Starting phenix.real_space_refine on Thu Aug 6 03:21:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10ep_75114/08_2026/10ep_75114.cif Found real_map, /net/cci-nas-00/data/ceres_data/10ep_75114/08_2026/10ep_75114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10ep_75114/08_2026/10ep_75114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10ep_75114/08_2026/10ep_75114.map" model { file = "/net/cci-nas-00/data/ceres_data/10ep_75114/08_2026/10ep_75114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10ep_75114/08_2026/10ep_75114.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 42 5.16 5 C 8055 2.51 5 N 2172 2.21 5 O 2400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12669 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 6371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 807, 6371 Classifications: {'peptide': 807} Link IDs: {'PTRANS': 57, 'TRANS': 749} Chain: "A" Number of atoms: 6298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 6298 Classifications: {'peptide': 797} Link IDs: {'PTRANS': 57, 'TRANS': 739} Chain breaks: 1 Time building chain proxies: 2.65, per 1000 atoms: 0.21 Number of scatterers: 12669 At special positions: 0 Unit cell: (104.12, 160.29, 98.64, 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 42 16.00 O 2400 8.00 N 2172 7.00 C 8055 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: 0.98 Conformation dependent library (CDL) restraints added in 693.3 milliseconds 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2986 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 26 sheets defined 16.4% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.695A pdb=" N ILE B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 154 removed outlier: 3.786A pdb=" N ARG B 154 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 327 Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.585A pdb=" N ARG B 377 " --> pdb=" O PRO B 374 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 378 " --> pdb=" O CYS B 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 374 through 378' Processing helix chain 'B' and resid 456 through 460 removed outlier: 3.520A pdb=" N GLY B 459 " --> pdb=" O PRO B 456 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 460 " --> pdb=" O LEU B 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 456 through 460' Processing helix chain 'B' and resid 697 through 702 Processing helix chain 'B' and resid 719 through 724 Processing helix chain 'B' and resid 748 through 767 Processing helix chain 'B' and resid 781 through 794 Processing helix chain 'B' and resid 809 through 813 removed outlier: 3.796A pdb=" N LEU B 812 " --> pdb=" O ASN B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 833 Processing helix chain 'B' and resid 839 through 843 removed outlier: 3.850A pdb=" N LYS B 842 " --> pdb=" O SER B 839 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 843 " --> pdb=" O ALA B 840 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 839 through 843' Processing helix chain 'B' and resid 861 through 875 removed outlier: 3.799A pdb=" N SER B 865 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 912 Processing helix chain 'A' and resid 114 through 122 removed outlier: 3.923A pdb=" N ILE A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 removed outlier: 3.644A pdb=" N ASP A 151 " --> pdb=" O PRO A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 327 removed outlier: 3.638A pdb=" N ALA A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 removed outlier: 3.535A pdb=" N ARG A 377 " --> pdb=" O PRO A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 726 removed outlier: 3.791A pdb=" N LEU A 721 " --> pdb=" O SER A 718 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TRP A 722 " --> pdb=" O ALA A 719 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 723 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA A 724 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 726 " --> pdb=" O LEU A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 747 removed outlier: 3.576A pdb=" N ASP A 747 " --> pdb=" O GLU A 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 744 through 747' Processing helix chain 'A' and resid 748 through 768 removed outlier: 3.669A pdb=" N VAL A 754 " --> pdb=" O VAL A 750 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 755 " --> pdb=" O GLU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 794 removed outlier: 3.560A pdb=" N ASN A 789 " --> pdb=" O PHE A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 835 removed outlier: 3.901A pdb=" N TYR A 831 " --> pdb=" O ALA A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 840 Processing helix chain 'A' and resid 862 through 875 removed outlier: 3.717A pdb=" N ASP A 866 " --> pdb=" O THR A 862 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 868 " --> pdb=" O GLN