Starting phenix.real_space_refine on Wed Sep 25 02:54:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n58_24182/09_2024/7n58_24182.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n58_24182/09_2024/7n58_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n58_24182/09_2024/7n58_24182.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n58_24182/09_2024/7n58_24182.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n58_24182/09_2024/7n58_24182.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n58_24182/09_2024/7n58_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-5461/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: 6.05, per 1000 atoms: 0.65 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: 2.38 Conformation dependent library (CDL) restraints added in 1.1 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: 1.06 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: 2.78 Time building geometry restraints manager: 2.79 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: 0.00 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: 1.640 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.190 Process input model: 24.200 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.030 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.024 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: 0.2152 time to fit residues: 37.5258 Evaluate side-chains 98 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9490 Z= 0.205 Angle : 0.659 10.690 12842 Z= 0.346 Chirality : 0.041 0.149 1506 Planarity : 0.005 0.060 1630 Dihedral : 4.127 15.616 1298 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.42 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: 0.25 (0.24), residues: 1196 helix: 1.26 (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 0.008 0.001 TRP A 170 HIS 0.005 0.001 HIS A 574 PHE 0.014 0.001 PHE B 271 TYR 0.025 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 fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 ILE cc_start: 0.7897 (tt) cc_final: 0.7565 (tt) REVERT: B 407 GLN cc_start: 0.5452 (mt0) cc_final: 0.5097 (tm-30) REVERT: B 573 ILE cc_start: 0.7892 (tt) cc_final: 0.7523 (tt) outliers start: 11 outliers final: 7 residues processed: 114 average time/residue: 0.2154 time to fit residues: 35.0400 Evaluate side-chains 107 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 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 60 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 108 optimal weight: 0.0270 chunk 37 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.9442 ------------------------------------------------------------------------------- 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 679 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.2078 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= 0.196 Angle : 0.589 8.410 12842 Z= 0.311 Chirality : 0.041 0.156 1506 Planarity : 0.004 0.052 1630 Dihedral : 4.034 15.142 1298 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.59 % Allowed : 12.70 % Favored : 85.71 % 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: 0.58 (0.24), residues: 1196 helix: 1.65 (0.19), residues: 724 sheet: 0.60 (0.65), residues: 44 loop : -1.95 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 170 HIS 0.006 0.001 HIS A 574 PHE 0.016 0.002 PHE A 302 TYR 0.019 0.002 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 131 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 159 GLN cc_start: 0.6929 (tp40) cc_final: 0.6377 (tt0) REVERT: A 573 ILE cc_start: 0.7847 (tt) cc_final: 0.7518 (tt) REVERT: A 632 LYS cc_start: 0.4557 (mttt) cc_final: 0.3847 (tttm) REVERT: B 159 GLN cc_start: 0.7050 (tp40) cc_final: 0.6185 (tt0) REVERT: B 573 ILE cc_start: 0.7894 (tt) cc_final: 0.7529 (tt) outliers start: 16 outliers final: 12 residues processed: 123 average time/residue: 0.2199 time to fit residues: 37.7746 Evaluate side-chains 114 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 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 107 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 250 HIS ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9490 Z= 0.269 Angle : 0.632 7.780 12842 Z= 0.340 Chirality : 0.043 0.145 1506 Planarity : 0.005 0.066 1630 Dihedral : 4.323 17.400 1298 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.48 % Allowed : 14.09 % Favored : 83.43 % 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: 1.52 (0.19), residues: 726 sheet: 0.38 (0.55), residues: 70 loop : -2.53 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 304 HIS 0.008 0.001 HIS A 574 PHE 0.022 0.002 PHE B 601 TYR 0.015 0.002 TYR B 360 ARG 0.010 0.001 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 145 