Starting phenix.real_space_refine on Wed Sep 25 12:43:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xg6_22174/09_2024/6xg6_22174.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xg6_22174/09_2024/6xg6_22174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xg6_22174/09_2024/6xg6_22174.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xg6_22174/09_2024/6xg6_22174.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xg6_22174/09_2024/6xg6_22174.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xg6_22174/09_2024/6xg6_22174.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 479 atoms to isotropic. 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: 9 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 Mg 2 5.21 5 S 43 5.16 5 Be 2 3.05 5 C 6203 2.51 5 N 1708 2.21 5 O 1855 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9825 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4856 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 588} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4903 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 594} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.46, per 1000 atoms: 0.66 Number of scatterers: 9825 At special positions: 0 Unit cell: (94.424, 92.796, 135.124, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) K 2 19.00 S 43 16.00 P 4 15.00 Mg 2 11.99 F 6 9.00 O 1855 8.00 N 1708 7.00 C 6203 6.00 Be 2 4.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.1 seconds 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2328 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 11 sheets defined 47.0% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.816A pdb=" N ASP A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 135 removed outlier: 4.227A pdb=" N ARG A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 Processing helix chain 'A' and resid 178 through 186 removed outlier: 3.703A pdb=" N ALA A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 210 removed outlier: 3.563A pdb=" N MET A 210 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.671A pdb=" N PHE A 264 " --> pdb=" O CYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.766A pdb=" N MET A 301 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.883A pdb=" N HIS A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 313 " --> pdb=" O TRP A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 410 through 433 Processing helix chain 'A' and resid 433 through 444 Processing helix chain 'A' and resid 444 through 455 removed outlier: 3.577A pdb=" N MET A 448 " --> pdb=" O TYR A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 466 removed outlier: 3.705A pdb=" N LYS A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 504 through 511 Processing helix chain 'A' and resid 511 through 520 removed outlier: 4.392A pdb=" N LYS A 520 " --> pdb=" O ALA A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 540 Processing helix chain 'A' and resid 551 through 553 No H-bonds generated for 'chain 'A' and resid 551 through 553' Processing helix chain 'A' and resid 575 through 590 removed outlier: 4.061A pdb=" N GLU A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 584 " --> pdb=" O GLU A 580 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 624 removed outlier: 3.500A pdb=" N ARG A 619 " --> pdb=" O MET A 615 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N HIS A 620 " --> pdb=" O GLY A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 639 removed outlier: 3.909A pdb=" N ALA A 635 " --> pdb=" O GLN A 631 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLN A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 637 " --> pdb=" O GLU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 661 removed outlier: 4.111A pdb=" N ASN A 655 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLN A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA A 659 " --> pdb=" O ASN A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 681 removed outlier: 3.501A pdb=" N GLN A 666 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 667 " --> pdb=" O GLY A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 701 removed outlier: 4.447A pdb=" N ARG A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU A 695 " --> pdb=" O GLY A 691 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 698 " --> pdb=" O ASN A 694 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYS A 699 " --> pdb=" O GLU A 695 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 Processing helix chain 'B' and resid 110 through 134 removed outlier: 4.351A pdb=" N ARG B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 178 through 186 removed outlier: 3.987A pdb=" N ALA B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 261 through 265 removed outlier: 3.941A pdb=" N PHE B 264 " --> pdb=" O CYS B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 307 through 319 removed outlier: 3.548A pdb=" N GLU B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 357 Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 408 through 433 removed outlier: 3.919A pdb=" N LYS B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 455 removed outlier: 3.552A pdb=" N LYS B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N PHE