A 864 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 912 Processing sheet with id=AA1, first strand: chain 'B' and resid 128 through 131 removed outlier: 3.528A pdb=" N LEU B 141 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 157 through 159 removed outlier: 3.687A pdb=" N THR B 170 " --> pdb=" O ASP B 165 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 205 through 211 removed outlier: 3.594A pdb=" N ARG B 223 " --> pdb=" O LYS B 205 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL B 209 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA B 219 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N TRP B 211 " --> pdb=" O HIS B 217 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N HIS B 217 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 220 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 244 " --> pdb=" O ASP B 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 225 through 226 Processing sheet with id=AA5, first strand: chain 'B' and resid 263 through 265 removed outlier: 3.554A pdb=" N LYS B 340 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.757A pdb=" N ARG A 880 " --> pdb=" O ILE A 847 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N CYS A 800 " --> pdb=" O ILE A 775 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 777 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 802 " --> pdb=" O VAL A 777 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N LEU A 684 " --> pdb=" O ARG A 772 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS A 774 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU A 730 " --> pdb=" O PRO A 685 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 687 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 729 " --> pdb=" O TYR A 671 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN A 652 " --> pdb=" O LEU A 672 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 348 through 351 removed outlier: 6.900A pdb=" N SER B 363 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU B 351 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU B 361 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP B 385 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS B 380 " --> pdb=" O ASP B 397 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASP B 397 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL B 382 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG B 393 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR B 386 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N PHE B 391 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 416 through 420 removed outlier: 3.535A pdb=" N ARG B 416 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE B 418 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N TYR B 429 " --> pdb=" O ILE B 418 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRP B 420 " --> pdb=" O THR B 427 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR B 427 " --> pdb=" O TRP B 420 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TRP B 430 " --> pdb=" O TYR B 450 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS B 466 " --> pdb=" O VAL B 449 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N MET B 451 " --> pdb=" O VAL B 464 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL B 464 " --> pdb=" O MET B 451 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 471 through 479 removed outlier: 6.281A pdb=" N TYR B 486 " --> pdb=" O GLY B 473 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE B 475 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU B 484 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TRP B 477 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N LEU B 482 " --> pdb=" O TRP B 477 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR B 495 " --> pdb=" O ASP B 514 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP B 514 " --> pdb=" O THR B 495 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR B 497 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 510 " --> pdb=" O VAL B 499 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 526 through 527 removed outlier: 3.815A pdb=" N GLY B 556 " --> pdb=" O PHE B 567 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 568 " --> pdb=" O TRP B 582 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TRP B 582 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU B 570 " --> pdb=" O ARG B 580 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG B 580 " --> pdb=" O LEU B 570 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 529 through 531 Processing sheet with id=AB3, first strand: chain 'B' and resid 542 through 543 Processing sheet with id=AB4, first strand: chain 'B' and resid 592 through 596 removed outlier: 7.101A pdb=" N LEU B 613 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LEU B 596 " --> pdb=" O