Starting phenix.real_space_refine on Thu Mar 13 23:43:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n58_24182/03_2025/7n58_24182.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n58_24182/03_2025/7n58_24182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n58_24182/03_2025/7n58_24182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n58_24182/03_2025/7n58_24182.map" model { file = "/net/cci-nas-00/data/ceres_data/7n58_24182/03_2025/7n58_24182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n58_24182/03_2025/7n58_24182.cif" } resolution = 3.4 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 5952 2.51 5 N 1598 2.21 5 O 1742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9326 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4663 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 13, 'TRANS': 586} Chain: "B" Number of atoms: 4663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4663 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 13, 'TRANS': 586} Time building chain proxies: 5.65, per 1000 atoms: 0.61 Number of scatterers: 9326 At special positions: 0 Unit cell: (112.005, 98.325, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1742 8.00 N 1598 7.00 C 5952 6.00 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: 2.30 Conformation dependent library (CDL) restraints added in 1.0 seconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2240 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 8 sheets defined 66.9% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 117 through 132 removed outlier: 3.646A pdb=" N MET A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 169 removed outlier: 4.281A pdb=" N ARG A 140 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A 153 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Proline residue: A 161 - end of helix removed outlier: 3.518A pdb=" N VAL A 168 " --> pdb=" O PHE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 183 removed outlier: 3.762A pdb=" N THR A 182 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR A 183 " --> pdb=" O SER A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 179 through 183' Processing helix chain 'A' and resid 197 through 245 removed outlier: 3.889A pdb=" N VAL A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG A 229 " --> pdb=" O LYS A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 253 removed outlier: 3.667A pdb=" N HIS A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 279 removed outlier: 3.584A pdb=" N LEU A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 292 Processing helix chain 'A' and resid 293 through 296 Processing helix chain 'A' and resid 299 through 348 removed outlier: 3.715A pdb=" N TRP A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 327 " --> pdb=" O TRP A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 355 removed outlier: 3.744A pdb=" N VAL A 352 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 411 removed outlier: 3.602A pdb=" N LYS A 364 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER A 391 " --> pdb=" O ASN A 387 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 431 removed outlier: 4.014A pdb=" N VAL A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 removed outlier: 4.310A pdb=" N LEU A 436 " --> pdb=" O PRO A 432 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER A 438 " --> pdb=" O ASN A 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 432 through 438' Processing helix chain 'A' and resid 438 through 457 removed outlier: 4.732A pdb=" N GLU A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 removed outlier: 3.956A pdb=" N ARG A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 555 Processing helix chain 'A' and resid 569 through 575 Processing helix chain 'A' and resid 581 through 593 Processing helix chain 'A' and resid 594 through 599 removed outlier: 3.507A pdb=" N SER A 599 " --> pdb=" O HIS A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 633 removed outlier: 4.596A pdb=" N LEU A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A 632 " --> pdb=" O ARG A 628 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER A 633 " --> pdb=" O THR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 662 removed outlier: 3.596A pdb=" N GLU A 653 " --> pdb=" O THR A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 702 removed outlier: 3.545A