B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET B 448 " --> pdb=" O TYR B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 466 removed outlier: 3.519A pdb=" N LYS B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU B 462 " --> pdb=" O GLN B 458 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP B 463 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 490 removed outlier: 3.589A pdb=" N ALA B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 488 " --> pdb=" O SER B 484 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG B 489 " --> pdb=" O GLU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 510 Processing helix chain 'B' and resid 511 through 518 Processing helix chain 'B' and resid 531 through 540 Processing helix chain 'B' and resid 550 through 557 Processing helix chain 'B' and resid 575 through 591 removed outlier: 3.719A pdb=" N GLU B 581 " --> pdb=" O LYS B 577 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG B 587 " --> pdb=" O MET B 583 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 589 " --> pdb=" O TRP B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 624 Processing helix chain 'B' and resid 632 through 639 removed outlier: 3.539A pdb=" N GLN B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEU B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 639 " --> pdb=" O ALA B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 661 removed outlier: 3.802A pdb=" N ASN B 655 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA B 659 " --> pdb=" O ASN B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 680 removed outlier: 3.586A pdb=" N ALA B 665 " --> pdb=" O GLU B 661 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN B 666 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 701 removed outlier: 3.811A pdb=" N VAL B 690 " --> pdb=" O PRO B 686 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY B 691 " --> pdb=" O ARG B 687 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 89 removed outlier: 3.877A pdb=" N HIS A 88 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE B 239 " --> pdb=" O HIS A 88 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 219 " --> pdb=" O TYR B 229 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG B 214 " --> pdb=" O HIS B 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 239 through 242 removed outlier: 3.761A pdb=" N SER A 219 " --> pdb=" O TYR A 229 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG A 214 " --> pdb=" O HIS A 256 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 245 Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 331 removed outlier: 4.208A pdb=" N TYR A 327 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A 365 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 481 through 482 removed outlier: 4.016A pdb=" N GLU A 471 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N LEU A 525 " --> pdb=" O ASN A 496 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR A 498 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N CYS A 527 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 500 " --> pdb=" O CYS A 527 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 597 through 599 removed outlier: 6.123A pdb=" N LYS A 598 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 325 through 333 removed outlier: 6.711A pdb=" N ALA B 364 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N SER B 393 " --> pdb=" O ALA B 364 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR B 366 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 481 through 482 removed outlier: 4.154A pdb=" N GLU B 471 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR B 499 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 598 through 599 removed outlier: 6.697A pdb=" N LYS B 598 " --> pdb=" O ILE B 644 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1218 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: 3.16 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3240 1.34 - 1.46: 1814 1.46 - 1.58: 4854 1.58 - 1.69: 7 1.69 - 1.81: 78 Bond restraints: 9993 Sorted by residual: bond pdb=" F2 BEF A 902 " pdb="BE BEF A 902 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" F2 BEF B 902 " pdb="BE BEF B 902 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" F3 BEF B 902 " pdb="BE BEF B 902 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" F3 BEF A 902 " pdb="BE BEF A 902 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" F1 BEF A 902 " pdb="BE BEF A 902 " ideal model delta sigma weight residual 1.476 1.534 -0.058 2.00e-02 2.50e+03 8.32e+00 ... (remaining 9988 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 13388 2.53 - 5.06: 68 5.06 - 7.59: 19 7.59 - 10.12: 2 10.12 - 12.65: 3 Bond angle restraints: 13480 Sorted by residual: angle pdb=" CA PRO B 662 " pdb=" N PRO B 662 " pdb=" CD PRO B 662 " ideal model delta sigma weight residual 112.00 104.59 7.41 1.40e+00 5.10e-01 2.80e+01 angle pdb=" F2 BEF B 902 " pdb="BE BEF B 902 " pdb=" F3 BEF B 902 " ideal model delta sigma weight residual 119.96 107.31 12.65 3.00e+00 1.11e-01 1.78e+01 angle pdb=" F2 BEF A 902 " pdb="BE BEF A 902 " pdb=" F3 BEF A 902 " ideal model delta sigma weight residual 119.96 107.42 12.54 3.00e+00 1.11e-01 1.75e+01 