LYS B 611 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N LYS B 611 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE B 612 " --> pdb=" O GLN B 628 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B 628 " --> pdb=" O ILE B 612 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 652 through 659 removed outlier: 3.865A pdb=" N GLN B 652 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 669 " --> pdb=" O SER B 731 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 729 " --> pdb=" O TYR B 671 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU B 730 " --> pdb=" O PRO B 685 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU B 687 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU B 684 " --> pdb=" O LYS B 774 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ALA B 776 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N CYS B 686 " --> pdb=" O ALA B 776 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N GLY B 778 " --> pdb=" O CYS B 686 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE B 688 " --> pdb=" O GLY B 778 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N HIS B 780 " --> pdb=" O PHE B 688 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N CYS B 800 " --> pdb=" O ILE B 775 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 804 " --> pdb=" O GLY B 779 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 128 through 131 removed outlier: 3.541A pdb=" N ALA A 128 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 156 through 159 Processing sheet with id=AB8, first strand: chain 'A' and resid 206 through 211 removed outlier: 4.315A pdb=" N VAL A 209 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA A 219 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N TRP A 211 " --> pdb=" O HIS A 217 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N HIS A 217 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 273 through 275 Processing sheet with id=AC1, first strand: chain 'A' and resid 351 through 353 removed outlier: 3.563A pdb=" N ASP A 352 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 360 " --> pdb=" O TRP A 385 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 380 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A 396 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL A 384 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN A 394 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N THR A 386 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N VAL A 392 " --> pdb=" O THR A 386 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 415 through 419 removed outlier: 7.388A pdb=" N MET A 415 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR A 433 " --> pdb=" O MET A 415 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER A 417 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 431 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR A 429 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 415 through 419 removed outlier: 7.388A pdb=" N MET A 415 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR A 433 " --> pdb=" O MET A 415 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER A 417 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 431 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR A 429 " --> pdb=" O ASN A 419 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TRP A 430 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A 447 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 449 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU A 465 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 483 through 489 removed outlier: 3.853A pdb=" N ARG A 494 " --> pdb=" O TRP A 489 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 495 " --> pdb=" O PHE A 513 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE A 513 " --> pdb=" O THR A 495 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.574A pdb=" N ASN A 555 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 554 " --> pdb=" O ASP A 569 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY A 556 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU A 570 " --> pdb=" O ARG A 580 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ARG A 580 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ASP A 572 " --> pdb=" O LYS A 578 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS A 578 " --> pdb=" O ASP A 572 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 529 through 531 Processing sheet with id=AC7, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AC8, first strand: chain 'A' and resid 593 through 596 removed outlier: 6.995A pdb=" N LEU A 613 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEU A 596 " --> pdb=" O LYS A 611 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LYS A 611 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 