Starting phenix.real_space_refine on Wed Jul 30 22:44:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b6n_44271/07_2025/9b6n_44271.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b6n_44271/07_2025/9b6n_44271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b6n_44271/07_2025/9b6n_44271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b6n_44271/07_2025/9b6n_44271.map" model { file = "/net/cci-nas-00/data/ceres_data/9b6n_44271/07_2025/9b6n_44271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b6n_44271/07_2025/9b6n_44271.cif" } resolution = 3.31 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 ------------------------------------------------------------------------------- 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= 1.000 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 52 5.16 5 C 8380 2.51 5 N 2281 2.21 5 O 2513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13226 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3812 Classifications: {'peptide': 474} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 440} Chain breaks: 3 Chain: "B" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3812 Classifications: {'peptide': 474} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 440} Chain breaks: 3 Chain: "C" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3812 Classifications: {'peptide': 474} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 440} Chain breaks: 3 Chain: "H" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 957 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 833 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Time building chain proxies: 7.99, per 1000 atoms: 0.60 Number of scatterers: 13226 At special positions: 0 Unit cell: (124.8, 123.968, 109.824, 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 52 16.00 O 2513 8.00 N 2281 7.00 C 8380 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS H 106 " - pdb=" SG CYS H 111 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 92 " distance=2.03 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: 2.83 Conformation dependent library (CDL) restraints added in 1.6 seconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3044 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 42 sheets defined 9.0% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 262 through 266 Processing helix chain 'A' and resid 288 through 293 removed outlier: 4.283A pdb=" N HIS A 292 " --> pdb=" O ARG A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.821A pdb=" N ASN A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.590A pdb=" N PHE A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 563 through 568 removed outlier: 4.332A pdb=" N THR A 568 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 288 through 293 removed outlier: 4.253A pdb=" N HIS B 292 " --> pdb=" O ARG B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.756A pdb=" N ASN B 304 " --> pdb=" O ARG B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.689A pdb=" N PHE B 400 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 435 removed outlier: 4.101A pdb=" N LEU B 435 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 496 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 563 through 567 Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.176A pdb=" N HIS C 292 " --> pdb=" O ARG C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.844A pdb=" N ASN C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 359 removed outlier: 3.722A pdb=" N SER C 358 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA C 359 " --> pdb=" O LEU C 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 355 through 359' Processing helix chain 'C' and resid 396 through 400 removed outlier: 3.563A pdb=" N PHE C 400 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 removed outlier: 4.076A pdb=" N LEU C 435 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 569 removed outlier: 3.511A pdb=" N LYS C 567 " --> pdb=" O GLU C 564 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR C 568 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 67 removed outlier: 3.643A pdb=" N LYS H 67 " --> pdb=" O ALA H 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 64 through 67' Processing helix chain 'H' and resid 89 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 231 through 235 removed outlier: 7.799A pdb=" N THR A 676 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N PHE A 318 " --> pdb=" O THR A 676 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLN A 678 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LYS A 316 " --> pdb=" O GLN A 678 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER A 680 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN A 314 " --> pdb=" O SER A 680 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU A 682 " --> pdb=" O ARG A 312 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG A 312 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLU A 684 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU A 686 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE A 308 " --> pdb=" O GLU A 686 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLN A 688 " --> pdb=" O TRP A 306 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 371 through 373 removed outlier: 9.269A pdb=" N PHE A 372 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR A 246 " --> pdb=" O PHE A 372 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N THR A 676 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N PHE A 318 " --> pdb=" O THR A 676 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLN A 678 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LYS A 316 " --> pdb=" O GLN A 678 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER A 680 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN A 314 " --> pdb=" O SER A 680 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU A 682 " --> pdb=" O ARG A 312 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG A 312 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLU A 684 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU A 686 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE A 308 " --> pdb=" O