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 1.010 Fit side-chains REVERT: A 159 GLN cc_start: 0.7053 (tp40) cc_final: 0.6463 (tt0) REVERT: A 323 TRP cc_start: 0.7386 (t-100) cc_final: 0.6581 (t60) REVERT: A 573 ILE cc_start: 0.7873 (tt) cc_final: 0.7562 (tt) REVERT: A 632 LYS cc_start: 0.4918 (mttt) cc_final: 0.4181 (tttm) REVERT: B 323 TRP cc_start: 0.7480 (t-100) cc_final: 0.6480 (t60) REVERT: B 364 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6457 (mptt) REVERT: B 573 ILE cc_start: 0.7879 (tt) cc_final: 0.7493 (tt) REVERT: B 638 LEU cc_start: 0.7149 (tp) cc_final: 0.6913 (pp) REVERT: B 668 ILE cc_start: 0.7153 (mp) cc_final: 0.6806 (pt) outliers start: 25 outliers final: 13 residues processed: 136 average time/residue: 0.2252 time to fit residues: 43.0288 Evaluate side-chains 115 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 364 LYS 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 96 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 250 HIS ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 GLN ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9490 Z= 0.175 Angle : 0.552 6.667 12842 Z= 0.297 Chirality : 0.039 0.141 1506 Planarity : 0.005 0.058 1630 Dihedral : 4.123 15.272 1298 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.08 % Allowed : 16.57 % Favored : 81.35 % 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: 0.55 (0.24), residues: 1196 helix: 1.79 (0.19), residues: 728 sheet: 0.41 (0.54), residues: 70 loop : -2.50 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 304 HIS 0.005 0.001 HIS A 574 PHE 0.011 0.001 PHE A 302 TYR 0.013 0.001 TYR B 205 ARG 0.005 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 123 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 323 TRP cc_start: 0.7313 (t-100) cc_final: 0.6498 (t60) REVERT: A 370 LYS cc_start: 0.7310 (tppt) cc_final: 0.6956 (ttmm) REVERT: A 407 GLN cc_start: 0.5877 (mt0) cc_final: 0.4802 (tm-30) REVERT: A 573 ILE cc_start: 0.7908 (tt) cc_final: 0.7614 (tt) REVERT: A 632 LYS cc_start: 0.4834 (mttt) cc_final: 0.4124 (tttm) REVERT: B 159 GLN cc_start: 0.7107 (tp40) cc_final: 0.6303 (tt0) REVERT: B 442 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7572 (mm-30) REVERT: B 573 ILE cc_start: 0.7898 (tt) cc_final: 0.7533 (tt) REVERT: B 638 LEU cc_start: 0.7160 (tp) cc_final: 0.6894 (pp) REVERT: B 668 ILE cc_start: 0.7072 (mp) cc_final: 0.6748 (pt) outliers start: 21 outliers final: 15 residues processed: 112 average time/residue: 0.2342 time to fit residues: 36.1884 Evaluate side-chains 113 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 MET 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 364 LYS Chi-restraints excluded: chain B residue 566 ASN 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 0.0670 chunk 60 optimal weight: 8.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 243 HIS B 250 HIS ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 ASN ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9490 Z= 0.153 Angle : 0.522 6.379 12842 Z= 0.280 Chirality : 0.038 0.138 1506 Planarity : 0.004 0.057 1630 Dihedral : 3.927 14.041 1298 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.88 % Allowed : 17.26 % Favored : 80.85 % 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: 0.78 (0.24), residues: 1196 helix: 1.97 (0.19), residues: 730 sheet: 0.49 (0.55), residues: 70 loop : -2.43 (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 0.008 0.001 PHE A 302 TYR 0.014 0.002 TYR A 349 ARG 0.008 0.000 ARG A 590 *********************** 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 123 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 323 TRP cc_start: 0.7282 (t-100) cc_final: 0.6452 (t60) REVERT: A 366 ASP cc_start: 0.7517 (t70) cc_final: 0.7046 (t70) REVERT: A 370 LYS cc_start: 0.7305 (tppt) cc_final: 0.7032 (ttmm) REVERT: A 407 GLN cc_start: 0.5734 (mt0) cc_final: 0.4725 (tm-30) REVERT: A 573 ILE cc_start: 0.7980 (tt) cc_final: 0.7697 (tt) REVERT: A 632 LYS cc_start: 0.4900 (mttt) cc_final: 0.4225 (tttm) REVERT: B 159 GLN cc_start: 0.7105 (tp40) cc_final: 0.6344 (tt0) REVERT: B 370 LYS cc_start: 0.6999 (tppt) cc_final: 0.6575 (ttmm) REVERT: B 442 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7582 (mm-30) REVERT: B 573 ILE cc_start: 0.7888 (tt) cc_final: 0.7516 (tt) REVERT: B 638 LEU cc_start: 0.7178 (tp) cc_final: 0.6880 (pp) REVERT: B 668 ILE cc_start: 0.7017 (mp) cc_final: 0.6690 (pt) outliers start: 19 outliers final: 15 residues processed: 116 average time/residue: 0.2339 time to fit residues: 37.8877 Evaluate side-chains 114 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 MET 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 364 LYS Chi-restraints excluded: chain B residue 