pdb=" N LEU A 700 " --> pdb=" O PRO A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 716 Processing helix chain 'B' and resid 118 through 132 Processing helix chain 'B' and resid 136 through 169 removed outlier: 4.281A pdb=" N ARG B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA B 153 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Proline residue: B 161 - end of helix removed outlier: 3.519A pdb=" N VAL B 168 " --> pdb=" O PHE B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 183 removed outlier: 3.761A pdb=" N THR B 182 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR B 183 " --> pdb=" O SER B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 179 through 183' Processing helix chain 'B' and resid 197 through 245 removed outlier: 3.888A pdb=" N VAL B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG B 229 " --> pdb=" O LYS B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.667A pdb=" N HIS B 250 " --> pdb=" O ASP B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 279 removed outlier: 3.584A pdb=" N LEU B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 292 Processing helix chain 'B' and resid 293 through 296 Processing helix chain 'B' and resid 299 through 348 removed outlier: 3.715A pdb=" N TRP B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR B 306 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 322 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TRP B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE B 327 " --> pdb=" O TRP B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 355 removed outlier: 3.744A pdb=" N VAL B 352 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 411 removed outlier: 3.601A pdb=" N LYS B 364 " --> pdb=" O TYR B 360 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER B 391 " --> pdb=" O ASN B 387 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE B 394 " --> pdb=" O GLN B 390 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA B 397 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 431 removed outlier: 4.014A pdb=" N VAL B 422 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 438 removed outlier: 4.311A pdb=" N LEU B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER B 438 " --> pdb=" O ASN B 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 432 through 438' Processing helix chain 'B' and resid 438 through 457 removed outlier: 4.732A pdb=" N GLU B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 removed outlier: 3.955A pdb=" N ARG B 523 " --> pdb=" O SER B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 555 Processing helix chain 'B' and resid 569 through 575 Processing helix chain 'B' and resid 581 through 593 Processing helix chain 'B' and resid 594 through 599 removed outlier: 3.507A pdb=" N SER B 599 " --> pdb=" O HIS B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 633 removed outlier: 4.597A pdb=" N LEU B 631 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS B 632 " --> pdb=" O ARG B 628 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER B 633 " --> pdb=" O THR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 662 removed outlier: 3.595A pdb=" N GLU B 653 " --> pdb=" O THR B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 702 removed outlier: 3.544A pdb=" N LEU B 700 " --> pdb=" O PRO B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 716 Processing sheet with id=AA1, first strand: chain 'A' and resid 501 through 502 removed outlier: 3.737A pdb=" N ILE A 479 " --> pdb=" O VAL A 502 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU A 482 " --> pdb=" O ASN A 535 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN A 535 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 484 through 486 removed outlier: 4.819A pdb=" N VAL A 484 " --> pdb=" O GLY A 497 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 486 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 495 " --> pdb=" O PHE A 486 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 556 through 557 removed outlier: 6.907A pdb=" N GLY A 556 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 670 " --> pdb=" O CYS A 639 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY A 512 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER A 507 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL A 684 " --> pdb=" O SER A 507 