Starting phenix.real_space_refine on Thu Sep 18 01:10:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b6n_44271/09_2025/9b6n_44271.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b6n_44271/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9b6n_44271/09_2025/9b6n_44271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b6n_44271/09_2025/9b6n_44271.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b6n_44271/09_2025/9b6n_44271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b6n_44271/09_2025/9b6n_44271.map" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.07, per 1000 atoms: 0.23 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: 0.74 Conformation dependent library (CDL) restraints added in 451.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.50 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: 2.36 Time building geometry restraints manager: 1.04 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: 0.610 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.170 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.850 ------------------------------------------------------------------------------- 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 : 11.71 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.014 0.002 ARG B 734 TYR 0.046 0.003 TYR L 31 PHE 0.020 0.003 PHE C 534 TRP 0.028 0.003 TRP H 47 HIS 0.019 0.002 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00790 (13621) covalent geometry : angle 0.90661 (18534) SS BOND : bond 0.00275 ( 3) SS BOND : angle 0.73030 ( 6) hydrogen bonds : bond 0.22928 ( 293) hydrogen bonds : angle 9.66763 ( 846) *********************** 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 : 0.580 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: 0.1335 time to fit residues: 50.3390 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 : 0.526 ------------------------------------------------------------------------------- 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 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 651 ASN 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 H 35 ASN L 6 GLN L 83 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.094838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.083592 restraints weight = 18705.583| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 0.91 r_work: 0.2594 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13624 Z= 0.108 Angle : 0.541 7.638 18540 Z= 0.288 Chirality : 0.043 0.154 1896 Planarity : 0.004 0.035 2440 Dihedral : 5.137 33.347 1816 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.31 % Allowed : 4.50 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.18), residues: 1630 helix: -2.84 (0.52), residues: 66 sheet: -0.80 (0.22), residues: 407 loop : -0.54 (0.16), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 730 TYR 0.017 0.001 TYR B 350 PHE 0.012 0.002 PHE C 367 TRP 0.011 0.001 TRP H 47 HIS 0.007 0.001 HIS C 423 Details of bonding type rmsd covalent geometry : bond 0.00242 (13621) covalent geometry : angle 0.54055 (18534) SS BOND : bond 0.00416 ( 3) SS BOND : angle 0.59193 ( 6) hydrogen bonds : bond 0.03395 ( 293) hydrogen bonds : angle 6.42249 ( 846) *********************** 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 211 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 238 ARG cc_start: 0.7752 (mtm110) cc_final: 0.7046 (mtp85) REVERT: A 419 ASN cc_start: 0.8127 (t0) cc_final: 0.7745 (m-40) REVERT: A 550 ARG cc_start: 0.8294 (ttt-90) cc_final: 0.8012 (mtp180) REVERT: A 579 GLN cc_start: 0.8187 (mt0) cc_final: 0.7893 (mt0) REVERT: A 691 ASN cc_start: 0.7130 (t0) cc_final: 0.6843 (t0) REVERT: A 707 LYS cc_start: 0.8090 (pttt) cc_final: 0.7700 (ptmm) REVERT: A 710 ASN cc_start: 0.7797 (m-40) cc_final: 0.7370 (m-40) REVERT: B 233 GLN cc_start: 0.8126 (mt0) cc_final: 0.7405 (mp10) REVERT: B 238 ARG cc_start: 0.7885 (mtm110) cc_final: 0.7239 (mtt90) REVERT: B 312 ARG cc_start: 0.8270 (mtt90) cc_final: 0.7891 (mtp85) REVERT: B 613 TYR cc_start: 0.8688 (m-80) cc_final: 0.8424 (m-80) REVERT: C 233 GLN cc_start: 0.8505 (mt0) cc_final: 