angle pdb=" F1 BEF A 902 " pdb="BE BEF A 902 " pdb=" F3 BEF A 902 " ideal model delta sigma weight residual 120.12 109.96 10.16 3.00e+00 1.11e-01 1.15e+01 angle pdb=" F1 BEF B 902 " pdb="BE BEF B 902 " pdb=" F3 BEF B 902 " ideal model delta sigma weight residual 120.12 110.11 10.01 3.00e+00 1.11e-01 1.11e+01 ... (remaining 13475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.87: 5661 22.87 - 45.74: 402 45.74 - 68.62: 33 68.62 - 91.49: 21 91.49 - 114.36: 2 Dihedral angle restraints: 6119 sinusoidal: 2536 harmonic: 3583 Sorted by residual: dihedral pdb=" O1B ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PB ADP A 901 " pdb=" PA ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 -174.36 114.36 1 2.00e+01 2.50e-03 3.39e+01 dihedral pdb=" O2A ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PA ADP B 901 " pdb=" PB ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 -172.11 112.11 1 2.00e+01 2.50e-03 3.30e+01 dihedral pdb=" O2A ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PA ADP A 901 " pdb=" PB ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 -131.18 71.18 1 2.00e+01 2.50e-03 1.63e+01 ... (remaining 6116 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 950 0.029 - 0.058: 385 0.058 - 0.087: 109 0.087 - 0.116: 66 0.116 - 0.144: 9 Chirality restraints: 1519 Sorted by residual: chirality pdb=" CB ILE A 113 " pdb=" CA ILE A 113 " pdb=" CG1 ILE A 113 " pdb=" CG2 ILE A 113 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA ILE B 254 " pdb=" N ILE B 254 " pdb=" C ILE B 254 " pdb=" CB ILE B 254 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.85e-01 chirality pdb=" CA ILE B 143 " pdb=" N ILE B 143 " pdb=" C ILE B 143 " pdb=" CB ILE B 143 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 1516 not shown) Planarity restraints: 1714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 661 " 0.094 5.00e-02 4.00e+02 1.37e-01 3.01e+01 pdb=" N PRO B 662 " -0.237 5.00e-02 4.00e+02 pdb=" CA PRO B 662 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 662 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 380 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 381 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 381 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 381 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 475 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO A 476 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 476 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 476 " -0.017 5.00e-02 4.00e+02 ... (remaining 1711 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.67: 160 2.67 - 3.28: 10575 3.28 - 3.90: 19907 3.90 - 4.52: 26408 4.52 - 5.14: 40528 Nonbonded interactions: 97578 Sorted by model distance: nonbonded pdb=" F1 BEF A 902 " pdb="MG MG A 903 " model vdw 2.048 2.120 nonbonded pdb=" OD1 ASN A 119 " pdb="MG MG A 903 " model vdw 2.096 2.170 nonbonded pdb=" OD1 ASN B 119 " pdb="MG MG B 903 " model vdw 2.105 2.170 nonbonded pdb=" O1B ADP B 901 " pdb="MG MG B 903 " model vdw 2.127 2.170 nonbonded pdb=" O1A ADP B 901 " pdb="MG MG B 903 " model vdw 2.144 2.170 ... (remaining 97573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 70 through 554 or resid 573 through 626 or resid 631 throu \ gh 704 or resid 901 through 904)) selection = (chain 'B' and (resid 70 through 351 or resid 363 through 554 or resid 573 throu \ gh 704 or resid 901 through 904)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.030 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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 0.096 9993 Z= 0.157 Angle : 0.548 12.652 13480 Z= 0.267 Chirality : 0.038 0.144 1519 Planarity : 0.004 0.137 1714 Dihedral : 15.405 114.361 3791 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: 0.46 (0.25), residues: 1206 helix: 0.92 (0.25), residues: 495 sheet: 1.25 (0.42), residues: 177 loop : -0.55 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 309 HIS 0.002 0.000 HIS B 129 PHE 0.011 0.001 PHE A 112 TYR 0.006 0.001 TYR A 106 ARG 0.004 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.185 Fit side-chains REVERT: A 94 THR cc_start: 0.6615 (p) cc_final: 0.6403 (p) REVERT: A 495 ARG cc_start: 0.6708 (ptm-80) cc_final: 0.6346 (ttp80) REVERT: A 606 HIS cc_start: 0.7263 (m90) cc_final: 0.6952 (m90) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2510 time to fit residues: 58.0079 Evaluate side-chains 119 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.067 9993 Z= 0.612 Angle : 0.838 9.969 13480 Z= 0.423 Chirality : 0.051 0.195 1519 Planarity : 0.006 0.077 1714 Dihedral : 7.240 137.605 1356 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.26 % Allowed : 11.21 % Favored : 86.53 % 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: -0.23 (0.25), residues: 1206 helix: 0.33 (0.23), residues: 501 sheet: 0.06 (0.39), residues: 193 loop : -0.59 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 299 HIS 0.013 0.002 HIS A 88 PHE 0.015 0.002 PHE A 264 TYR 0.016 0.003 TYR A 437 ARG 0.010 0.001 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 1.197 Fit side-chains REVERT: A 292 MET cc_start: 0.5587 (pmm) cc_final: 0.5279 (pmm) outliers start: 24 outliers final: 14 residues processed: 136 average time/residue: 0.2355 time to fit