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA A 509 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU A 686 " --> pdb=" O ALA A 509 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL A 511 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE A 683 " --> pdb=" O GLN A 694 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN A 694 " --> pdb=" O ILE A 683 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 685 " --> pdb=" O VAL A 692 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 567 through 568 Processing sheet with id=AA5, first strand: chain 'B' and resid 501 through 502 removed outlier: 3.737A pdb=" N ILE B 479 " --> pdb=" O VAL B 502 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU B 482 " --> pdb=" O ASN B 535 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN B 535 " --> pdb=" O GLU B 482 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 484 through 486 removed outlier: 4.819A pdb=" N VAL B 484 " --> pdb=" O GLY B 497 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 486 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 495 " --> pdb=" O PHE B 486 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 556 through 557 removed outlier: 6.908A pdb=" N GLY B 556 " --> pdb=" O LEU B 638 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 670 " --> pdb=" O CYS B 639 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY B 512 " --> pdb=" O ALA B 671 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER B 507 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL B 684 " --> pdb=" O SER B 507 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA B 509 " --> pdb=" O VAL B 684 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU B 686 " --> pdb=" O ALA B 509 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL B 511 " --> pdb=" O LEU B 686 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE B 683 " --> pdb=" O GLN B 694 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN B 694 " --> pdb=" O ILE B 683 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 685 " --> pdb=" O VAL B 692 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 567 through 568 548 hydrogen bonds defined for protein. 1626 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3028 1.34 - 1.46: 1371 1.46 - 1.57: 5029 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 9490 Sorted by residual: bond pdb=" CB GLU B 651 " pdb=" CG GLU B 651 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.70e+00 bond pdb=" CB GLU A 651 " pdb=" CG GLU A 651 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.67e+00 bond pdb=" CB LYS A 632 " pdb=" CG LYS A 632 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.39e+00 bond pdb=" CB LYS B 632 " pdb=" CG LYS B 632 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CD LYS A 632 " pdb=" CE LYS A 632 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.28e+00 ... (remaining 9485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 12431 2.07 - 4.13: 331 4.13 - 6.20: 64 6.20 - 8.26: 14 8.26 - 10.33: 2 Bond angle restraints: 12842 Sorted by residual: angle pdb=" N VAL A 158 " pdb=" CA VAL A 158 " pdb=" C VAL A 158 " ideal model delta sigma weight residual 113.39 107.51 5.88 1.47e+00 4.63e-01 1.60e+01 angle pdb=" N VAL B 158 " pdb=" CA VAL B 158 " pdb=" C VAL B 158 " ideal model delta sigma weight residual 113.39 107.54 5.85 1.47e+00 4.63e-01 1.58e+01 angle pdb=" CA ARG A 232 " pdb=" CB ARG A 232 " pdb=" CG ARG A 232 " ideal model delta sigma weight residual 114.10 107.07 7.03 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA ARG B 232 " pdb=" CB ARG B 232 " pdb=" CG ARG B 232 " ideal model delta sigma weight residual 114.10 107.10 7.00 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CB LYS B 632 " pdb=" CG LYS B 632 " pdb=" CD LYS B 632 " ideal model delta sigma weight residual 111.30 103.96 7.34 2.30e+00 1.89e-01 1.02e+01 ... (remaining 12837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.39: 5006 14.39 - 28.78: 491 28.78 - 43.17: 141 43.17 - 57.56: 26 57.56 - 71.95: 12 Dihedral angle restraints: 5676 sinusoidal: 2206 harmonic: 3470 Sorted by residual: dihedral pdb=" CA PRO B 696 " pdb=" C PRO B 696 " pdb=" N HIS B 697 " pdb=" CA HIS B 697 " ideal model delta harmonic sigma weight residual 180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA PRO A 696 " pdb=" C PRO A 696 " pdb=" N HIS A 697 " pdb=" CA HIS A 697 " ideal model delta harmonic sigma weight residual -180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA GLU B 373 " pdb=" CB GLU B 373 " pdb=" CG GLU B 373 " pdb=" CD GLU B 373 " ideal model delta sinusoidal sigma weight residual -60.00 -104.54 44.54 3 1.50e+01 4.44e-03 8.01e+00 ... (remaining 5673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 986 0.036 - 0.073: 366 0.073 - 0.109: 101 0.109 - 0.145: 41 0.145 - 0.182: 12 Chirality restraints: 1506 Sorted by residual: chirality pdb=" CA GLU B 458 " pdb=" N GLU B 458 " pdb=" C GLU B 458 " pdb=" CB GLU B 458 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" CA GLU A 458 " pdb=" N GLU A 458 " pdb=" C GLU A 458 " pdb=" CB GLU A 458 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA ILE A 293 " pdb=" N ILE A 293 " pdb=" C ILE A 293 " pdb=" CB ILE A 293 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.70e-01 ... (remaining 1503 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 188 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.71e+01 pdb=" N PRO A 189 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 188 " -0.067 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 189 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 189 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 189 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 213 " -0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C SER B 213 " 0.062 2.00e-02 2.50e+03 pdb=" O SER B 213 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA B 214 " -0.021 2.00e-02 2.50e+03 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 212 2.70 - 3.25: 10201 3.25 - 3.80: 13940 3.80 - 4.35: 18003 4.35 - 4.90: 28592 Nonbonded interactions: 70948 Sorted by model distance: nonbonded pdb=" O ASP A 449 " pdb=" OG SER A 452 " model vdw 2.146 3.040 nonbonded pdb=" O ASP B 449 " pdb=" OG SER B 452 " model vdw 2.147 3.040 nonbonded pdb=" O GLY B 176 " pdb=" OG1 THR B 177 " model vdw 2.223 3.040 nonbonded pdb=" O GLY A 176 " pdb=" OG1 THR A 177 " model vdw 2.224 3.040 nonbonded pdb=" NE2 GLN A 445 " pdb=" OD2 ASP A 449 " model vdw 2.259 3.120 ... (remaining 70943 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.060 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 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 : 0.004 0.049 9490 Z= 0.224 Angle : 0.841 10.328 12842 Z= 0.468 Chirality : 0.045 0.182 1506 Planarity : 0.007 0.104 1630 Dihedral : 13.091 71.950 3436 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: -0.83 (0.23), residues: 1196 helix: 0.34 (0.19), residues: 734 sheet: -0.40 (0.52), residues: 70 loop : -2.25 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 304 HIS 0.004 0.001 HIS B 595 PHE 0.026 0.002 PHE A 271 TYR 0.035 0.002 TYR A 354 ARG 0.011 0.001 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 ILE cc_start: 0.7990 (tt) cc_final: 0.7687 (tt) REVERT: B 573 ILE cc_start: 0.8013 (tt) cc_final: 0.7699 (tt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2255 time to fit residues: 39.2044 Evaluate side-chains 98 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 0.3980 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.206090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.175021 restraints weight = 14075.633| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 2.55 r_work: 0.4075 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9490 Z= 0.206 Angle : 0.659 10.618 12842 Z= 0.346 Chirality : 0.041 0.149 1506 Planarity : 0.005 0.060 1630 Dihedral : 4.129 15.620 1298 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.09 % Allowed : 9.42 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.24), residues: 1196 helix: 1.27 (0.19), residues: 730 sheet: 0.19 (0.56), residues: 70 loop : -1.96 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 170 HIS 0.005 0.001 HIS A 574 PHE 0.014 0.001 PHE B 271 TYR 0.026 0.002 TYR B 354 ARG 0.005 0.001 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 ILE cc_start: 0.8211 (tt) cc_final: 0.7909 (tt) REVERT: B 276 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8211 (ttm) REVERT: B 407 GLN cc_start: 0.5678 (mt0) cc_final: 0.5253 (tm-30) REVERT: B 573 ILE cc_start: 0.8211 (tt) cc_final: 0.7870 (tt) outliers start: 11 outliers final: 7 residues processed: 114 average time/residue: 0.2454 time to fit residues: 39.4488 Evaluate side-chains 108 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 70 optimal weight: 2.9990 chunk 48 optimal weight: 0.0370 chunk 29 optimal weight: 0.0470 chunk 59 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 78 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 108 optimal weight: 0.0070 chunk 7 optimal weight: 0.0040 chunk 44 optimal weight: 4.9990 overall best weight: 0.