Starting phenix.real_space_refine on Fri Feb 14 15:32:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xg6_22174/02_2025/6xg6_22174.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xg6_22174/02_2025/6xg6_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/cci-nas-00/data/ceres_data/6xg6_22174/02_2025/6xg6_22174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xg6_22174/02_2025/6xg6_22174.map" model { file = "/net/cci-nas-00/data/ceres_data/6xg6_22174/02_2025/6xg6_22174.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xg6_22174/02_2025/6xg6_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-5592/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: 5.86, per 1000 atoms: 0.60 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: 2.37 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: 1.18 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: 3.31 Time building geometry restraints manager: 2.73 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: 1.740 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.650 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.310 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.089 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: 0.2646 time to fit residues: 61.3698 Evaluate side-chains 119 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.118688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098005 restraints weight = 16837.386| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.21 r_work: 0.3175 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.173 Fit side-chains REVERT: A 292 MET cc_start: 0.5898 (pmm) cc_final: 0.5623 (pmm) outliers start: 24 outliers final: 14 residues processed: 136 average time/residue: 0.2545 time to fit residues: 48.2677 Evaluate side-chains 111 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 44 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.125292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.103533 restraints weight = 16937.736| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.34 r_work: 0.3266 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3302 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= 0.168 Angle : 0.583 7.941 13480 Z= 0.290 Chirality : 0.041 0.184 1519 Planarity : 0.004 0.065 1714 Dihedral : 6.449 109.035 1356 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.07 % Allowed : 13.56 % 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: 0.25 (0.25), residues: 1206 helix: 1.00 (0.25), residues: 495 sheet: 0.28 (0.39), residues: 183 loop : -0.62 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 231 HIS 0.004 0.001 HIS B 144 PHE 0.012 0.001 PHE A 112 TYR 0.010 0.001 TYR A 514 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 138 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.083 Fit side-chains REVERT: A 292 MET cc_start: 0.5597 (pmm) cc_final: 0.5261 (pmm) REVERT: A 327 TYR cc_start: 0.8793 (m-80) cc_final: 0.8518 (m-80) REVERT: A 623 ARG cc_start: 0.6732 (mtm110) cc_final: 0.6505 (mtm110) REVERT: A 643 GLU cc_start: 0.7991 (mp0) cc_final: 0.7502 (mt-10) REVERT: B 95 LYS cc_start: 0.8280 (mptt) cc_final: 0.8035 (mmtt) outliers start: 22 outliers final: 13 residues processed: 131 average time/residue: 0.2590 time to fit residues: 46.4302 Evaluate side-chains 116 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ILE 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 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 490 MET 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 55 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 112 optimal weight: 0.0570 chunk 93 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.123525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.102308 restraints weight = 16789.987| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.30 r_work: 0.3237 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9993 Z= 0.219 Angle : 0.583 9.076 13480 Z= 0.290 Chirality : 0.042 0.176 1519 Planarity : 0.004 0.061 1714 Dihedral : 6.450 112.290 1356 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.45 % Allowed : 15.25 % 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: 0.22 (0.25), residues: 1206 helix: 1.11 (0.25), residues: 496 sheet: -0.07 (0.38), residues: 190 loop : -0.64 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 231 HIS 0.004 0.001 HIS B 144 PHE 0.012 0.001 PHE B 621 TYR 0.012 0.001 TYR A 514 ARG 0.007 0.000 ARG A 103 *********************** 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 to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 1.047 Fit side-chains REVERT: A 496 ASN cc_start: 0.7702 (p0) cc_final: 0.7449 (p0) REVERT: B 95 LYS cc_start: 0.8350 (mptt) cc_final: 0.8130 (mmtt) REVERT: B 98 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8532 (mt) outliers start: 26 outliers final: 19 residues processed: 128 average time/residue: 0.2253 time to fit residues: 40.8512 Evaluate side-chains 125 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ILE 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 536 LEU Chi-restraints excluded: chain B residue 551 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 0 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 42 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.123976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.102607 restraints weight = 16709.463| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.29 r_work: 0.3241 