residues: 44.6133 Evaluate side-chains 111 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 552 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 419 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9993 Z= 0.192 Angle : 0.596 8.324 13480 Z= 0.297 Chirality : 0.041 0.177 1519 Planarity : 0.004 0.065 1714 Dihedral : 6.554 112.721 1356 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.17 % Allowed : 13.47 % Favored : 84.37 % 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: 0.22 (0.25), residues: 1206 helix: 1.00 (0.25), residues: 487 sheet: 0.15 (0.38), residues: 184 loop : -0.58 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 231 HIS 0.005 0.001 HIS B 144 PHE 0.011 0.001 PHE A 112 TYR 0.011 0.001 TYR A 327 ARG 0.006 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 1.132 Fit side-chains REVERT: A 327 TYR cc_start: 0.8685 (m-80) cc_final: 0.8400 (m-80) REVERT: B 95 LYS cc_start: 0.7971 (mptt) cc_final: 0.7741 (mmtt) outliers start: 23 outliers final: 17 residues processed: 129 average time/residue: 0.2416 time to fit residues: 43.1342 Evaluate side-chains 117 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 551 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 279 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9993 Z= 0.267 Angle : 0.613 9.081 13480 Z= 0.305 Chirality : 0.042 0.173 1519 Planarity : 0.004 0.061 1714 Dihedral : 6.593 114.853 1356 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.73 % Allowed : 14.97 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1206 helix: 1.02 (0.25), residues: 493 sheet: -0.18 (0.38), residues: 185 loop : -0.57 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 231 HIS 0.004 0.001 HIS B 144 PHE 0.011 0.001 PHE B 621 TYR 0.012 0.002 TYR A 514 ARG 0.008 0.000 ARG A 623 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 108 time to evaluate : 1.089 Fit side-chains REVERT: A 88 HIS cc_start: 0.6535 (OUTLIER) cc_final: 0.4645 (p-80) REVERT: A 496 ASN cc_start: 0.7500 (p0) cc_final: 0.7296 (p0) REVERT: A 643 GLU cc_start: 0.7782 (mp0) cc_final: 0.7436 (mp0) REVERT: B 98 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8622 (mt) REVERT: B 661 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6295 (pm20) outliers start: 29 outliers final: 21 residues processed: 128 average time/residue: 0.2203 time to fit residues: 40.1133 Evaluate side-chains 126 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN B 506 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 9993 Z= 0.431 Angle : 0.700 8.771 13480 Z= 0.351 Chirality : 0.046 0.172 1519 Planarity : 0.005 0.058 1714 Dihedral : 7.028 125.146 1356 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.86 % Allowed : 16.10 % Favored : 80.04 % 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: -0.37 (0.25), residues: 1206 helix: 0.57 (0.24), residues: 512 sheet: -0.58 (0.36), residues: 182 loop : -0.86 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 299 HIS 0.009 0.002 HIS A 88 PHE 0.012 0.002 PHE A 264 TYR 0.015 0.002 TYR A 437 ARG 0.005 0.001 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 107 time to evaluate : 1.431 Fit side-chains REVERT: A 88 HIS cc_start: 0.7081 (OUTLIER) cc_final: 0.5499 (p-80) REVERT: A 643 GLU cc_start: 0.7751 (mp0) cc_final: 0.7350 (mp0) outliers start: 41 outliers final: 27 residues processed: 140 average time/residue: 0.2168 time to fit residues: 43.5649 Evaluate side-chains 130 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 0.0370 chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN B 506 HIS B 655 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9993 Z= 0.171 Angle : 0.583 9.045 13480 Z= 0.289 Chirality : 0.041 0.177 1519 Planarity : 0.004 0.058 1714 Dihedral : 6.503 107.351 1356 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.58 % Allowed : 17.14 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.03 (0.25), residues: 1206 helix: 0.99 (0.24), residues: 502 sheet: -0.44 (0.37), residues: 184 loop : -0.78 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 231 HIS 0.010 0.001 HIS B 506 PHE 0.013 0.001 PHE B 621 TYR 0.011 0.001 TYR A 514 ARG 0.007 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 122 time to evaluate : 1.084 Fit side-chains REVERT: A 88 HIS cc_start: 0.6515 (OUTLIER) cc_final: 0.4765 (p-80) outliers start: 38 outliers final: 23 residues processed: 151 average time/residue: 0.2135 time to fit residues: 45.6021 Evaluate side-chains 135 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 98 optimal weight: 0.0570 chunk 65 optimal weight: 0.8980 chunk 116 optimal weight: 0.0670 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 310 GLN B 506 HIS B 655 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9993 Z= 0.183 Angle : 0.587 8.375 13480 Z= 0.291 Chirality : 0.041 0.172 1519 Planarity : 0.004 0.058 1714 Dihedral : 6.412 109.562 1356 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.11 % Allowed : 18.27 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1206 helix: 1.06 (0.24), residues: 502 sheet: -0.27 (0.38), residues: 184 loop : -0.75 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 231 HIS 0.003 0.001 HIS B 144 PHE 0.012 0.001 PHE A 112 TYR 0.011 0.001 TYR A 514 ARG 0.008 