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.210317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.178339 restraints weight = 14113.020| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 2.68 r_work: 0.4111 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9490 Z= 0.146 Angle : 0.551 7.498 12842 Z= 0.289 Chirality : 0.039 0.159 1506 Planarity : 0.004 0.054 1630 Dihedral : 3.783 13.849 1298 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.19 % Allowed : 12.50 % Favored : 86.31 % 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: 1.00 (0.24), residues: 1196 helix: 1.94 (0.19), residues: 732 sheet: 0.80 (0.57), residues: 68 loop : -1.93 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 132 HIS 0.003 0.001 HIS B 574 PHE 0.010 0.001 PHE B 271 TYR 0.021 0.001 TYR A 354 ARG 0.003 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.974 Fit side-chains REVERT: A 159 GLN cc_start: 0.7176 (tp40) cc_final: 0.6658 (tt0) REVERT: A 407 GLN cc_start: 0.6090 (mt0) cc_final: 0.4846 (tm-30) REVERT: A 573 ILE cc_start: 0.8230 (tt) cc_final: 0.7936 (tt) REVERT: B 246 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7315 (m-30) REVERT: B 573 ILE cc_start: 0.8329 (tt) cc_final: 0.8024 (tt) REVERT: B 653 GLU cc_start: 0.5420 (mm-30) cc_final: 0.5093 (mm-30) outliers start: 12 outliers final: 9 residues processed: 125 average time/residue: 0.2224 time to fit residues: 39.0110 Evaluate side-chains 112 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 26 optimal weight: 1.9990 chunk 73 optimal weight: 0.0170 chunk 83 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN A 679 GLN B 250 HIS ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN B 566 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.205610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.173505 restraints weight = 14159.270| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 2.68 r_work: 0.4059 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9490 Z= 0.161 Angle : 0.539 6.559 12842 Z= 0.285 Chirality : 0.039 0.164 1506 Planarity : 0.004 0.052 1630 Dihedral : 3.746 14.372 1298 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.98 % Allowed : 14.09 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.24), residues: 1196 helix: 2.01 (0.19), residues: 730 sheet: 0.82 (0.56), residues: 68 loop : -1.95 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 170 HIS 0.008 0.001 HIS A 485 PHE 0.011 0.001 PHE A 302 TYR 0.014 0.001 TYR B 360 ARG 0.007 0.000 ARG A 590 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.986 Fit side-chains REVERT: A 159 GLN cc_start: 0.7189 (tp40) cc_final: 0.6707 (tt0) REVERT: A 407 GLN cc_start: 0.6211 (mt0) cc_final: 0.4905 (tm-30) REVERT: A 573 ILE cc_start: 0.8287 (tt) cc_final: 0.8002 (tt) REVERT: B 159 GLN cc_start: 0.7341 (tp40) cc_final: 0.6544 (tt0) REVERT: B 407 GLN cc_start: 0.6015 (mt0) cc_final: 0.5424 (tm-30) REVERT: B 441 ARG cc_start: 0.8161 (ptp90) cc_final: 0.7675 (ptp90) REVERT: B 573 ILE cc_start: 0.8267 (tt) cc_final: 0.7956 (tt) outliers start: 20 outliers final: 12 residues processed: 123 average time/residue: 0.2115 time to fit residues: 37.0432 Evaluate side-chains 117 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 0 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 110 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN ** B 714 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 = 0.4409 r_free = 0.4409 target = 0.201671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.169853 restraints weight = 14232.064| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 2.54 r_work: 0.4022 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9490 Z= 0.190 Angle : 0.547 6.060 12842 Z= 0.294 Chirality : 0.040 0.163 1506 Planarity : 0.004 0.052 1630 Dihedral : 3.816 15.183 1298 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.88 % Allowed : 15.08 % Favored : 83.04 % 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: 0.96 (0.24), residues: 1196 helix: 2.00 (0.19), residues: 