GLU A 686 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLN A 688 " --> pdb=" O TRP A 306 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 261 removed outlier: 7.552A pdb=" N THR A 279 " --> pdb=" O TYR A 379 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N TYR A 379 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N TRP A 281 " --> pdb=" O TYR A 377 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 261 removed outlier: 5.862A pdb=" N ASN A 651 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 427 through 428 removed outlier: 6.146A pdb=" N ALA A 427 " --> pdb=" O ARG A 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 451 removed outlier: 6.810A pdb=" N LYS A 462 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR A 450 " --> pdb=" O THR A 460 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 479 through 480 removed outlier: 6.352A pdb=" N ILE A 479 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET A 605 " --> pdb=" O PHE B 629 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 483 through 484 Processing sheet with id=AA9, first strand: chain 'A' and resid 488 through 490 Processing sheet with id=AB1, first strand: chain 'A' and resid 514 through 517 removed outlier: 4.107A pdb=" N GLY C 578 " --> pdb=" O VAL C 596 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 542 through 544 Processing sheet with id=AB3, first strand: chain 'A' and resid 593 through 596 removed outlier: 4.095A pdb=" N GLY A 578 " --> pdb=" O VAL A 596 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 619 through 621 Processing sheet with id=AB5, first strand: chain 'A' and resid 627 through 629 removed outlier: 3.854A pdb=" N MET C 605 " --> pdb=" O PHE A 629 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE C 479 " --> pdb=" O VAL C 606 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 231 through 235 removed outlier: 3.525A pdb=" N ASP B 231 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N PHE B 372 " --> pdb=" O THR B 244 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR B 246 " --> pdb=" O PHE B 372 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 231 through 235 removed outlier: 3.525A pdb=" N ASP B 231 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N THR B 676 " --> pdb=" O ASN B 319 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN B 319 " --> pdb=" O THR B 676 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLN B 678 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU B 317 " --> pdb=" O GLN B 678 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER B 680 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE B 315 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU B 682 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU B 313 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLU B 684 " --> pdb=" O LYS B 311 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 258 through 261 removed outlier: 7.560A pdb=" N THR B 279 " --> pdb=" O TYR B 379 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N TYR B 379 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TRP B 281 " --> pdb=" O TYR B 377 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 258 through 261 removed outlier: 5.556A pdb=" N ASN B 651 " --> pdb=" O PRO B 280 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN B 646 " --> pdb=" O ASP B 347 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 427 through 428 removed outlier: 6.431A pdb=" N ALA B 427 " --> pdb=" O ARG B 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 445 through 451 removed outlier: 6.839A pdb=" N LYS B 462 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR B 450 " --> pdb=" O THR B 460 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 479 through 480 removed outlier: 6.287A pdb=" N ILE B 479 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET B 605 " --> pdb=" O PHE C 629 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 488 through 490 Processing sheet with id=AC5, first strand: chain 'B' and resid 542 through 544 Processing sheet with id=AC6, first strand: chain 'B' and resid 593 through 596 removed outlier: 3.868A pdb=" N GLY B 578 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 619 through 621 Processing sheet with id=AC8, first strand: chain 'C' and resid 231 through 235 removed outlier: 6.255A pdb=" N THR C 676 " --> pdb=" O ASN C 319 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN C 319 " --> pdb=" O THR C 676 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLN C 678 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU C 317 " --> pdb=" O GLN C 678 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER C 680 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE C 315 " --> pdb=" O SER C 680 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU C 682 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU C 313 " --> pdb=" O GLU C 682 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLU C 684 " --> pdb=" O LYS C 311 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 371 through 373 removed outlier: 9.372A pdb=" N PHE C 372 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR C 246 " --> pdb=" O PHE C 372 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THR C 676 " --> pdb=" O ASN C 319 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN C 319 " --> pdb=" O THR C 676 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLN C 678 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU C 317 " --> pdb=" O GLN C 678 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER C 680 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE C 315 " --> pdb=" O SER C 680 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU C 682 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU C 313 " --> pdb=" O GLU C 682 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLU C 684 " --> pdb=" O LYS C 311 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 258 through 261 removed outlier: 7.715A pdb=" N TYR C 277 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR C 381 " --> pdb=" O TYR C 277 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR C 279 " --> pdb=" O TYR C 379 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N