0.8232 (mt0) REVERT: C 237 ASP cc_start: 0.8139 (p0) cc_final: 0.7821 (p0) REVERT: C 316 LYS cc_start: 0.8200 (mttt) cc_final: 0.7730 (tttt) REVERT: C 349 ASP cc_start: 0.8132 (m-30) cc_final: 0.7904 (m-30) REVERT: C 514 ARG cc_start: 0.8622 (mtm180) cc_final: 0.8392 (mtp180) REVERT: C 588 GLN cc_start: 0.7992 (mp10) cc_final: 0.7588 (mm-40) REVERT: H 46 GLU cc_start: 0.8075 (tt0) cc_final: 0.7697 (tt0) REVERT: L 53 SER cc_start: 0.8814 (t) cc_final: 0.8446 (p) outliers start: 19 outliers final: 15 residues processed: 204 average time/residue: 0.1142 time to fit residues: 33.6835 Evaluate side-chains 170 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 94 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 142 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 38 optimal weight: 0.2980 chunk 140 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 overall best weight: 6.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN A 585 GLN A 678 GLN B 319 ASN B 428 HIS B 704 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.088877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.077086 restraints weight = 19216.100| |-----------------------------------------------------------------------------| r_work (start): 0.2582 rms_B_bonded: 1.01 r_work: 0.2488 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2394 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13624 Z= 0.262 Angle : 0.621 8.456 18540 Z= 0.326 Chirality : 0.047 0.142 1896 Planarity : 0.005 0.044 2440 Dihedral : 5.241 32.018 1806 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.42 % Allowed : 6.02 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.18), residues: 1630 helix: -2.48 (0.58), residues: 66 sheet: -0.61 (0.23), residues: 418 loop : -0.53 (0.16), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 100 TYR 0.028 0.002 TYR L 31 PHE 0.016 0.002 PHE C 534 TRP 0.015 0.002 TRP B 509 HIS 0.008 0.002 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00640 (13621) covalent geometry : angle 0.62119 (18534) SS BOND : bond 0.00462 ( 3) SS BOND : angle 0.86141 ( 6) hydrogen bonds : bond 0.03878 ( 293) hydrogen bonds : angle 6.22686 ( 846) *********************** 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 189 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 238 ARG cc_start: 0.7756 (mtm110) cc_final: 0.6991 (mtp85) REVERT: A 312 ARG cc_start: 0.8177 (mtt90) cc_final: 0.7859 (mtm-85) REVERT: A 419 ASN cc_start: 0.8100 (t0) cc_final: 0.7685 (m-40) REVERT: A 485 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.7324 (ttm170) REVERT: A 654 VAL cc_start: 0.8289 (t) cc_final: 0.7956 (m) REVERT: A 691 ASN cc_start: 0.7172 (t0) cc_final: 0.6828 (t0) REVERT: A 707 LYS cc_start: 0.8215 (pttt) cc_final: 0.7675 (ptmm) REVERT: A 710 ASN cc_start: 0.7680 (m-40) cc_final: 0.7224 (m-40) REVERT: B 233 GLN cc_start: 0.8201 (mt0) cc_final: 0.7351 (mm110) REVERT: B 238 ARG cc_start: 0.7944 (mtm110) cc_final: 0.7128 (mtt90) REVERT: B 312 ARG cc_start: 0.8307 (mtt90) cc_final: 0.7883 (mtp85) REVERT: B 485 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8491 (ttm170) REVERT: B 613 TYR cc_start: 0.8830 (m-80) cc_final: 0.8515 (m-80) REVERT: C 233 GLN cc_start: 0.8431 (mt0) cc_final: 0.8096 (mt0) REVERT: C 316 LYS cc_start: 0.8096 (mttt) cc_final: 0.7558 (tttt) REVERT: C 384 ASP cc_start: 0.7591 (t70) cc_final: 0.7295 (t0) REVERT: C 514 ARG cc_start: 0.8645 (mtm180) cc_final: 0.8444 (mtp180) REVERT: C 588 GLN cc_start: 0.8056 (mp10) cc_final: 0.7566 (mm-40) REVERT: C 640 MET cc_start: 0.9368 (mtt) cc_final: 0.9109 (mtt) REVERT: H 93 THR cc_start: 0.8556 (t) cc_final: 0.8243 (m) REVERT: H 101 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8117 (tm-30) REVERT: H 106 CYS cc_start: 0.7226 (m) cc_final: 0.7004 (m) REVERT: L 53 SER cc_start: 0.8854 (t) cc_final: 0.8549 (p) outliers start: 35 outliers final: 24 residues processed: 178 average time/residue: 0.1197 time to fit residues: 30.5444 Evaluate side-chains 173 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 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 