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 113 time to evaluate : 1.296 Fit side-chains REVERT: A 88 HIS cc_start: 0.6313 (OUTLIER) cc_final: 0.4529 (p-80) outliers start: 33 outliers final: 25 residues processed: 137 average time/residue: 0.2105 time to fit residues: 42.0302 Evaluate side-chains 135 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 109 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 6.9990 chunk 22 optimal weight: 0.0970 chunk 74 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 101 optimal weight: 0.3980 chunk 108 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 506 HIS B 655 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9993 Z= 0.173 Angle : 0.580 8.986 13480 Z= 0.287 Chirality : 0.041 0.153 1519 Planarity : 0.004 0.057 1714 Dihedral : 6.346 108.216 1356 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.30 % Allowed : 18.36 % Favored : 78.34 % 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: 0.15 (0.25), residues: 1206 helix: 1.12 (0.25), residues: 500 sheet: -0.18 (0.38), residues: 184 loop : -0.75 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 231 HIS 0.003 0.001 HIS B 506 PHE 0.013 0.001 PHE B 621 TYR 0.012 0.001 TYR B 513 ARG 0.009 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 113 time to evaluate : 1.005 Fit side-chains REVERT: A 88 HIS cc_start: 0.6231 (OUTLIER) cc_final: 0.4479 (p-80) REVERT: B 695 GLU cc_start: 0.8367 (tp30) cc_final: 0.8165 (tp30) outliers start: 35 outliers final: 26 residues processed: 140 average time/residue: 0.2037 time to fit residues: 41.1193 Evaluate side-chains 136 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 506 HIS ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9993 Z= 0.317 Angle : 0.655 9.280 13480 Z= 0.323 Chirality : 0.044 0.160 1519 Planarity : 0.004 0.057 1714 Dihedral : 6.715 117.555 1356 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.20 % Allowed : 19.30 % Favored : 77.50 % 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 (0.25), residues: 1206 helix: 0.94 (0.24), residues: 504 sheet: -0.35 (0.37), residues: 184 loop : -0.81 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 309 HIS 0.005 0.001 HIS A 88 PHE 0.013 0.002 PHE B 621 TYR 0.018 0.002 TYR B 513 ARG 0.010 0.001 ARG A 623 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 108 time to evaluate : 1.174 Fit side-chains REVERT: A 88 HIS cc_start: 0.6840 (OUTLIER) cc_final: 0.5052 (p-80) REVERT: A 327 TYR cc_start: 0.8669 (m-80) cc_final: 0.8344 (m-80) REVERT: A 643 GLU cc_start: 0.7744 (mp0) cc_final: 0.7376 (mp0) outliers start: 34 outliers final: 30 residues processed: 133 average time/residue: 0.2092 time to fit residues: 40.8836 Evaluate side-chains 133 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 102 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 120 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 506 HIS ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9993 Z= 0.231 Angle : 0.627 9.934 13480 Z= 0.307 Chirality : 0.042 0.148 1519 Planarity : 0.004 0.057 1714 Dihedral : 6.610 111.953 1356 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.92 % Allowed : 19.77 % Favored : 77.31 % 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 (0.25), residues: 1206 helix: 0.95 (0.24), residues: 503 sheet: -0.29 (0.37), residues: 182 loop : -0.85 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 309 HIS 0.004 0.001 HIS B 144 PHE 0.014 0.001 PHE B 621 TYR 0.015 0.001 TYR B 513 ARG 0.010 0.000 ARG A 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 109 time to evaluate : 1.217 Fit side-chains REVERT: A 88 HIS cc_start: 0.6691 (OUTLIER) cc_final: 0.4905 (p-80) outliers start: 31 outliers final: 29 residues processed: 131 average time/residue: 0.2065 time to fit residues: 39.5140 Evaluate side-chains 138 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 108 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.0270 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.0370 chunk 96 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 98 optimal weight: 0.0030 chunk 12 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 overall best weight: 0.3726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN A 655 ASN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 506 HIS ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.125747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.103702 restraints weight = 16413.838| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.34 r_work: 0.3268 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9993 Z= 0.153 Angle : 0.596 11.316 13480 Z= 0.292 Chirality : 0.041 0.149 1519 Planarity : 0.004 0.056 1714 Dihedral : 6.361 104.623 1356 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.54 % Allowed : 20.62 % Favored : 76.84 % 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 (0.25), residues: 1206 helix: 1.10 (0.25), residues: 502 sheet: -0.08 (0.38), residues: 182 loop : -0.80 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 231 HIS 0.008 0.001 HIS B 506 PHE 0.015 0.001 PHE B 621 TYR 0.011 0.001 TYR B 514 ARG 0.011 0.001 ARG A 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2121.49 seconds wall clock time: 38 minutes 42.92 seconds (2322.92 seconds total)