TYR C 379 " --> pdb=" O THR C 279 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TRP C 281 " --> pdb=" O TYR C 377 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 258 through 261 removed outlier: 5.907A pdb=" N ASN C 651 " --> pdb=" O PRO C 280 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN C 646 " --> pdb=" O ASP C 347 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 427 through 428 removed outlier: 6.158A pdb=" N ALA C 427 " --> pdb=" O ARG C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 445 through 451 removed outlier: 6.703A pdb=" N LYS C 462 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR C 450 " --> pdb=" O THR C 460 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 483 through 484 Processing sheet with id=AD6, first strand: chain 'C' and resid 488 through 490 Processing sheet with id=AD7, first strand: chain 'C' and resid 542 through 544 Processing sheet with id=AD8, first strand: chain 'C' and resid 619 through 621 removed outlier: 6.055A pdb=" N ALA C 620 " --> pdb=" O MET C 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.766A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AE2, first strand: chain 'H' and resid 60 through 62 removed outlier: 6.674A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AE4, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AE5, first strand: chain 'L' and resid 9 through 10 removed outlier: 3.592A pdb=" N MET L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLN L 37 " --> pdb=" O TYR L 46 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 9 through 10 351 hydrogen bonds defined for protein. 846 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: 5.37 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2947 1.33 - 1.45: 3414 1.45 - 1.57: 7174 1.57 - 1.69: 0 1.69 - 1.81: 86 Bond restraints: 13621 Sorted by residual: bond pdb=" CA HIS B 642 " pdb=" C HIS B 642 " ideal model delta sigma weight residual 1.522 1.491 0.032 1.05e-02 9.07e+03 9.01e+00 bond pdb=" CA TYR L 90 " pdb=" CB TYR L 90 " ideal model delta sigma weight residual 1.528 1.486 0.041 1.39e-02 5.18e+03 8.88e+00 bond pdb=" C HIS B 642 " pdb=" O HIS B 642 " ideal model delta sigma weight residual 1.239 1.205 0.034 1.17e-02 7.31e+03 8.35e+00 bond pdb=" C ILE A 374 " pdb=" O ILE A 374 " ideal model delta sigma weight residual 1.245 1.210 0.035 1.34e-02 5.57e+03 6.66e+00 bond pdb=" N HIS B 642 " pdb=" CA HIS B 642 " ideal model delta sigma weight residual 1.462 1.437 0.025 1.15e-02 7.56e+03 4.75e+00 ... (remaining 13616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 18030 2.40 - 4.81: 450 4.81 - 7.21: 37 7.21 - 9.62: 14 9.62 - 12.02: 3 Bond angle restraints: 18534 Sorted by residual: angle pdb=" C HIS B 642 " pdb=" N PRO B 643 " pdb=" CA PRO B 643 " ideal model delta sigma weight residual 120.38 129.72 -9.34 1.03e+00 9.43e-01 8.22e+01 angle pdb=" N GLY B 539 " pdb=" CA GLY B 539 " pdb=" C GLY B 539 " ideal model delta sigma weight residual 112.73 120.80 -8.07 1.20e+00 6.94e-01 4.52e+01 angle pdb=" C GLU B 723 " pdb=" N PRO B 724 " pdb=" CA PRO B 724 " ideal model delta sigma weight residual 119.05 126.44 -7.39 1.11e+00 8.12e-01 4.44e+01 angle pdb=" N TYR L 98 " pdb=" CA TYR L 98 " pdb=" C TYR L 98 " ideal model delta sigma weight residual 111.36 118.10 -6.74 1.09e+00 8.42e-01 3.82e+01 angle pdb=" C GLU C 723 " pdb=" N PRO C 724 " pdb=" CA PRO C 724 " ideal model delta sigma weight residual 119.05 125.71 -6.66 1.11e+00 8.12e-01 3.60e+01 ... (remaining 18529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 7659 17.60 - 35.20: 246 35.20 - 52.80: 33 52.80 - 70.40: 2 70.40 - 87.99: 11 Dihedral angle restraints: 7951 sinusoidal: 3171 harmonic: 4780 Sorted by residual: dihedral pdb=" CA LEU A 256 " pdb=" C LEU A 256 " pdb=" N TYR A 257 " pdb=" CA TYR A 257 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA ASN C 383 " pdb=" C ASN C 383 " pdb=" N ASP C 384 " pdb=" CA ASP C 384 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA TYR A 484 " pdb=" C TYR A 484 " pdb=" N ARG A 485 " pdb=" CA ARG A 485 " ideal model delta harmonic sigma weight residual -180.00 -159.83 -20.17 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 7948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1328 0.055 - 0.109: 444 0.109 - 0.164: 91 0.164 - 0.218: 26 0.218 - 0.273: 7 Chirality restraints: 1896 Sorted by residual: chirality pdb=" CG LEU L 14 " pdb=" CB LEU L 14 " pdb=" CD1 LEU L 14 " pdb=" CD2 LEU L 14 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA LEU L 50 " pdb=" N LEU L 50 " pdb=" C LEU L 50 " pdb=" CB LEU L 50 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA VAL A 596 " pdb=" N VAL A 596 " pdb=" C VAL A 596 " pdb=" CB VAL A 596 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1893 not shown) Planarity restraints: 2440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 497 " -0.024 2.00e-02 2.50e+03 4.72e-02 2.22e+01 pdb=" C ASN C 497 " 0.082 2.00e-02 2.50e+03 pdb=" O ASN C 497 " -0.031 2.00e-02 2.50e+03 pdb=" N ASN C 498 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 31 " 0.022 2.00e-02 2.50e+03 1.89e-02 7.15e+00 pdb=" CG TYR L 31 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR L 31 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR L 31 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR L 31 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR L 31 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR L 31 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR L 31 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 290 " -0.014 2.00e-02 2.50e+03 1.67e-02 4.17e+00 pdb=" CG HIS A 290 " 0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS A 290 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS A 290 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS A 290 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 290 " -0.005 2.00e-02 2.50e+03 ... (remaining 2437 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1761 2.75 - 3.28: 12132 3.28 - 3.82: 22165 3.82 - 4.36: 28178 4.36 - 4.90: 48321 Nonbonded interactions: 112557 Sorted by model distance: nonbonded pdb=" O TRP B 247 " pdb=" OG1 THR B 676 " model vdw 2.206 3.040 nonbonded pdb=" O TRP C 