728 sheet: 0.83 (0.56), residues: 68 loop : -2.12 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 170 HIS 0.006 0.001 HIS A 574 PHE 0.015 0.002 PHE B 565 TYR 0.016 0.001 TYR B 360 ARG 0.003 0.000 ARG A 590 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.897 Fit side-chains REVERT: A 159 GLN cc_start: 0.7183 (tp40) cc_final: 0.6694 (tt0) REVERT: A 407 GLN cc_start: 0.6140 (mt0) cc_final: 0.4900 (tm-30) REVERT: A 410 MET cc_start: 0.6419 (mmm) cc_final: 0.5887 (tmm) REVERT: A 573 ILE cc_start: 0.8235 (tt) cc_final: 0.7958 (tt) REVERT: A 632 LYS cc_start: 0.4851 (mttt) cc_final: 0.4045 (tttm) REVERT: B 159 GLN cc_start: 0.7240 (tp40) cc_final: 0.6464 (tt0) REVERT: B 407 GLN cc_start: 0.5959 (mt0) cc_final: 0.5340 (tm-30) REVERT: B 573 ILE cc_start: 0.8270 (tt) cc_final: 0.7942 (tt) outliers start: 19 outliers final: 13 residues processed: 119 average time/residue: 0.2669 time to fit residues: 44.2582 Evaluate side-chains 116 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 678 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 58 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 113 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN B 566 ASN ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.200258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.168558 restraints weight = 14168.888| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 2.53 r_work: 0.4009 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9490 Z= 0.179 Angle : 0.534 5.978 12842 Z= 0.286 Chirality : 0.039 0.148 1506 Planarity : 0.004 0.053 1630 Dihedral : 3.843 15.183 1298 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.88 % Allowed : 16.37 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.92 (0.24), residues: 1196 helix: 2.01 (0.19), residues: 730 sheet: 0.68 (0.57), residues: 68 loop : -2.22 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 304 HIS 0.005 0.001 HIS A 574 PHE 0.012 0.001 PHE B 601 TYR 0.014 0.001 TYR B 360 ARG 0.003 0.000 ARG A 706 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 1.351 Fit side-chains REVERT: A 159 GLN cc_start: 0.7263 (tp40) cc_final: 0.6769 (tt0) REVERT: A 323 TRP cc_start: 0.7410 (t-100) cc_final: 0.6499 (t60) REVERT: A 407 GLN cc_start: 0.6186 (mt0) cc_final: 0.5007 (tm-30) REVERT: A 410 MET cc_start: 0.6405 (mmm) cc_final: 0.6000 (tmm) REVERT: A 573 ILE cc_start: 0.8299 (tt) cc_final: 0.8027 (tt) REVERT: A 632 LYS cc_start: 0.4974 (mttt) cc_final: 0.4157 (tttm) REVERT: B 159 GLN cc_start: 0.7264 (tp40) cc_final: 0.6474 (tt0) REVERT: B 407 GLN cc_start: 0.5948 (mt0) cc_final: 0.5371 (tm-30) REVERT: B 442 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7810 (mm-30) REVERT: B 573 ILE cc_start: 0.8249 (tt) cc_final: 0.7922 (tt) REVERT: B 638 LEU cc_start: 0.7249 (tp) cc_final: 0.7030 (pp) REVERT: B 668 ILE cc_start: 0.7173 (mp) cc_final: 0.6882 (pt) REVERT: B 709 GLN cc_start: 0.2397 (OUTLIER) cc_final: 0.2087 (pt0) outliers start: 19 outliers final: 12 residues processed: 127 average time/residue: 0.3188 time to fit residues: 56.1413 Evaluate side-chains 118 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 709 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 18 optimal weight: 0.0770 chunk 92 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 97 optimal weight: 0.3980 chunk 115 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 5 optimal weight: 0.0170 chunk 58 optimal weight: 7.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.200673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.169117 restraints weight = 14358.574| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.55 r_work: 0.4018 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9490 Z= 0.163 Angle : 0.524 6.599 12842 Z= 0.281 Chirality : 0.039 0.133 1506 Planarity : 0.004 0.074 1630 Dihedral : 3.761 15.058 1298 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.69 % Allowed : 17.66 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1196 helix: 2.04 (0.19), residues: 734 sheet: 0.66 (0.57), residues: 68 loop : -2.22 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 304 HIS 0.005 0.001 HIS A 574 PHE 0.009 0.001 PHE B 601 TYR 0.015 0.001 TYR B 349 ARG 0.003 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.025 Fit side-chains REVERT: A 159 GLN cc_start: 0.7242 (tp40) cc_final: 0.6779 (tt0) REVERT: A 323 TRP cc_start: 