612 " --> pdb=" O GLN A 628 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN A 628 " --> pdb=" O ILE A 612 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 936 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: 2.37 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4168 1.34 - 1.46: 2889 1.46 - 1.58: 5869 1.58 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 12994 Sorted by residual: bond pdb=" N SER A 504 " pdb=" CA SER A 504 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.24e+00 bond pdb=" C GLU A 455 " pdb=" N PRO A 456 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.77e-01 bond pdb=" CA TRP B 630 " pdb=" C TRP B 630 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.23e-02 6.61e+03 6.53e-01 bond pdb=" CA SER A 504 " pdb=" C SER A 504 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.34e-02 5.57e+03 6.38e-01 bond pdb=" C SER B 444 " pdb=" N PRO B 445 " ideal model delta sigma weight residual 1.334 1.352 -0.018 2.34e-02 1.83e+03 6.06e-01 ... (remaining 12989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 17299 1.09 - 2.19: 239 2.19 - 3.28: 119 3.28 - 4.38: 10 4.38 - 5.47: 6 Bond angle restraints: 17673 Sorted by residual: angle pdb=" N ILE B 372 " pdb=" CA ILE B 372 " pdb=" C ILE B 372 " ideal model delta sigma weight residual 113.20 110.70 2.50 9.60e-01 1.09e+00 6.80e+00 angle pdb=" C SER A 504 " pdb=" CA SER A 504 " pdb=" CB SER A 504 " ideal model delta sigma weight residual 110.42 115.34 -4.92 1.99e+00 2.53e-01 6.12e+00 angle pdb=" C GLU B 545 " pdb=" N ASN B 546 " pdb=" CA ASN B 546 " ideal model delta sigma weight residual 121.54 125.07 -3.53 1.91e+00 2.74e-01 3.42e+00 angle pdb=" C TRP B 630 " pdb=" CA TRP B 630 " pdb=" CB TRP B 630 " ideal model delta sigma weight residual 112.76 109.39 3.37 1.86e+00 2.89e-01 3.28e+00 angle pdb=" C GLY A 503 " pdb=" N SER A 504 " pdb=" CA SER A 504 " ideal model delta sigma weight residual 121.54 124.86 -3.32 1.91e+00 2.74e-01 3.02e+00 ... (remaining 17668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 6941 17.18 - 34.35: 731 34.35 - 51.53: 124 51.53 - 68.71: 22 68.71 - 85.88: 9 Dihedral angle restraints: 7827 sinusoidal: 3180 harmonic: 4647 Sorted by residual: dihedral pdb=" CA ASP A 336 " pdb=" CB ASP A 336 " pdb=" CG ASP A 336 " pdb=" OD1 ASP A 336 " ideal model delta sinusoidal sigma weight residual -30.00 -86.54 56.54 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CB GLU A 455 " pdb=" CG GLU A 455 " pdb=" CD GLU A 455 " pdb=" OE1 GLU A 455 " ideal model delta sinusoidal sigma weight residual 0.00 85.88 -85.88 1 3.00e+01 1.11e-03 9.90e+00 dihedral pdb=" CA ASP B 681 " pdb=" CB ASP B 681 " pdb=" CG ASP B 681 " pdb=" OD1 ASP B 681 " ideal model delta sinusoidal sigma weight residual -30.00 -83.76 53.76 1 2.00e+01 2.50e-03 9.81e+00 ... (remaining 7824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1183 0.026 - 0.053: 461 0.053 - 0.079: 115 0.079 - 0.106: 105 0.106 - 0.132: 62 Chirality restraints: 1926 Sorted by residual: chirality pdb=" CA ILE B 276 " pdb=" N ILE B 276 " pdb=" C ILE B 276 " pdb=" CB ILE B 276 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA VAL A 344 " pdb=" N VAL A 344 " pdb=" C VAL A 344 " pdb=" CB VAL A 344 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.01e-01 chirality pdb=" CA ILE A 276 " pdb=" N ILE A 276 " pdb=" C ILE A 276 " pdb=" CB ILE A 276 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1923 not shown) Planarity restraints: 2304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 344 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO A 345 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 345 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 345 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 424 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.99e+00 pdb=" N PRO A 425 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 425 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 425 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 645 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO B 646 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 646 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 646 " -0.018 5.00e-02 4.00e+02 ... (remaining 2301 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 7043 3.05 - 3.52: 11554 3.52 - 3.98: 17781 3.98 - 4.44: 19646 4.44 - 4.90: 33868 Nonbonded interactions: 89892 Sorted by model distance: nonbonded pdb=" N ILE A 406 " pdb=" N ALA A 407 " model vdw 2.593 2.560 nonbonded pdb=" N ALA A 346 " pdb=" O ALA A 346 " model vdw 2.629 2.496 nonbonded pdb=" N ALA B 346 " pdb=" O ALA B 346 " model vdw 2.630 2.496 nonbonded pdb=" N ASP B 479 " pdb=" O ASP B 479 " model vdw 2.635 2.496 nonbonded pdb=" O ASP A 403 " pdb=" OD1 ASP A 403 " model vdw 2.636 3.040 ... (remaining 89887 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' and (resid 108 through 695 or resid 706 through 915)) } 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: 0.540 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.810 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 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 : 0.002 0.027 12994 Z= 0.080 Angle : 0.411 5.470 17673 Z= 0.210 Chirality : 0.040 0.132 1926 Planarity : 0.003 0.039 2304 Dihedral : 13.943 85.882 4841 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.21), residues: 1598 helix: 0.94 (0.37), residues: 212 sheet: 0.35 (0.27), residues: 395 loop : -0.86 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 173 TYR 0.007 0.000 TYR A 521 PHE 0.008 0.000 PHE B 695 TRP 0.004 0.000 TRP B 630 HIS 0.001 0.000 HIS B 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00159 / 0.08 (12994) covalent geometry : angle 0.41089 / 0.21 (17673) hydrogen bonds : bond 0.26861 / 18.92 ( 347) hydrogen bonds : angle 8.38842 / 6.06 ( 936) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 116 GLU cc_start: 0.7534 (mp0) cc_final: 0.7326 (mp0) REVERT: B 156 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8117 (mt-10) REVERT: B 288 LEU cc_start: 0.8917 (mm) cc_final: 0.8640 (mm) REVERT: B 528 MET cc_start: 0.9055 (mtp) cc_final: 0.8710 (mtp) REVERT: A 383 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6495 (mp0) REVERT: A 496 ARG cc_start: 0.7258 (mtp180) cc_final: 0.6888 (mtm110) REVERT: A 597 MET cc_start: 0.8396 (mmp) cc_final: 0.7775 (mmm) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1039 time to fit residues: 10.7856 Evaluate side-chains 47 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 169 ASN B 875 HIS A 169 ASN A 366 HIS A 546 ASN A 574 ASN A 780 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.101788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.072208 restraints weight = 25035.867| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.73 r_work: 0.2860 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12994 Z= 0.093 Angle : 0.453 5.268 17673 Z= 0.232 Chirality : 0.041 0.142 1926 Planarity : 0.004 0.039 2304 Dihedral : 2.824 10.218 1756 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.36 % Allowed : 6.41 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.21), residues: 1598 helix: 1.46 (0.38), residues: 214 sheet: 0.29 (0.27), residues: 414 loop : -0.82 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 781 TYR 0.011 0.001 TYR B 472 PHE 0.007 0.001 PHE B 785 TRP 0.007 0.001 TRP A 236 HIS 0.002 0.000 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (12994) covalent geometry : angle 0.45299 / 0.23 (17673) hydrogen bonds : bond 0.04671 / 3.39 ( 347) hydrogen bonds : angle 5.61494 / 4.11 ( 936) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: B 116 GLU cc_start: 0.7704 (mp0) cc_final: 0.7503 (mp0) REVERT: B 288 LEU cc_start: 0.8969 (mm) cc_final: 0.8740 (mm) REVERT: B 528 MET cc_start: 0.9096 (mtp) cc_final: 0.8846 (mtp) REVERT: A 169 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8377 (t0) REVERT: A 383 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6383 (mp0) REVERT: A 496 ARG cc_start: 0.6714 (mtp180) cc_final: 0.6482 (mtp85) REVERT: A 597 MET cc_start: 0.8283 (mmp) cc_final: 0.7662 (mmm) REVERT: A 879 CYS cc_start: 0.7522 (p) cc_final: 0.7297 (p) outliers start: 5 outliers final: 3 residues processed: 62 average time/residue: 0.1038 time to fit residues: 10.2689 Evaluate side-chains 53 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 395 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 29 optimal weight: 0.0980 chunk 149 optimal weight: 4.9990 chunk 139 optimal weight: 0.3980 chunk 142 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 17 optimal weight: 0.0770 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 169 ASN B 409 ASN A 169 ASN A 546 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.098620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.068698 restraints weight = 25259.821| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.72 r_work: 0.2791 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12994 Z= 0.112 Angle : 0.458 5.538 17673 Z= 0.233 Chirality : 0.041 0.143 1926 Planarity : 0.004 0.044 2304 Dihedral : 2.999 11.665 1756 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.65 % Allowed : 7.63 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.21), residues: 1598 helix: 1.56 (0.38), residues: 217 sheet: 0.29 (0.26), residues: 422 loop : -0.95 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 810 TYR 0.011 0.001 TYR B 472 PHE 0.011 0.001 PHE B 263 TRP 0.008 0.001 TRP A 236 HIS 0.005 0.001 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (12994) covalent geometry : angle 0.45786 / 0.23 (17673) hydrogen bonds : bond 0.04651 / 3.33 ( 347) hydrogen bonds : angle 5.13496 / 3.73 ( 936) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.455 Fit side-chains REVERT: B 116 GLU cc_start: 0.7793 (mp0) cc_final: 0.7591 (mp0) REVERT: B 288 LEU cc_start: 0.9003 (mm) cc_final: 0.8775 (mm) REVERT: B 528 MET cc_start: 0.9083 (mtp) cc_final: 0.8753 (mtp) REVERT: A 383 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6588 (mp0) REVERT: A 597 MET cc_start: 0.8371 (mmp) cc_final: 0.7618 (mmm) outliers start: 9 outliers final: 4 residues processed: 56 average time/residue: 0.0967 time to fit residues: 8.2218 Evaluate side-chains 51 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 395 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 76 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 169 ASN B 636 GLN A 169 ASN A 546 ASN ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.093811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.063421 restraints weight = 25378.149| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.78 r_work: 0.2685 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12994 Z= 0.192 Angle : 0.547 5.771 17673 Z= 0.282 Chirality : 0.044 0.162 1926 Planarity : 0.005 0.056 2304 Dihedral : 3.716 14.465 1756 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.94 % Allowed : 8.71 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.21), residues: 1598 helix: 1.43 (0.38), residues: 217 sheet: 0.10 (0.26), residues: 420 loop : -1.19 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 515 TYR 0.015 0.001 TYR B 472 PHE 0.022 0.002 PHE A 727 TRP 0.013 0.001 TRP A 236 HIS 0.005 0.001 HIS A 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.19 (12994) covalent geometry : angle 0.54688 / 0.28 (17673) hydrogen bonds : bond 0.05962 / 4.23 ( 347) hydrogen bonds : angle 5.14673 / 3.71 ( 936) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.498 Fit side-chains REVERT: B 288 LEU cc_start: 0.9182 (mm) cc_final: 0.8949 (mm) REVERT: B 441 MET cc_start: 0.8138 (mmm) cc_final: 0.7734 (ttt) REVERT: B 528 MET cc_start: 0.8976 (mtp) cc_final: 0.8757 (mtp) REVERT: A 597 MET cc_start: 0.8326 (mmp) cc_final: 0.7679 (mmm) outliers start: 13 outliers final: 7 residues processed: 55 average time/residue: 0.0831 time to fit residues: 7.7899 Evaluate side-chains 50 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 466 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 131 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 115 optimal weight: 20.0000 chunk 156 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 169 ASN B 636 GLN A 169 ASN A 546 ASN A 622 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.095583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.065367 restraints weight = 25141.216| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 3.70 r_work: 0.2722 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12994 Z= 0.100 Angle : 0.467 6.139 17673 Z= 0.237 Chirality : 0.042 0.147 1926 Planarity : 0.004 0.049 2304 Dihedral : 3.463 14.162 1756 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.01 % Allowed : 9.43 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.21), residues: 1598 helix: 1.50 (0.38), residues: 216 sheet: 0.17 (0.26), residues: 419 loop : -1.12 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 390 TYR 0.010 0.001 TYR B 472 PHE 0.011 0.001 PHE A 727 TRP 0.010 0.001 TRP A 825 HIS 0.002 0.000 HIS A 886 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (12994) covalent geometry : angle 0.46653 / 0.24 (17673) hydrogen bonds : bond 0.04248 / 3.05 ( 347) hydrogen bonds : angle 4.80873 / 3.47 ( 936) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.524 Fit side-chains REVERT: B 288 LEU cc_start: 0.9187 (mm) cc_final: 0.8964 (mm) REVERT: B 441 MET cc_start: 0.8192 (mmm) cc_final: 0.7706 (ttt) REVERT: B 528 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8755 (mtp) REVERT: B 839 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8587 (t) REVERT: A 169 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.7528 (t0) REVERT: A 597 MET cc_start: 0.8417 (mmp) cc_final: 0.7695 (mmm) outliers start: 14 outliers final: 7 residues processed: 53 average time/residue: 0.0804 time to fit residues: 7.3409 Evaluate side-chains 52 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 839 SER Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 466 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 130 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 169 ASN A 169 ASN A 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.094674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.064516 restraints weight = 25060.846| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.69 r_work: 0.2705 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12994 Z= 0.139 Angle : 0.487 5.931 17673 Z= 0.249 Chirality : 0.042 0.153 1926 Planarity : 0.004 0.050 2304 Dihedral : 3.526 13.710 1756 