247 " pdb=" OG1 THR C 676 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR C 252 " pdb=" O ILE C 374 " model vdw 2.212 3.040 nonbonded pdb=" OG1 THR B 279 " pdb=" O TYR B 377 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR C 350 " pdb=" O PRO C 643 " model vdw 2.234 3.040 ... (remaining 112552 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' selection = chain 'C' } 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: 0.860 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: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 33.070 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 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:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 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 : 0.008 0.056 13624 Z= 0.359 Angle : 0.907 12.019 18540 Z= 0.538 Chirality : 0.059 0.273 1896 Planarity : 0.005 0.047 2440 Dihedral : 9.755 87.994 4898 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.62 % Allowed : 1.45 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.16), residues: 1630 helix: -4.56 (0.25), residues: 66 sheet: -1.39 (0.19), residues: 473 loop : -1.01 (0.15), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP H 47 HIS 0.019 0.002 HIS A 290 PHE 0.020 0.003 PHE C 534 TYR 0.046 0.003 TYR L 31 ARG 0.014 0.002 ARG B 734 Details of bonding type rmsd hydrogen bonds : bond 0.22928 ( 293) hydrogen bonds : angle 9.66763 ( 846) SS BOND : bond 0.00275 ( 3) SS BOND : angle 0.73030 ( 6) covalent geometry : bond 0.00790 (13621) covalent geometry : angle 0.90661 (18534) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 264 time to evaluate : 1.511 Fit side-chains REVERT: A 238 ARG cc_start: 0.7759 (mtm110) cc_final: 0.7188 (mtp85) REVERT: A 297 ASP cc_start: 0.8325 (m-30) cc_final: 0.8044 (m-30) REVERT: A 419 ASN cc_start: 0.8172 (t0) cc_final: 0.7812 (m-40) REVERT: A 675 SER cc_start: 0.8539 (p) cc_final: 0.8308 (t) REVERT: A 691 ASN cc_start: 0.7171 (t0) cc_final: 0.6880 (t0) REVERT: A 707 LYS cc_start: 0.8242 (pttt) cc_final: 0.7823 (ptmm) REVERT: A 710 ASN cc_start: 0.7666 (m-40) cc_final: 0.7303 (m-40) REVERT: B 233 GLN cc_start: 0.8010 (mt0) cc_final: 0.7442 (mm110) REVERT: B 238 ARG cc_start: 0.7955 (mtm110) cc_final: 0.7409 (mtt90) REVERT: B 312 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7805 (mtp85) REVERT: B 347 ASP cc_start: 0.8187 (t0) cc_final: 0.7589 (p0) REVERT: B 613 TYR cc_start: 0.8857 (m-80) cc_final: 0.8521 (m-80) REVERT: C 231 ASP cc_start: 0.7658 (p0) cc_final: 0.7199 (t0) REVERT: C 233 GLN cc_start: 0.8466 (mt0) cc_final: 0.8199 (mt0) REVERT: C 312 ARG cc_start: 0.8117 (mtt90) cc_final: 0.7857 (mtp-110) REVERT: C 316 LYS cc_start: 0.8048 (mttt) cc_final: 0.7683 (tttt) REVERT: C 349 ASP cc_start: 0.8088 (m-30) cc_final: 0.7874 (m-30) REVERT: C 514 ARG cc_start: 0.8659 (mtm180) cc_final: 0.8306 (mtp180) REVERT: C 563 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8180 (mm-30) REVERT: C 588 GLN cc_start: 0.7721 (mp10) cc_final: 0.7342 (mm-40) outliers start: 9 outliers final: 5 residues processed: 272 average time/residue: 0.2948 time to fit residues: 111.0770 Evaluate side-chains 172 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 167 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 725 ARG Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain L residue 55 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 ASN A 428 HIS A 430 GLN A 515 ASN A 570 ASN A 585 GLN A 592 GLN A 608 GLN A 624 HIS A 646 GLN A 651 ASN A 700 GLN B 319 ASN B 343 GLN B 430 GLN B 452 ASN B 496 ASN B 546 GLN B 585 GLN B 608 GLN B 646 GLN B 700 GLN B 704 ASN B 710 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 HIS ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN C 608 GLN C 646 GLN C 651 ASN C 673 GLN L 6 GLN L 83 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.092454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.080774 restraints weight = 18705.057| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 0.93 r_work: 0.2561 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13624 Z= 0.148 Angle : 0.580 8.090 18540 Z= 0.309 Chirality : 0.045 0.155 1896 Planarity : 0.004 0.039 2440 Dihedral : 5.397 39.369 1816 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.38 % Allowed : 4.57 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.18), residues: 1630 helix: -2.97 (0.50), residues: 66 sheet: -0.87 (0.23), residues: 400 loop : -0.65 (0.16), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.008 0.001 HIS C 423 PHE 0.014 0.002 PHE B 501 TYR 0.023 0.002 TYR B 350 ARG 0.004 0.001 ARG C 734 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 293) hydrogen bonds : angle 6.63428 ( 846) SS BOND : bond 0.00299 ( 3) SS BOND : angle 0.54237 ( 6) covalent geometry : bond 0.00349 (13621) covalent geometry : angle 0.58025 (18534) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 1.656 Fit side-chains revert: symmetry clash REVERT: A 238 ARG cc_start: 0.7809 (mtm110) cc_final: 0.7098 (mtp85) REVERT: A 419 ASN cc_start: 0.8098 (t0) cc_final: 0.7727 (m-40) REVERT: A 579 GLN cc_start: 0.8277 (mt0) cc_final: 0.7939 (mt0) REVERT: A 691 ASN cc_start: 0.7160 (t0) cc_final: 0.6810 (t0) REVERT: A 707 LYS cc_start: 0.8097 (pttt) cc_final: 0.7630 (ptmm) REVERT: A 710 ASN cc_start: 0.7765 (m-40) cc_final: 0.7330 (m-40) REVERT: B 233 GLN cc_start: 0.8114 (mt0) cc_final: 0.7422 (mp10) REVERT: B 238 ARG cc_start: 0.7930 (mtm110) cc_final: 0.7248 (mtt90) REVERT: B 312 ARG cc_start: 0.8264 (mtt90) cc_final: 0.7878 (mtp85) REVERT: B 613 TYR cc_start: 0.8744 (m-80) cc_final: 0.8433 (m-80) REVERT: C 233 GLN cc_start: 0.8477 (mt0) cc_final: 0.8186 (mt0) REVERT: C 316 LYS cc_start: 0.8172 (mttt) cc_final: 0.7692 (tttt) REVERT: C 349 ASP cc_start: 0.8117 (m-30) cc_final: 0.7893 (m-30) REVERT: C 514 ARG cc_start: 0.8629 (mtm180) cc_final: 0.8402 (mtp180) REVERT: C 563 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8099 (mm-30) REVERT: C 588 GLN cc_start: 0.8060 (mp10) cc_final: 0.7638 (mm-40) REVERT: H 46 GLU cc_start: 0.8057 (tt0) cc_final: 0.7664 (tt0) REVERT: H 106 CYS cc_start: 0.7138 (m) cc_final: 0.6906 (m) REVERT: L 57 ASN cc_start: 0.7954 (t0) cc_final: 0.7732 (t0) outliers start: 20 outliers final: 18 residues processed: 192 average time/residue: 0.2630 time to fit residues: 74.1368 Evaluate side-chains 172 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 55 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 72 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 45 optimal weight: 0.0370 chunk 80 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 overall best weight: 5.