0.7450 (t-100) cc_final: 0.6539 (t60) REVERT: A 366 ASP cc_start: 0.7503 (t0) cc_final: 0.7151 (t70) REVERT: A 407 GLN cc_start: 0.6185 (mt0) cc_final: 0.5041 (tm-30) REVERT: A 410 MET cc_start: 0.6387 (mmm) cc_final: 0.6014 (tmm) REVERT: A 573 ILE cc_start: 0.8388 (tt) cc_final: 0.8113 (tt) REVERT: A 632 LYS cc_start: 0.5072 (mttt) cc_final: 0.4275 (tttm) REVERT: B 159 GLN cc_start: 0.7283 (tp40) cc_final: 0.6504 (tt0) REVERT: B 370 LYS cc_start: 0.6955 (tppt) cc_final: 0.6574 (ttmm) REVERT: B 407 GLN cc_start: 0.5888 (mt0) cc_final: 0.5403 (tm-30) REVERT: B 442 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7816 (mm-30) REVERT: B 573 ILE cc_start: 0.8257 (tt) cc_final: 0.7936 (tt) REVERT: B 638 LEU cc_start: 0.7300 (tp) cc_final: 0.7047 (pp) REVERT: B 668 ILE cc_start: 0.7072 (mp) cc_final: 0.6795 (pt) REVERT: B 709 GLN cc_start: 0.2459 (OUTLIER) cc_final: 0.2130 (pt0) outliers start: 17 outliers final: 12 residues processed: 120 average time/residue: 0.2282 time to fit residues: 38.0206 Evaluate side-chains 117 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 709 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 25 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.198077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.166332 restraints weight = 14401.159| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.55 r_work: 0.3987 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9490 Z= 0.192 Angle : 0.549 6.914 12842 Z= 0.295 Chirality : 0.040 0.167 1506 Planarity : 0.005 0.066 1630 Dihedral : 3.876 15.410 1298 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.88 % Allowed : 18.25 % Favored : 79.86 % 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: 0.75 (0.24), residues: 1196 helix: 1.92 (0.19), residues: 732 sheet: 0.51 (0.59), residues: 68 loop : -2.41 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 304 HIS 0.005 0.001 HIS A 574 PHE 0.014 0.001 PHE B 601 TYR 0.015 0.002 TYR B 349 ARG 0.004 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 159 GLN cc_start: 0.7261 (tp40) cc_final: 0.6741 (tt0) REVERT: A 323 TRP cc_start: 0.7478 (t-100) cc_final: 0.6403 (t60) REVERT: A 366 ASP cc_start: 0.7664 (t0) cc_final: 0.7134 (t70) REVERT: A 407 GLN cc_start: 0.6286 (mt0) cc_final: 0.5141 (tm-30) REVERT: A 410 MET cc_start: 0.6494 (mmm) cc_final: 0.6081 (tmm) REVERT: A 573 ILE cc_start: 0.8372 (tt) cc_final: 0.8090 (tt) REVERT: A 632 LYS cc_start: 0.5147 (mttt) cc_final: 0.4349 (tttm) REVERT: B 159 GLN cc_start: 0.7308 (tp40) cc_final: 0.6512 (tt0) REVERT: B 370 LYS cc_start: 0.7163 (tppt) cc_final: 0.6752 (ttmm) REVERT: B 407 GLN cc_start: 0.5952 (mt0) cc_final: 0.5414 (tm-30) REVERT: B 442 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7939 (mm-30) REVERT: B 552 ARG cc_start: 0.5807 (mtt180) cc_final: 0.5547 (mpt-90) REVERT: B 573 ILE cc_start: 0.8306 (tt) cc_final: 0.7965 (tt) REVERT: B 638 LEU cc_start: 0.7341 (tp) cc_final: 0.7138 (pp) REVERT: B 668 ILE cc_start: 0.7104 (mp) cc_final: 0.6828 (pt) outliers start: 19 outliers final: 15 residues processed: 124 average time/residue: 0.2139 time to fit residues: 37.1430 Evaluate side-chains 120 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 709 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 68 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN B 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.200288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.168860 restraints weight = 14287.646| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 2.52 r_work: 0.4014 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9490 Z= 0.154 Angle : 0.526 7.563 12842 Z= 0.279 Chirality : 0.038 0.166 1506 Planarity : 0.004 0.061 1630 Dihedral : 3.792 15.298 1298 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.49 % Allowed : 19.25 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1196 helix: 2.03 (0.19), residues: 732 sheet: 0.46 (0.58), residues: 68 loop : -2.39 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 323 HIS 0.004 0.001 HIS A 574 PHE 0.010 0.001 PHE B 302 TYR 0.016 0.001 TYR B 349 ARG 0.005 0.000 ARG B 341 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 159 GLN cc_start: 0.7267 (tp40) cc_final: 0.6791 (tt0) REVERT: A 323 TRP cc_start: 0.7437 (t-100) cc_final: 0.6555 (t60) REVERT: A 366 ASP cc_start: 0.7719 (t0) cc_final: 0.7199 (t70) REVERT: A 407 GLN