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.86 % Allowed : 10.08 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.21), residues: 1598 helix: 1.52 (0.38), residues: 216 sheet: 0.08 (0.26), residues: 425 loop : -1.19 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 390 TYR 0.011 0.001 TYR B 472 PHE 0.012 0.001 PHE B 263 TRP 0.009 0.001 TRP A 825 HIS 0.003 0.001 HIS A 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (12994) covalent geometry : angle 0.48674 / 0.25 (17673) hydrogen bonds : bond 0.04651 / 3.31 ( 347) hydrogen bonds : angle 4.78780 / 3.45 ( 936) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.336 Fit side-chains REVERT: B 288 LEU cc_start: 0.9207 (mm) cc_final: 0.8989 (mm) REVERT: B 839 SER cc_start: 0.9045 (OUTLIER) cc_final: 0.8587 (t) REVERT: A 169 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.7630 (t0) REVERT: A 597 MET cc_start: 0.8426 (mmp) cc_final: 0.7675 (mmm) outliers start: 12 outliers final: 7 residues processed: 50 average time/residue: 0.0795 time to fit residues: 6.7278 Evaluate side-chains 50 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 839 SER Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 466 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 115 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 14 optimal weight: 0.0470 chunk 32 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 86 optimal weight: 0.0980 chunk 46 optimal weight: 0.0370 chunk 111 optimal weight: 2.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 169 ASN A 169 ASN A 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.096543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.066484 restraints weight = 25000.879| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.69 r_work: 0.2744 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12994 Z= 0.078 Angle : 0.453 6.224 17673 Z= 0.228 Chirality : 0.041 0.143 1926 Planarity : 0.004 0.046 2304 Dihedral : 3.342 13.847 1756 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.86 % Allowed : 10.66 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.21), residues: 1598 helix: 1.60 (0.38), residues: 213 sheet: 0.19 (0.26), residues: 420 loop : -1.08 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 390 TYR 0.010 0.001 TYR B 749 PHE 0.007 0.001 PHE B 263 TRP 0.010 0.001 TRP A 722 HIS 0.002 0.000 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00173 / 0.08 (12994) covalent geometry : angle 0.45261 / 0.23 (17673) hydrogen bonds : bond 0.03489 / 2.52 ( 347) hydrogen bonds : angle 4.56891 / 3.31 ( 936) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.515 Fit side-chains REVERT: B 839 SER cc_start: 0.9037 (OUTLIER) cc_final: 0.8576 (t) REVERT: A 169 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.7507 (t0) REVERT: A 597 MET cc_start: 0.8413 (mmp) cc_final: 0.7669 (mmm) outliers start: 12 outliers final: 8 residues processed: 50 average time/residue: 0.0878 time to fit residues: 7.6086 Evaluate side-chains 50 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 839 SER Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 466 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 81 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 169 ASN A 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.093523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.063428 restraints weight = 25267.928| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.72 r_work: 0.2684 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12994 Z= 0.189 Angle : 0.526 5.737 17673 Z= 0.269 Chirality : 0.043 0.160 1926 Planarity : 0.004 0.051 2304 Dihedral : 3.659 13.527 1756 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.79 % Allowed : 11.09 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.21), residues: 1598 helix: 1.56 (0.38), residues: 216 sheet: 0.04 (0.26), residues: 409 loop : -1.27 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 810 TYR 0.014 0.001 TYR B 472 PHE 0.015 0.002 PHE A 727 TRP 0.011 0.001 TRP B 722 HIS 0.005 0.001 HIS A 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 (12994) covalent geometry : angle 0.52589 / 0.27 (17673) hydrogen bonds : bond 0.05308 / 3.74 ( 347) hydrogen bonds : angle 4.77173 / 3.43 ( 936) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.457 Fit side-chains REVERT: B 839 SER cc_start: 0.9006 (OUTLIER) cc_final: 0.8537 (t) REVERT: A 169 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.7672 (t0) REVERT: A 597 MET cc_start: 0.8432 (mmp) cc_final: 0.7809 (mmm) outliers start: 11 outliers final: 7 residues processed: 49 average time/residue: 0.0838 time to fit residues: 7.0167 Evaluate side-chains 50 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 839 SER Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 466 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 106 optimal weight: 5.9990 chunk 17 optimal weight: 