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN A 585 GLN A 678 GLN B 343 GLN B 428 HIS B 651 ASN B 704 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN L 28 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.089461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.076342 restraints weight = 19198.600| |-----------------------------------------------------------------------------| r_work (start): 0.2566 rms_B_bonded: 1.11 r_work: 0.2495 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2399 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13624 Z= 0.223 Angle : 0.594 8.071 18540 Z= 0.312 Chirality : 0.046 0.145 1896 Planarity : 0.005 0.037 2440 Dihedral : 5.170 35.291 1806 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.21 % Allowed : 5.88 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.99 (0.18), residues: 1630 helix: -2.45 (0.58), residues: 66 sheet: -0.60 (0.23), residues: 418 loop : -0.54 (0.16), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 509 HIS 0.006 0.001 HIS C 423 PHE 0.014 0.002 PHE C 534 TYR 0.023 0.002 TYR L 31 ARG 0.005 0.001 ARG L 100 Details of bonding type rmsd hydrogen bonds : bond 0.03725 ( 293) hydrogen bonds : angle 6.17643 ( 846) SS BOND : bond 0.00185 ( 3) SS BOND : angle 0.34526 ( 6) covalent geometry : bond 0.00545 (13621) covalent geometry : angle 0.59388 (18534) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 2.272 Fit side-chains REVERT: A 238 ARG cc_start: 0.7741 (mtm110) cc_final: 0.6948 (mtp85) REVERT: A 419 ASN cc_start: 0.8086 (t0) cc_final: 0.7690 (m-40) REVERT: A 485 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8697 (ttt180) REVERT: A 654 VAL cc_start: 0.8280 (t) cc_final: 0.7944 (m) REVERT: A 691 ASN cc_start: 0.7115 (t0) cc_final: 0.6787 (t0) REVERT: A 707 LYS cc_start: 0.8119 (pttt) cc_final: 0.7582 (ptmm) REVERT: A 710 ASN cc_start: 0.7694 (m-40) cc_final: 0.7237 (m-40) REVERT: B 233 GLN cc_start: 0.8220 (mt0) cc_final: 0.7375 (mm110) REVERT: B 238 ARG cc_start: 0.7914 (mtm110) cc_final: 0.7095 (mtt90) REVERT: B 312 ARG cc_start: 0.8301 (mtt90) cc_final: 0.7889 (mtp85) REVERT: B 485 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8563 (ttt180) REVERT: C 233 GLN cc_start: 0.8418 (mt0) cc_final: 0.8094 (mt0) REVERT: C 316 LYS cc_start: 0.8085 (mttt) cc_final: 0.7556 (tttt) REVERT: C 384 ASP cc_start: 0.7581 (t70) cc_final: 0.7288 (t0) REVERT: C 514 ARG cc_start: 0.8639 (mtm180) cc_final: 0.8423 (mtp180) REVERT: C 588 GLN cc_start: 0.8050 (mp10) cc_final: 0.7563 (mm-40) REVERT: C 640 MET cc_start: 0.9371 (mtt) cc_final: 0.9112 (mtt) REVERT: H 101 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8035 (tm-30) outliers start: 32 outliers final: 23 residues processed: 187 average time/residue: 0.3094 time to fit residues: 82.2933 Evaluate side-chains 181 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 55 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 16 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 109 optimal weight: 0.0170 chunk 67 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 585 GLN B 704 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.092080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.080789 restraints weight = 18658.195| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 0.92 r_work: 0.2554 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2462 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13624 Z= 0.106 Angle : 0.489 6.586 18540 Z= 0.257 Chirality : 0.042 0.143 1896 Planarity : 0.004 0.040 2440 Dihedral : 4.583 20.740 1806 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.59 % Allowed : 7.47 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.68 (0.19), residues: 1630 helix: -2.17 (0.60), residues: 66 sheet: -0.26 (0.24), residues: 419 loop : -0.38 (0.17), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.005 0.001 HIS C 423 PHE 0.009 0.001 PHE B 535 TYR 0.011 0.001 TYR B 350 ARG 0.004 0.000 ARG L 100 Details of bonding type rmsd hydrogen bonds : bond 0.02895 ( 293) hydrogen bonds : angle 5.59913 ( 846) SS BOND : bond 0.00280 ( 3) SS BOND : angle 0.55318 ( 6) covalent geometry : bond 0.00248 (13621) covalent geometry : angle 0.48940 (18534) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 1.624 Fit side-chains REVERT: A 238 ARG cc_start: 0.7731 (mtm110) cc_final: 0.7003 (mtp85) REVERT: A 419 ASN cc_start: 0.8094 (t0) cc_final: 0.7670 (m-40) REVERT: A 691 ASN cc_start: 0.7070 (t0) cc_final: 0.6738 (t0) REVERT: A 707 LYS cc_start: 0.8098 (pttt) cc_final: 0.7609 (ptmm) REVERT: A 710 ASN cc_start: 0.7715 (m-40) cc_final: 0.7246 (m-40) REVERT: B 233 GLN cc_start: 0.8225 (mt0) cc_final: 0.7475 (mm110) REVERT: B 238 ARG cc_start: 0.7837 (mtm110) cc_final: 0.7161 (mtt90) REVERT: B 312 ARG cc_start: 0.8264 (mtt90) cc_final: 0.7949 (mtp85) REVERT: B 613 TYR cc_start: 0.8782 (m-80) cc_final: 0.8337 (m-80) REVERT: B 682 GLU cc_start: 0.8190 (tt0) cc_final: 0.7959 (tt0) REVERT: C 233 GLN cc_start: 0.8403 (mt0) cc_final: 0.8092 (mt0) REVERT: C 316 LYS cc_start: 0.8160 (mttt) cc_final: 0.7693 (tttt) REVERT: C 384 ASP cc_start: 0.7546 (t70) cc_final: 0.7275 (t0) REVERT: C 514 ARG cc_start: 0.8662 (mtm180) cc_final: 0.8442 (mtp180) REVERT: C 588 GLN cc_start: 0.7979 (mp10) cc_final: 0.7557 (mm-40) REVERT: C 640 MET cc_start: 0.9314 (mtt) cc_final: 0.9036 (mtt) REVERT: C 641 LYS cc_start: 0.8671 (mtmt) cc_final: 0.8330 (mmtt) REVERT: H 73 SER cc_start: 0.8837 (t) cc_final: 0.8552 (p) REVERT: H 93 THR cc_start: 0.8580 (t) cc_final: 0.8289 (m) REVERT: L 93 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7988 (tt0) outliers start: 23 outliers final: 16 residues processed: 175 average time/residue: 0.3077 time to fit residues: 76.0434 Evaluate side-chains 167 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 