566 ASN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.0040 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.0870 chunk 84 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 115 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.4172 ------------------------------------------------------------------------------- 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 243 HIS ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.3226 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= 0.142 Angle : 0.509 6.317 12842 Z= 0.272 Chirality : 0.038 0.137 1506 Planarity : 0.004 0.058 1630 Dihedral : 3.794 13.874 1298 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.79 % Allowed : 18.75 % Favored : 79.46 % 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: 0.90 (0.25), residues: 1196 helix: 2.07 (0.19), residues: 730 sheet: 0.52 (0.55), residues: 70 loop : -2.39 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 323 HIS 0.003 0.001 HIS A 574 PHE 0.007 0.001 PHE B 669 TYR 0.014 0.001 TYR B 349 ARG 0.005 0.000 ARG A 232 *********************** 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 122 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 323 TRP cc_start: 0.7233 (t-100) cc_final: 0.6391 (t60) REVERT: A 366 ASP cc_start: 0.7558 (t70) cc_final: 0.6971 (t70) REVERT: A 370 LYS cc_start: 0.7328 (tppt) cc_final: 0.7077 (ttmm) REVERT: A 407 GLN cc_start: 0.5711 (mt0) cc_final: 0.4707 (tm-30) REVERT: A 573 ILE cc_start: 0.8015 (tt) cc_final: 0.7709 (tt) REVERT: A 632 LYS cc_start: 0.4897 (mttt) cc_final: 0.4296 (tttm) REVERT: B 159 GLN cc_start: 0.7011 (tp40) cc_final: 0.6270 (tt0) REVERT: B 370 LYS cc_start: 0.7122 (tppt) cc_final: 0.6681 (ttmm) REVERT: B 407 GLN cc_start: 0.5683 (mt0) cc_final: 0.5024 (tm-30) REVERT: B 442 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7612 (mm-30) REVERT: B 573 ILE cc_start: 0.7882 (tt) cc_final: 0.7518 (tt) REVERT: B 638 LEU cc_start: 0.7171 (tp) cc_final: 0.6862 (pp) REVERT: B 668 ILE cc_start: 0.6970 (mp) cc_final: 0.6637 (pt) REVERT: B 709 GLN cc_start: 0.2471 (OUTLIER) cc_final: 0.2022 (pt0) outliers start: 18 outliers final: 14 residues processed: 117 average time/residue: 0.2095 time to fit residues: 34.8031 Evaluate side-chains 114 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 364 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 595 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.3433 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 6.666 12842 Z= 0.293 Chirality : 0.039 0.134 1506 Planarity : 0.005 0.058 1630 Dihedral : 3.871 14.640 1298 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.98 % Allowed : 18.95 % Favored : 79.07 % 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 (0.25), residues: 1196 helix: 1.98 (0.19), residues: 732 sheet: 0.35 (0.57), residues: 70 loop : -2.51 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 170 HIS 0.004 0.001 HIS A 574 PHE 0.012 0.001 PHE B 601 TYR 0.016 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 127 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 323 TRP cc_start: 0.7307 (t-100) cc_final: 0.6475 (t60) REVERT: A 366 ASP cc_start: 0.7657 (t70) cc_final: 0.6977 (t70) REVERT: A 370 LYS cc_start: 0.7401 (tppt) cc_final: 0.7078 (ttpp) REVERT: A 407 GLN cc_start: 0.5884 (mt0) cc_final: 0.4867 (tm-30) REVERT: A 573 ILE cc_start: 0.8014 (tt) cc_final: 0.7702 (tt) REVERT: A 632 LYS cc_start: 0.5049 (mttt) cc_final: 0.4419 (tttp) REVERT: B 323 TRP cc_start: 0.7430 (t-100) cc_final: 0.6444 (t60) REVERT: B 364 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.6339 (mptt) REVERT: B 370 LYS cc_start: 0.7115 (tppt) cc_final: 0.6766 (ttmm) REVERT: B 442 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7663 (mm-30) REVERT: B 552 ARG cc_start: 0.5737 (mtt180) cc_final: 0.5440 (mpt-90) REVERT: B 573 ILE cc_start: 0.7991 (tt) cc_final: 0.7595 (tt) REVERT: B 638 LEU cc_start: 0.7174 (tp) cc_final: 0.6937 (pp) REVERT: B 668 ILE cc_start: 0.7066 (mp) cc_final: 0.6749 (pt) outliers start: 20 outliers final: 15 residues processed: 119 average time/residue: 0.2157 time to fit residues: 36.1089 Evaluate side-chains 122 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 364 LYS Chi-restraints excluded: chain B residue 564 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.6980 chunk 101 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.3697 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= 0.196 Angle : 0.553 7.270 12842 Z= 0.297 Chirality : 0.040 0.194 1506 Planarity : 0.005 0.056 1630 Dihedral : 3.995 16.201 1298 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.79 % Allowed : 19.94 % Favored : 78.27 % 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: 0.67 (0.24), residues: 1196 helix: 1.98 (0.19), residues: 730 sheet: 0.28 (0.56), residues: 70 loop : -2.66 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 170 HIS 0.005 0.001 HIS A 574 PHE 0.012 0.001 PHE B 601 TYR 0.016 0.002 TYR A 349 ARG 0.004 0.000 ARG A 232 *********************** 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 fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 323 TRP cc_start: 0.7358 (t-100) cc_final: 0.6311 (t60) REVERT: A 366 ASP cc_start: 0.7685 (t70) cc_final: 0.7055 (t70) REVERT: A 370 LYS cc_start: 0.7427 (tppt) cc_final: 0.7169 (ttpp) REVERT: A 407 GLN cc_start: 0.5794 (mt0) cc_final: 0.4805 (tm-30) REVERT: A 573 ILE cc_start: 0.8009 (tt) cc_final: 0.7687 (tt) REVERT: A 632 LYS cc_start: 0.5107 (mttt) cc_final: 0.4505 (tttp) REVERT: B 159 GLN cc_start: 0.7375 (tp40) cc_final: 0.6975 (tp40) REVERT: B 323 TRP cc_start: 0.7454 (t-100) cc_final: 0.6491 (t60) REVERT: B 364 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.6472 (mptt) REVERT: B 370 LYS cc_start: 0.7180 (tppt) cc_final: 0.6902 (ttmm) REVERT: B 442 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7637 (mm-30) REVERT: B 573 ILE cc_start: 0.7989 (tt) cc_final: 0.7601 (tt) REVERT: B 638 LEU cc_start: 0.7296 (tp) cc_final: 0.7073 (pp) REVERT: B 668 ILE cc_start: 0.7052 (mp) cc_final: 0.6722 (pt) outliers start: 18 outliers final: 15 residues processed: 117 average time/residue: 0.2314 time to fit residues: 37.4240 Evaluate side-chains 116 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 364 LYS Chi-restraints excluded: chain B residue 564 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 54 optimal weight: 0.0870 chunk 79 optimal weight: 0.3980 chunk 119 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9490 Z= 0.158 Angle : 0.537 7.431 12842 Z= 0.285 Chirality : 0.038 0.145 1506 Planarity : 0.004 0.057 1630 Dihedral : 3.844 14.495 1298 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.79 % Allowed : 19.94 % Favored : 78.27 % 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: 0.87 (0.24), residues: 1196 helix: 2.14 (0.19), residues: 720 sheet: 0.45 (0.57), residues: 70 loop : -2.47 (0.26), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 323 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 0.004 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 117 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 323 TRP cc_start: 0.7289 (t-100) cc_final: 0.6433 (t60) REVERT: A 366 ASP cc_start: 0.7647 (t70) cc_final: 0.7048 (t70) REVERT: A 407 GLN cc_start: 0.5774 (mt0) cc_final: 0.4844 (tm-30) REVERT: A 573 ILE cc_start: 0.8030 (tt) cc_final: 0.7733 (tt) REVERT: A 632 LYS cc_start: 0.5044 (mttt) cc_final: 0.4507 (tttp) REVERT: B 159 GLN cc_start: 0.7339 (tp40) cc_final: 0.6931 (tp40) REVERT: B 323 TRP cc_start: 0.7387 (t-100) cc_final: 0.6410 (t60) REVERT: B 370 LYS cc_start: 0.7114 (tppt) cc_final: 0.6893 (ttmm) REVERT: B 442 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7609 (mm-30) REVERT: B 573 ILE cc_start: 0.7981 (tt) cc_final: 0.7579 (tt) REVERT: B 630 PHE cc_start: 0.6180 (OUTLIER) cc_final: 0.5898 (m-80) REVERT: B 638 LEU cc_start: 0.7308 (tp) cc_final: 0.7031 (pp) REVERT: B 668 ILE cc_start: 0.6899 (mp) cc_final: 0.6563 (pt) outliers start: 18 outliers final: 15 residues processed: 110 average time/residue: 0.2235 time to fit residues: 34.1022 Evaluate side-chains 115 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 564 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 630 PHE 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 87 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 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** ** 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 = 0.4341 r_free = 0.4341 target = 0.194750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.163863 restraints weight = 14187.476| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.49 r_work: 0.3959 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.3870 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= 0.193 Angle : 0.564 7.324 12842 Z= 0.302 Chirality : 0.040 0.216 1506 Planarity : 0.005 0.057 1630 Dihedral : 3.946 16.051 1298 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.59 % Allowed : 20.24 % Favored : 78.17 % 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: 0.64 (0.24), residues: 1196 helix: 1.92 (0.19), residues: 742 sheet: 0.30 (0.57), residues: 70 loop : -2.74 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 170 HIS 0.005 0.001 HIS A 574 PHE 0.012 0.001 PHE B 601 TYR 0.017 0.002 TYR B 349 ARG 0.005 0.000 ARG A 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1979.45 seconds wall clock time: 36 minutes 3.18 seconds (2163.18 seconds total)