0.0060 chunk 44 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 169 ASN A 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.094341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.064117 restraints weight = 25107.202| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.76 r_work: 0.2695 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12994 Z= 0.123 Angle : 0.486 6.843 17673 Z= 0.247 Chirality : 0.042 0.151 1926 Planarity : 0.004 0.050 2304 Dihedral : 3.608 13.932 1756 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.01 % Allowed : 11.09 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.21), residues: 1598 helix: 1.59 (0.38), residues: 216 sheet: 0.09 (0.26), residues: 403 loop : -1.26 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 390 TYR 0.010 0.001 TYR B 472 PHE 0.011 0.001 PHE B 263 TRP 0.009 0.001 TRP A 825 HIS 0.003 0.001 HIS A 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 (12994) covalent geometry : angle 0.48649 / 0.25 (17673) hydrogen bonds : bond 0.04513 / 3.21 ( 347) hydrogen bonds : angle 4.62791 / 3.31 ( 936) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.309 Fit side-chains REVERT: B 839 SER cc_start: 0.8985 (OUTLIER) cc_final: 0.8511 (t) REVERT: A 169 ASN cc_start: 0.8373 (OUTLIER) cc_final: 0.7683 (t0) REVERT: A 597 MET cc_start: 0.8394 (mmp) cc_final: 0.7630 (mmm) outliers start: 14 outliers final: 9 residues processed: 52 average time/residue: 0.0789 time to fit residues: 7.0594 Evaluate side-chains 51 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 839 SER Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 466 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 84 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 46 optimal weight: 0.8980 chunk 45 optimal weight: 0.0970 chunk 23 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 169 ASN A 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.095065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.064974 restraints weight = 25212.864| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.70 r_work: 0.2714 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12994 Z= 0.096 Angle : 0.473 7.060 17673 Z= 0.237 Chirality : 0.042 0.150 1926 Planarity : 0.004 0.049 2304 Dihedral : 3.524 15.419 1756 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.86 % Allowed : 11.16 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.21), residues: 1598 helix: 1.62 (0.38), residues: 216 sheet: 0.13 (0.26), residues: 403 loop : -1.22 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 171 TYR 0.010 0.001 TYR B 472 PHE 0.009 0.001 PHE B 263 TRP 0.009 0.001 TRP A 722 HIS 0.003 0.000 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (12994) covalent geometry : angle 0.47278 / 0.24 (17673) hydrogen bonds : bond 0.04005 / 2.86 ( 347) hydrogen bonds : angle 4.52605 / 3.25 ( 936) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.361 Fit side-chains REVERT: B 839 SER cc_start: 0.9018 (OUTLIER) cc_final: 0.8545 (t) REVERT: A 169 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7855 (t0) REVERT: A 597 MET cc_start: 0.8434 (mmp) cc_final: 0.7683 (mmm) outliers start: 12 outliers final: 10 residues processed: 52 average time/residue: 0.0759 time to fit residues: 6.8231 Evaluate side-chains 54 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 839 SER Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 466 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 126 optimal weight: 2.9990 chunk 81 optimal weight: 0.0470 chunk 145 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 39 optimal weight: 0.0050 chunk 138 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.1896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.094983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.064866 restraints weight = 25274.752| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.70 r_work: 0.2712 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 12994 Z= 0.142 Angle : 0.777 59.174 17673 Z= 0.462 Chirality : 0.043 0.460 1926 Planarity : 0.005 0.113 2304 Dihedral : 3.550 16.908 1756 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.62 % Rotamer: Outliers : 0.79 % Allowed : 11.30 % Favored : 87.90 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.21), residues: 1598 helix: 1.61 (0.38), residues: 216 sheet: 0.13 (0.26), residues: 403 loop : -1.23 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 390 TYR 0.010 0.001 TYR B 472 PHE 0.009 0.001 PHE B 263 TRP 0.009 0.001 TRP A 722 HIS 0.003 0.000 HIS A 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (12994) covalent geometry : angle 0.77729 / 0.46 (17673) hydrogen bonds : bond 0.04036 / 2.88 ( 347) hydrogen bonds : angle 4.52514 / 3.25 ( 936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2410.41 seconds wall clock time: 42 minutes 1.96 seconds (2521.96 seconds total)