456 GLN Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 93 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 585 GLN ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.089858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.078046 restraints weight = 18899.724| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 1.00 r_work: 0.2509 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2414 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13624 Z= 0.176 Angle : 0.533 7.281 18540 Z= 0.279 Chirality : 0.044 0.148 1896 Planarity : 0.004 0.041 2440 Dihedral : 4.670 20.359 1805 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.87 % Allowed : 7.82 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.69 (0.19), residues: 1630 helix: -2.09 (0.62), residues: 66 sheet: -0.30 (0.24), residues: 418 loop : -0.38 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 509 HIS 0.005 0.001 HIS C 423 PHE 0.011 0.002 PHE C 629 TYR 0.015 0.002 TYR L 31 ARG 0.005 0.001 ARG A 550 Details of bonding type rmsd hydrogen bonds : bond 0.03179 ( 293) hydrogen bonds : angle 5.64215 ( 846) SS BOND : bond 0.00232 ( 3) SS BOND : angle 0.98474 ( 6) covalent geometry : bond 0.00425 (13621) covalent geometry : angle 0.53320 (18534) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 1.577 Fit side-chains REVERT: A 238 ARG cc_start: 0.7702 (mtm110) cc_final: 0.6931 (mtp85) REVERT: A 419 ASN cc_start: 0.8147 (t0) cc_final: 0.7706 (m-40) REVERT: A 691 ASN cc_start: 0.7227 (t0) cc_final: 0.6850 (t0) REVERT: A 707 LYS cc_start: 0.8123 (pttt) cc_final: 0.7591 (ptmm) REVERT: A 710 ASN cc_start: 0.7671 (m-40) cc_final: 0.7194 (m-40) REVERT: B 233 GLN cc_start: 0.8236 (mt0) cc_final: 0.7409 (mm110) REVERT: B 238 ARG cc_start: 0.7837 (mtm110) cc_final: 0.7069 (mtt90) REVERT: B 312 ARG cc_start: 0.8283 (mtt90) cc_final: 0.7893 (mtp85) REVERT: B 613 TYR cc_start: 0.8843 (m-80) cc_final: 0.8429 (m-80) REVERT: B 698 GLU cc_start: 0.8596 (mm-30) cc_final: 0.7550 (mp0) REVERT: C 233 GLN cc_start: 0.8404 (mt0) cc_final: 0.8079 (mt0) REVERT: C 316 LYS cc_start: 0.8124 (mttt) cc_final: 0.7602 (tttt) REVERT: C 384 ASP cc_start: 0.7642 (t70) cc_final: 0.7375 (t0) REVERT: C 588 GLN cc_start: 0.8004 (mp10) cc_final: 0.7573 (mm-40) REVERT: C 640 MET cc_start: 0.9348 (mtt) cc_final: 0.9110 (mtt) REVERT: C 641 LYS cc_start: 0.8721 (mtmt) cc_final: 0.8306 (mmtt) REVERT: H 73 SER cc_start: 0.8801 (t) cc_final: 0.8495 (p) REVERT: H 101 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8090 (tm-30) outliers start: 27 outliers final: 24 residues processed: 159 average time/residue: 0.2610 time to fit residues: 60.8118 Evaluate side-chains 164 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 456 GLN Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 55 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS H 84 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.088462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.077298 restraints weight = 19208.445| |-----------------------------------------------------------------------------| r_work (start): 0.2585 rms_B_bonded: 0.89 r_work: 0.2495 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2403 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13624 Z= 0.239 Angle : 0.575 7.557 18540 Z= 0.300 Chirality : 0.046 0.138 1896 Planarity : 0.004 0.043 2440 Dihedral : 4.872 20.412 1805 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.21 % Allowed : 8.17 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.80 (0.19), residues: 1630 helix: -2.09 (0.63), residues: 66 sheet: -0.27 (0.24), residues: 415 loop : -0.51 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 509 HIS 0.006 0.001 HIS C 423 PHE 0.012 0.002 PHE C 629 TYR 0.018 0.002 TYR L 31 ARG 0.005 0.001 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 293) hydrogen bonds : angle 5.80370 ( 846) SS BOND : bond 0.00242 ( 3) SS BOND : angle 1.32819 ( 6) covalent geometry : bond 0.00582 (13621) covalent geometry : angle 0.57464 (18534) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 1.283 Fit side-chains REVERT: A 238 ARG cc_start: 0.7785 (mtm110) cc_final: 0.7068 (mtp85) REVERT: A 419 ASN cc_start: 0.8155 (t0) cc_final: 0.7712 (m-40) REVERT: A 586 SER cc_start: 0.8862 (p) cc_final: 0.8338 (m) REVERT: A 691 ASN cc_start: 0.7357 (t0) cc_final: 0.7011 (t0) REVERT: A 707 LYS cc_start: 0.8174 (pttt) cc_final: 0.7663 (ptmm) REVERT: A 710 ASN cc_start: 0.7670 (m-40) cc_final: 0.7196 (m-40) REVERT: B 233 GLN cc_start: 0.8271 (mt0) cc_final: 0.7507 (mm110) REVERT: B 238 ARG cc_start: 0.7928 (mtm110) cc_final: 0.7145 (mtt90) REVERT: B 312 ARG cc_start: 0.8285 (mtt90) cc_final: 0.7956 (mtp85) REVERT: B 613 TYR cc_start: 0.8856 (m-80) cc_final: 0.8441 (m-80) REVERT: B 698 GLU cc_start: 0.8588 (mm-30) cc_final: 0.7559 (mp0) REVERT: C 233 GLN cc_start: 0.8415 (mt0) cc_final: 0.8005 (mt0) REVERT: C 316 LYS cc_start: 0.8133 (mttt) cc_final: 0.7617 (tttt) REVERT: C 384 ASP cc_start: 0.7706 (t70) cc_final: 0.7421 (t0) REVERT: C 588 GLN cc_start: 0.7996 (mp10) cc_final: 0.7566 (mm-40) REVERT: C 640 MET cc_start: 0.9324 (mtt) cc_final: 0.9097 (mtt) REVERT: C 641 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8369 (mmtt) REVERT: H 73 SER cc_start: 0.8816 (t) cc_final: 0.8549 (p) REVERT: H 101 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8081 (tm-30) outliers start: 32 outliers final: 27 residues processed: 170 average time/residue: 0.2625 time to fit residues: 65.4831 Evaluate side-chains 168 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 456 GLN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 30 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 109 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 81 optimal weight: 0.0370 chunk 138 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 592 GLN C 290 HIS ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.090680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.079517 restraints weight = 18820.174| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 0.89 r_work: 0.2531 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2440 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13624 Z= 0.114 Angle : 0.487 7.749 18540 