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9993 Z= 0.212 Angle : 0.584 9.237 13480 Z= 0.289 Chirality : 0.041 0.168 1519 Planarity : 0.004 0.062 1714 Dihedral : 6.434 111.843 1356 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.64 % Allowed : 16.01 % Favored : 81.36 % 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: 0.20 (0.25), residues: 1206 helix: 1.13 (0.25), residues: 496 sheet: -0.13 (0.38), residues: 185 loop : -0.67 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 231 HIS 0.003 0.001 HIS B 144 PHE 0.012 0.001 PHE B 621 TYR 0.012 0.001 TYR A 514 ARG 0.008 0.000 ARG A 623 *********************** 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 140 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 1.081 Fit side-chains REVERT: A 88 HIS cc_start: 0.6569 (OUTLIER) cc_final: 0.4707 (p-80) REVERT: A 292 MET cc_start: 0.5504 (pmm) cc_final: 0.5138 (pmm) REVERT: A 643 GLU cc_start: 0.8111 (mp0) cc_final: 0.7693 (mp0) REVERT: B 95 LYS cc_start: 0.8368 (mptt) cc_final: 0.8127 (mmtt) outliers start: 28 outliers final: 22 residues processed: 133 average time/residue: 0.2327 time to fit residues: 43.4663 Evaluate side-chains 129 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 115 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 506 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.124831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.103811 restraints weight = 16691.636| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.24 r_work: 0.3270 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9993 Z= 0.176 Angle : 0.569 9.054 13480 Z= 0.280 Chirality : 0.041 0.170 1519 Planarity : 0.004 0.059 1714 Dihedral : 6.346 109.901 1356 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.20 % Allowed : 15.44 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1206 helix: 1.21 (0.25), residues: 496 sheet: -0.05 (0.38), residues: 184 loop : -0.69 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 231 HIS 0.002 0.001 HIS A 129 PHE 0.011 0.001 PHE A 112 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 148 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 1.115 Fit side-chains REVERT: A 88 HIS cc_start: 0.6497 (OUTLIER) cc_final: 0.4666 (p-80) REVERT: A 292 MET cc_start: 0.5479 (pmm) cc_final: 0.4837 (ptp) REVERT: B 95 LYS cc_start: 0.8344 (mptt) cc_final: 0.8111 (mmtt) REVERT: B 98 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8515 (mt) REVERT: B 230 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7285 (tp40) outliers start: 34 outliers final: 25 residues processed: 141 average time/residue: 0.2315 time to fit residues: 46.4703 Evaluate side-chains 136 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS 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 98 LEU Chi-restraints excluded: chain B residue 132 VAL 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 698 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 36 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 116 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 87 optimal weight: 0.3980 chunk 26 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 HIS ** 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 506 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.123689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.102238 restraints weight = 16677.832| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.28 r_work: 0.3236 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9993 Z= 0.226 Angle : 0.598 9.275 13480 Z= 0.295 Chirality : 0.042 0.185 1519 Planarity : 0.004 0.057 1714 Dihedral : 6.438 112.282 1356 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.20 % Allowed : 15.82 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.18 (0.25), residues: 1206 helix: 1.14 (0.25), residues: 496 sheet: -0.15 (0.38), residues: 185 loop : -0.71 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 231 HIS 0.003 0.001 HIS B 330 PHE 0.011 0.001 PHE A 112 TYR 0.012 0.001 TYR A 437 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 143 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 1.155 Fit side-chains REVERT: A 88 HIS cc_start: 0.6672 (OUTLIER) cc_final: 0.4954 (p-80) REVERT: A 643 GLU cc_start: 0.7956 (mp0) cc_final: 0.7600 (mp0) REVERT: B 95 LYS cc_start: 0.8368 (mptt) cc_final: 0.8098 (mmtt) REVERT: B 98 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8600 (mt) outliers start: 34 outliers final: 29 residues processed: 135 average time/residue: 0.2280 time to fit residues: 44.3472 Evaluate side-chains 137 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 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 98 LEU Chi-restraints excluded: chain B residue 132 VAL 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 698 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 95 optimal weight: 2.9990 chunk 105 optimal weight: 0.1980 chunk 62 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 HIS ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 HIS B 645 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.123401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.102328 restraints weight = 16763.709| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.23 r_work: 0.3248 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3723 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= 0.215 Angle : 0.594 9.245 13480 Z= 0.293 Chirality : 0.042 0.160 1519 Planarity : 0.004 0.055 1714 Dihedral : 