 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 231 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.6738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19332 Z= 0.196 Angle : 0.595 11.113 26180 Z= 0.310 Chirality : 0.038 0.463 3024 Planarity : 0.004 0.041 3248 Dihedral : 4.211 17.107 2576 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.90 % Favored : 93.06 % Rotamer: Outliers : 4.00 % Allowed : 22.16 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.18), residues: 2304 helix: 1.10 (0.13), residues: 1420 sheet: -2.86 (0.60), residues: 56 loop : -2.02 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 733 HIS 0.011 0.002 HIS C 243 PHE 0.027 0.001 PHE B 624 TYR 0.022 0.001 TYR B 702 ARG 0.002 0.000 ARG B 503 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 372 time to evaluate : 3.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.2630 (mmt) cc_final: 0.2065 (tpt) REVERT: A 442 LYS cc_start: 0.7729 (mmtm) cc_final: 0.7235 (mttm) REVERT: A 622 LEU cc_start: 0.8336 (tp) cc_final: 0.7975 (tp) REVERT: A 625 MET cc_start: 0.7863 (mtp) cc_final: 0.7468 (mtp) REVERT: A 742 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8992 (mm) REVERT: B 223 MET cc_start: 0.2621 (mmt) cc_final: 0.2061 (tpt) REVERT: B 442 LYS cc_start: 0.7737 (mmtm) cc_final: 0.7216 (mttm) REVERT: B 453 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7713 (tp30) REVERT: B 482 MET cc_start: 0.7731 (tpt) cc_final: 0.6957 (tpp) REVERT: B 622 LEU cc_start: 0.8201 (tp) cc_final: 0.7725 (tp) REVERT: B 625 MET cc_start: 0.7684 (mtp) cc_final: 0.7091 (mtp) REVERT: C 223 MET cc_start: 0.2626 (mmt) cc_final: 0.2062 (tpt) REVERT: C 442 LYS cc_start: 0.7736 (mmtm) cc_final: 0.7242 (mttm) REVERT: C 482 MET cc_start: 0.7576 (tpt) cc_final: 0.6889 (tpp) REVERT: C 622 LEU cc_start: 0.8224 (tp) cc_final: 0.7762 (tp) REVERT: C 625 MET cc_start: 0.7649 (mtp) cc_final: 0.7056 (mtp) REVERT: C 742 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8982 (mm) REVERT: D 223 MET cc_start: 0.2625 (mmt) cc_final: 0.2065 (tpt) REVERT: D 442 LYS cc_start: 0.7740 (mmtm) cc_final: 0.7251 (mttm) REVERT: D 578 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.7003 (tmm) REVERT: D 622 LEU cc_start: 0.8215 (tp) cc_final: 0.7738 (tp) REVERT: D 625 MET cc_start: 0.7654 (mtp) cc_final: 0.7078 (mtp) outliers start: 83 outliers final: 76 residues processed: 421 average time/residue: 0.7864 time to fit residues: 493.4665 Evaluate side-chains 448 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 369 time to evaluate : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 553 TYR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 777 CYS Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 388 HIS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 553 TYR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 697 LEU Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 777 CYS Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 388 HIS Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 777 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 169 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 184 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 189 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.174610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.140126 restraints weight = 142780.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.145736 restraints weight = 75126.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.149478 restraints weight = 49580.791| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.6821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19332 Z= 0.178 Angle : 0.592 11.067 26180 Z= 0.306 Chirality : 0.038 0.462 3024 Planarity : 0.004 0.040 3248 Dihedral : 4.133 16.751 2576 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.16 % Favored : 93.79 % Rotamer: Outliers : 3.81 % Allowed : 22.54 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.18), residues: 2304 helix: 1.16 (0.13), residues: 1420 sheet: -2.83 (0.60), residues: 56 loop : -1.99 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 733 HIS 0.010 0.001 HIS B 243 PHE 0.023 0.001 PHE D 624 TYR 0.019 0.001 TYR B 702 ARG 0.002 0.000 ARG B 503 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9069.84 seconds wall clock time: 162 minutes 33.18 seconds (9753.18 seconds total)