Z= 0.255 Chirality : 0.042 0.163 1896 Planarity : 0.004 0.043 2440 Dihedral : 4.479 19.859 1805 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.73 % Allowed : 9.00 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.63 (0.20), residues: 1630 helix: -2.02 (0.63), residues: 66 sheet: -0.14 (0.25), residues: 415 loop : -0.39 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS C 423 PHE 0.009 0.001 PHE B 535 TYR 0.011 0.001 TYR C 257 ARG 0.005 0.000 ARG B 725 Details of bonding type rmsd hydrogen bonds : bond 0.02852 ( 293) hydrogen bonds : angle 5.47136 ( 846) SS BOND : bond 0.00198 ( 3) SS BOND : angle 1.17817 ( 6) covalent geometry : bond 0.00266 (13621) covalent geometry : angle 0.48654 (18534) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.494 Fit side-chains REVERT: A 238 ARG cc_start: 0.7702 (mtm110) cc_final: 0.7044 (mtp85) REVERT: A 419 ASN cc_start: 0.8114 (t0) cc_final: 0.7663 (m-40) REVERT: A 691 ASN cc_start: 0.7332 (t0) cc_final: 0.6979 (t0) REVERT: A 707 LYS cc_start: 0.8112 (pttt) cc_final: 0.7617 (ptmm) REVERT: A 710 ASN cc_start: 0.7661 (m-40) cc_final: 0.7246 (m-40) REVERT: B 233 GLN cc_start: 0.8235 (mt0) cc_final: 0.7444 (mm110) REVERT: B 238 ARG cc_start: 0.7910 (mtm110) cc_final: 0.7185 (mtt90) REVERT: B 312 ARG cc_start: 0.8281 (mtt90) cc_final: 0.7955 (mtp85) REVERT: B 613 TYR cc_start: 0.8795 (m-80) cc_final: 0.8411 (m-80) REVERT: B 682 GLU cc_start: 0.8198 (tt0) cc_final: 0.7856 (tt0) REVERT: B 698 GLU cc_start: 0.8585 (mm-30) cc_final: 0.7607 (mp0) REVERT: C 233 GLN cc_start: 0.8413 (mt0) cc_final: 0.8004 (mt0) REVERT: C 316 LYS cc_start: 0.8146 (mttt) cc_final: 0.7718 (tttt) REVERT: C 384 ASP cc_start: 0.7548 (t70) cc_final: 0.7281 (t0) REVERT: C 588 GLN cc_start: 0.7941 (mp10) cc_final: 0.7553 (mm-40) REVERT: C 640 MET cc_start: 0.9300 (mtt) cc_final: 0.9075 (mtt) REVERT: C 641 LYS cc_start: 0.8698 (mtmt) cc_final: 0.8328 (mmtt) REVERT: H 73 SER cc_start: 0.8843 (t) cc_final: 0.8585 (p) REVERT: H 101 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8099 (tm-30) outliers start: 25 outliers final: 21 residues processed: 160 average time/residue: 0.2631 time to fit residues: 62.2529 Evaluate side-chains 161 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 456 GLN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 118 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 123 optimal weight: 0.3980 chunk 6 optimal weight: 9.9990 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 HIS ** 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 = 0.2805 r_free = 0.2805 target = 0.091521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.080458 restraints weight = 18920.377| |-----------------------------------------------------------------------------| r_work (start): 0.2635 rms_B_bonded: 0.88 r_work: 0.2548 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13624 Z= 0.106 Angle : 0.470 6.831 18540 Z= 0.245 Chirality : 0.041 0.140 1896 Planarity : 0.004 0.042 2440 Dihedral : 4.258 19.490 1805 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.66 % Allowed : 9.00 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.54 (0.20), residues: 1630 helix: -1.98 (0.63), residues: 66 sheet: -0.10 (0.25), residues: 418 loop : -0.32 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 595 HIS 0.005 0.001 HIS C 423 PHE 0.009 0.001 PHE C 345 TYR 0.011 0.001 TYR C 257 ARG 0.004 0.000 ARG B 725 Details of bonding type rmsd hydrogen bonds : bond 0.02765 ( 293) hydrogen bonds : angle 5.26718 ( 846) SS BOND : bond 0.00215 ( 3) SS BOND : angle 1.28696 ( 6) covalent geometry : bond 0.00249 (13621) covalent geometry : angle 0.46939 (18534) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 1.619 Fit side-chains REVERT: A 238 ARG cc_start: 0.7669 (mtm110) cc_final: 0.6962 (mtp85) REVERT: A 419 ASN cc_start: 0.8088 (t0) cc_final: 0.7646 (m-40) REVERT: A 691 ASN cc_start: 0.7508 (t0) cc_final: 0.7119 (t0) REVERT: A 707 LYS cc_start: 0.8096 (pttt) cc_final: 0.7618 (ptmm) REVERT: A 710 ASN cc_start: 0.7625 (m-40) cc_final: 0.7220 (m-40) REVERT: B 233 GLN cc_start: 0.8189 (mt0) cc_final: 0.7397 (mm110) REVERT: B 238 ARG cc_start: 0.7929 (mtm110) cc_final: 0.7205 (mtt90) REVERT: B 312 ARG cc_start: 0.8273 (mtt90) cc_final: 0.7933 (mtp85) REVERT: B 613 TYR cc_start: 0.8791 (m-80) cc_final: 0.8456 (m-80) REVERT: B 682 GLU cc_start: 0.8144 (tt0) cc_final: 0.7851 (tt0) REVERT: B 698 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7629 (mp0) REVERT: C 233 GLN cc_start: 0.8420 (mt0) cc_final: 0.8027 (mt0) REVERT: C 237 ASP cc_start: 0.8095 (p0) cc_final: 0.7778 (p0) REVERT: C 316 LYS cc_start: 0.8159 (mttt) cc_final: 0.7746 (tttt) REVERT: C 384 ASP cc_start: 0.7549 (t70) cc_final: 0.7266 (t0) REVERT: C 588 GLN cc_start: 0.7923 (mp10) cc_final: 0.7529 (mm-40) REVERT: C 640 MET cc_start: 0.9294 (mtt) cc_final: 0.9045 (mtt) REVERT: C 641 LYS cc_start: 0.8702 (mtmt) cc_final: 0.8384 (mmtt) REVERT: H 73 SER cc_start: 0.8855 (t) cc_final: 0.8617 (p) REVERT: H 101 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8042 (tm-30) outliers start: 24 outliers final: 21 residues processed: 165 average time/residue: 0.2633 time to fit residues: 64.0430 Evaluate side-chains 164 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 456 GLN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.088965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.077100 restraints weight = 18789.560| |-----------------------------------------------------------------------------| r_work (start): 0.2580 rms_B_bonded: 0.99 r_work: 0.2489 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2396 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13624 Z= 0.200 Angle : 0.546 7.007 18540 Z= 0.285 Chirality : 0.045 0.212 1896 Planarity : 0.004 0.041 2440 Dihedral : 4.629 20.005 1805 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.87 % Allowed : 8.93 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.73 (0.20), residues: 1630 helix: -2.13 (0.53), residues: 84 sheet: -0.15 (0.25), residues: 418 loop : -0.45 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 509 HIS 0.007 0.001 HIS C 290 PHE 0.011 0.002 PHE C 629 TYR 0.014 0.002 TYR C 443 ARG 0.003 0.001 ARG B 725 Details of