6.437 111.889 1356 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.11 % Allowed : 16.10 % Favored : 80.79 % 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: 0.14 (0.25), residues: 1206 helix: 1.13 (0.25), residues: 496 sheet: -0.22 (0.38), residues: 185 loop : -0.74 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 231 HIS 0.004 0.001 HIS B 506 PHE 0.011 0.001 PHE A 112 TYR 0.012 0.001 TYR A 437 ARG 0.008 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 147 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 1.096 Fit side-chains REVERT: A 88 HIS cc_start: 0.6684 (OUTLIER) cc_final: 0.4972 (p-80) REVERT: B 95 LYS cc_start: 0.8357 (mptt) cc_final: 0.8090 (mmtt) REVERT: B 216 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7358 (tm-30) outliers start: 33 outliers final: 29 residues processed: 139 average time/residue: 0.2338 time to fit residues: 45.8773 Evaluate side-chains 138 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 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 132 VAL 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 698 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.124065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.103021 restraints weight = 16718.517| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.23 r_work: 0.3263 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9993 Z= 0.190 Angle : 0.599 9.150 13480 Z= 0.294 Chirality : 0.041 0.162 1519 Planarity : 0.004 0.054 1714 Dihedral : 6.392 111.127 1356 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.01 % Allowed : 16.67 % Favored : 80.32 % 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: 0.16 (0.25), residues: 1206 helix: 1.16 (0.25), residues: 494 sheet: -0.22 (0.38), residues: 185 loop : -0.73 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 231 HIS 0.003 0.001 HIS B 144 PHE 0.012 0.001 PHE A 112 TYR 0.014 0.001 TYR B 513 ARG 0.011 0.000 ARG A 495 *********************** 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 145 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.925 Fit side-chains REVERT: A 88 HIS cc_start: 0.6576 (OUTLIER) cc_final: 0.4857 (p-80) REVERT: A 643 GLU cc_start: 0.7957 (mp0) cc_final: 0.7588 (mp0) outliers start: 32 outliers final: 30 residues processed: 136 average time/residue: 0.2374 time to fit residues: 45.4752 Evaluate side-chains 138 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 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 132 VAL 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 72 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 117 optimal weight: 0.0980 chunk 69 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 50 optimal weight: 0.1980 chunk 14 optimal weight: 0.0020 chunk 91 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 HIS ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.126139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.105367 restraints weight = 16820.094| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.21 r_work: 0.3302 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9993 Z= 0.147 Angle : 0.584 10.501 13480 Z= 0.285 Chirality : 0.041 0.165 1519 Planarity : 0.004 0.054 1714 Dihedral : 6.243 105.698 1356 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.45 % Allowed : 17.61 % Favored : 79.94 % 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: 0.24 (0.25), residues: 1206 helix: 1.26 (0.25), residues: 494 sheet: -0.16 (0.37), residues: 185 loop : -0.72 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 231 HIS 0.003 0.001 HIS B 506 PHE 0.013 0.001 PHE B 112 TYR 0.010 0.001 TYR A 514 ARG 0.010 0.000 ARG A 495 ********************** 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 143 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 1.186 Fit side-chains REVERT: A 88 HIS cc_start: 0.6268 (OUTLIER) cc_final: 0.4625 (p-80) REVERT: A 623 ARG cc_start: 0.6413 (mtm110) cc_final: 0.6163 (ttp-110) outliers start: 26 outliers final: 24 residues processed: 135 average time/residue: 0.2277 time to fit residues: 44.1883 Evaluate side-chains 130 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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 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 132 VAL 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 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 698 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 92 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 83 optimal weight: 0.0030 chunk 98 optimal weight: 0.0030 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.126062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.104936 restraints weight = 16803.550| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.28 r_work: 0.3284 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9993 Z= 0.161 Angle : 0.589 10.247 13480 Z= 0.287 Chirality : 0.041 0.160 1519 Planarity : 0.004 0.053 1714 Dihedral : 6.249 107.458 1356 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.45 % Allowed : 17.89 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1206 helix: 1.29 (0.25), residues: 494 sheet: -0.08 (0.38), residues: 185 loop : -0.72 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 309 HIS 0.004 0.001 HIS B 144 PHE 0.012 0.001 PHE A 112 TYR 0.011 0.001 TYR B 513 ARG 0.010 0.001 ARG A 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4118.14 seconds wall clock time: 74 minutes 21.28 seconds (4461.28 seconds total)