cc_start: 0.6049 (mt0) cc_final: 0.4930 (tm-30) REVERT: A 410 MET cc_start: 0.6377 (mmm) cc_final: 0.6026 (tmm) REVERT: A 573 ILE cc_start: 0.8362 (tt) cc_final: 0.8082 (tt) REVERT: A 632 LYS cc_start: 0.5080 (mttt) cc_final: 0.4341 (tttm) REVERT: B 159 GLN cc_start: 0.7259 (tp40) cc_final: 0.6485 (tt0) REVERT: B 370 LYS cc_start: 0.7078 (tppt) cc_final: 0.6636 (ttmm) REVERT: B 407 GLN cc_start: 0.5863 (mt0) cc_final: 0.5411 (tm-30) REVERT: B 442 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7915 (mm-30) REVERT: B 573 ILE cc_start: 0.8267 (tt) cc_final: 0.7941 (tt) REVERT: B 638 LEU cc_start: 0.7337 (tp) cc_final: 0.7132 (pp) REVERT: B 668 ILE cc_start: 0.7049 (mp) cc_final: 0.6776 (pt) REVERT: B 709 GLN cc_start: 0.2357 (OUTLIER) cc_final: 0.1993 (pt0) outliers start: 15 outliers final: 14 residues processed: 116 average time/residue: 0.2430 time to fit residues: 39.3227 Evaluate side-chains 118 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 709 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 116 optimal weight: 0.0980 chunk 80 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 56 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.200841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.169493 restraints weight = 14355.617| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 2.55 r_work: 0.4022 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9490 Z= 0.146 Angle : 0.515 7.019 12842 Z= 0.274 Chirality : 0.038 0.140 1506 Planarity : 0.004 0.059 1630 Dihedral : 3.691 15.041 1298 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.59 % Allowed : 19.54 % Favored : 78.87 % 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: 0.93 (0.25), residues: 1196 helix: 2.09 (0.19), residues: 734 sheet: 0.52 (0.59), residues: 68 loop : -2.38 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 323 HIS 0.004 0.001 HIS B 574 PHE 0.008 0.001 PHE A 302 TYR 0.017 0.001 TYR B 349 ARG 0.004 0.000 ARG A 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 159 GLN cc_start: 0.7276 (tp40) cc_final: 0.6869 (tt0) REVERT: A 323 TRP cc_start: 0.7436 (t-100) cc_final: 0.6555 (t60) REVERT: A 366 ASP cc_start: 0.7648 (t0) cc_final: 0.7044 (t70) REVERT: A 410 MET cc_start: 0.6415 (mmm) cc_final: 0.6066 (tmm) REVERT: A 573 ILE cc_start: 0.8381 (tt) cc_final: 0.8113 (tt) REVERT: A 632 LYS cc_start: 0.5062 (mttt) cc_final: 0.4366 (tttm) REVERT: B 159 GLN cc_start: 0.7224 (tp40) cc_final: 0.6493 (tt0) REVERT: B 216 ASN cc_start: 0.8503 (t0) cc_final: 0.8219 (t0) REVERT: B 370 LYS cc_start: 0.7092 (tppt) cc_final: 0.6824 (ttmm) REVERT: B 407 GLN cc_start: 0.5863 (mt0) cc_final: 0.5427 (tm-30) REVERT: B 442 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7871 (mm-30) REVERT: B 573 ILE cc_start: 0.8363 (tt) cc_final: 0.8017 (tt) REVERT: B 632 LYS cc_start: 0.5097 (mttt) cc_final: 0.4879 (mttp) REVERT: B 668 ILE cc_start: 0.7035 (mp) cc_final: 0.6762 (pt) REVERT: B 709 GLN cc_start: 0.2306 (OUTLIER) cc_final: 0.1992 (pt0) outliers start: 16 outliers final: 15 residues processed: 114 average time/residue: 0.2310 time to fit residues: 36.5761 Evaluate side-chains 118 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 709 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.0570 chunk 75 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 109 optimal weight: 0.0040 chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.5910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.200694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.169452 restraints weight = 14271.219| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 2.54 r_work: 0.4021 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9490 Z= 0.153 Angle : 0.534 8.926 12842 Z= 0.279 Chirality : 0.039 0.237 1506 Planarity : 0.004 0.059 1630 Dihedral : 3.696 15.105 1298 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.69 % Allowed : 19.35 % Favored : 78.97 % 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: 0.91 (0.25), residues: 1196 helix: 2.08 (0.19), residues: 734 sheet: 0.52 (0.59), residues: 68 loop : -2.41 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 304 HIS 0.004 0.001 HIS A 574 PHE 0.008 0.001 PHE A 302 TYR 0.016 0.001 TYR B 349 ARG 0.005 0.000 ARG B 267 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4241.81 seconds wall clock time: 76 minutes 23.99 seconds (4583.99 seconds total)