bonding type rmsd hydrogen bonds : bond 0.03240 ( 293) hydrogen bonds : angle 5.58976 ( 846) SS BOND : bond 0.00255 ( 3) SS BOND : angle 1.81920 ( 6) covalent geometry : bond 0.00485 (13621) covalent geometry : angle 0.54470 (18534) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.454 Fit side-chains REVERT: A 238 ARG cc_start: 0.7714 (mtm110) cc_final: 0.6958 (mtp85) REVERT: A 419 ASN cc_start: 0.8125 (t0) cc_final: 0.7682 (m-40) REVERT: A 586 SER cc_start: 0.8849 (p) cc_final: 0.8342 (m) REVERT: A 691 ASN cc_start: 0.7709 (t0) cc_final: 0.7261 (t0) REVERT: A 707 LYS cc_start: 0.8124 (pttt) cc_final: 0.7577 (ptmm) REVERT: A 710 ASN cc_start: 0.7682 (m-40) cc_final: 0.7194 (m-40) REVERT: B 233 GLN cc_start: 0.8175 (mt0) cc_final: 0.7329 (mm110) REVERT: B 238 ARG cc_start: 0.7906 (mtm110) cc_final: 0.7109 (mtt90) REVERT: B 312 ARG cc_start: 0.8298 (mtt90) cc_final: 0.7890 (mtp85) REVERT: B 613 TYR cc_start: 0.8841 (m-80) cc_final: 0.8433 (m-80) REVERT: B 698 GLU cc_start: 0.8628 (mm-30) cc_final: 0.7566 (mp0) REVERT: C 233 GLN cc_start: 0.8423 (mt0) cc_final: 0.8004 (mt0) REVERT: C 316 LYS cc_start: 0.8078 (mttt) cc_final: 0.7528 (tttt) REVERT: C 384 ASP cc_start: 0.7652 (t70) cc_final: 0.7376 (t0) REVERT: C 588 GLN cc_start: 0.7940 (mp10) cc_final: 0.7539 (mm-40) REVERT: C 640 MET cc_start: 0.9325 (mtt) cc_final: 0.9111 (mtt) REVERT: C 641 LYS cc_start: 0.8716 (mtmt) cc_final: 0.8292 (mmtt) REVERT: H 73 SER cc_start: 0.8880 (t) cc_final: 0.8580 (p) REVERT: H 101 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8088 (tm-30) outliers start: 27 outliers final: 25 residues processed: 157 average time/residue: 0.2600 time to fit residues: 59.5674 Evaluate side-chains 163 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 456 GLN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 89 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 423 HIS ** 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 = 0.2768 r_free = 0.2768 target = 0.089075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.077257 restraints weight = 18820.081| |-----------------------------------------------------------------------------| r_work (start): 0.2587 rms_B_bonded: 0.99 r_work: 0.2495 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2402 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13624 Z= 0.167 Angle : 0.522 6.586 18540 Z= 0.273 Chirality : 0.043 0.198 1896 Planarity : 0.004 0.041 2440 Dihedral : 4.564 19.916 1805 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.66 % Allowed : 9.00 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.73 (0.20), residues: 1630 helix: -2.14 (0.53), residues: 84 sheet: -0.15 (0.25), residues: 418 loop : -0.45 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 509 HIS 0.006 0.001 HIS A 290 PHE 0.011 0.002 PHE C 629 TYR 0.013 0.002 TYR C 257 ARG 0.004 0.001 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 293) hydrogen bonds : angle 5.52650 ( 846) SS BOND : bond 0.00292 ( 3) SS BOND : angle 0.86682 ( 6) covalent geometry : bond 0.00402 (13621) covalent geometry : angle 0.52183 (18534) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 1.628 Fit side-chains REVERT: A 238 ARG cc_start: 0.7717 (mtm110) cc_final: 0.6958 (mtp85) REVERT: A 419 ASN cc_start: 0.8121 (t0) cc_final: 0.7672 (m-40) REVERT: A 586 SER cc_start: 0.8873 (p) cc_final: 0.8344 (m) REVERT: A 691 ASN cc_start: 0.7744 (t0) cc_final: 0.7448 (p0) REVERT: A 707 LYS cc_start: 0.8124 (pttt) cc_final: 0.7584 (ptmm) REVERT: A 710 ASN cc_start: 0.7694 (m-40) cc_final: 0.7213 (m-40) REVERT: B 233 GLN cc_start: 0.8208 (mt0) cc_final: 0.7353 (mm110) REVERT: B 238 ARG cc_start: 0.7912 (mtm110) cc_final: 0.7146 (mtt90) REVERT: B 312 ARG cc_start: 0.8304 (mtt90) cc_final: 0.7899 (mtp85) REVERT: B 613 TYR cc_start: 0.8826 (m-80) cc_final: 0.8412 (m-80) REVERT: B 682 GLU cc_start: 0.8161 (tt0) cc_final: 0.7817 (tt0) REVERT: B 698 GLU cc_start: 0.8610 (mm-30) cc_final: 0.7563 (mp0) REVERT: C 233 GLN cc_start: 0.8432 (mt0) cc_final: 0.8008 (mt0) REVERT: C 316 LYS cc_start: 0.8099 (mttt) cc_final: 0.7546 (tttt) REVERT: C 384 ASP cc_start: 0.7618 (t70) cc_final: 0.7331 (t0) REVERT: C 588 GLN cc_start: 0.7934 (mp10) cc_final: 0.7534 (mm-40) REVERT: C 640 MET cc_start: 0.9320 (mtt) cc_final: 0.9080 (mtt) REVERT: C 641 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8286 (mmtt) REVERT: H 73 SER cc_start: 0.8863 (t) cc_final: 0.8564 (p) REVERT: H 101 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8097 (tm-30) outliers start: 24 outliers final: 23 residues processed: 155 average time/residue: 0.2686 time to fit residues: 61.2846 Evaluate side-chains 161 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 456 GLN Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 3 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 28 optimal weight: 0.0070 chunk 126 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.088626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.076570 restraints weight = 19118.373| |-----------------------------------------------------------------------------| r_work (start): 0.2575 rms_B_bonded: 1.03 r_work: 0.2485 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2388 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13624 Z= 0.188 Angle : 0.542 6.990 18540 Z= 0.282 Chirality : 0.044 0.213 1896 Planarity : 0.004 0.041 2440 Dihedral : 4.643 20.039 1805 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.87 % Allowed : 9.00 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.76 (0.20), residues: 1630 helix: -2.17 (0.53), residues: 84 sheet: -0.16 (0.25), residues: 418 loop : -0.48 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 509 HIS 0.007 0.001 HIS C 290 PHE 0.011 0.002 PHE C 629 TYR 0.013 0.002 TYR B 701 ARG 0.004 0.001 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.03240 ( 293) hydrogen bonds : angle 5.52574 ( 846) SS BOND : bond 0.00403 ( 3) SS BOND : angle 2.55557 ( 6) covalent geometry : bond 0.00456 (13621) covalent geometry : angle 0.53981 (18534) =============================================================================== Job complete usr+sys time: 6582.53 seconds wall clock time: 114 minutes 29.52 seconds (6869.52 seconds total)