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 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 3 VAL 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 83 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 128 optimal weight: 10.0000 chunk 44 optimal weight: 0.0770 chunk 11 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.7340 ------------------------------------------------------------------------------- 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 570 ASN A 585 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.092236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.081030 restraints weight = 18925.394| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 0.91 r_work: 0.2554 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2462 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13624 Z= 0.103 Angle : 0.483 6.345 18540 Z= 0.254 Chirality : 0.042 0.144 1896 Planarity : 0.004 0.040 2440 Dihedral : 4.550 20.501 1806 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.25 % Allowed : 7.89 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.19), residues: 1630 helix: -2.20 (0.60), residues: 66 sheet: -0.27 (0.23), residues: 442 loop : -0.34 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 100 TYR 0.011 0.001 TYR B 350 PHE 0.010 0.001 PHE B 535 TRP 0.010 0.001 TRP H 47 HIS 0.005 0.001 HIS C 423 Details of bonding type rmsd covalent geometry : bond 0.00240 (13621) covalent geometry : angle 0.48303 (18534) SS BOND : bond 0.00269 ( 3) SS BOND : angle 0.57789 ( 6) hydrogen bonds : bond 0.02876 ( 293) hydrogen bonds : angle 5.55004 ( 846) *********************** 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 176 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 238 ARG cc_start: 0.7726 (mtm110) cc_final: 0.6995 (mtp85) REVERT: A 312 ARG cc_start: 0.8180 (mtt90) cc_final: 0.7886 (mtm-85) REVERT: A 419 ASN cc_start: 0.8067 (t0) cc_final: 0.7651 (m-40) REVERT: A 550 ARG cc_start: 0.8226 (ttt-90) cc_final: 0.7880 (mtp180) REVERT: A 579 GLN cc_start: 0.8295 (mt0) cc_final: 0.8021 (mt0) REVERT: A 691 ASN cc_start: 0.7049 (t0) cc_final: 0.6732 (t0) REVERT: A 707 LYS cc_start: 0.8157 (pttt) cc_final: 0.7698 (ptmm) REVERT: A 710 ASN cc_start: 0.7690 (m-40) cc_final: 0.7222 (m-40) REVERT: B 233 GLN cc_start: 0.8229 (mt0) cc_final: 0.7458 (mm110) REVERT: B 238 ARG cc_start: 0.7932 (mtm110) cc_final: 0.7215 (mtt90) REVERT: B 312 ARG cc_start: 0.8303 (mtt90) cc_final: 0.7967 (mtp85) REVERT: B 613 TYR cc_start: 0.8730 (m-80) cc_final: 0.8444 (m-80) REVERT: B 698 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7578 (mp0) REVERT: C 233 GLN cc_start: 0.8422 (mt0) cc_final: 0.8111 (mt0) REVERT: C 237 ASP cc_start: 0.8117 (p0) cc_final: 0.7770 (p0) REVERT: C 316 LYS cc_start: 0.8155 (mttt) cc_final: 0.7702 (tttt) REVERT: C 384 ASP cc_start: 0.7559 (t70) cc_final: 0.7288 (t0) REVERT: C 514 ARG cc_start: 0.8657 (mtm180) cc_final: 0.8441 (mtp180) REVERT: C 588 GLN cc_start: 0.7994 (mp10) cc_final: 0.7578 (mm-40) REVERT: C 640 MET cc_start: 0.9314 (mtt) cc_final: 0.9036 (mtt) REVERT: C 641 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8354 (mmtt) REVERT: H 93 THR cc_start: 0.8562 (t) cc_final: 0.8258 (m) REVERT: H 106 CYS cc_start: 0.7110 (m) cc_final: 0.6909 (m) outliers start: 18 outliers final: 15 residues processed: 170 average time/residue: 0.1300 time to fit residues: 31.1759 Evaluate side-chains 165 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 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 680 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 106 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 585 GLN ** C 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.089272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.077453 restraints weight = 19101.424| |-----------------------------------------------------------------------------| r_work (start): 0.2592 rms_B_bonded: 1.00 r_work: 0.2500 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2405 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13624 Z= 0.204 Angle : 0.554 7.586 18540 Z= 0.289 Chirality : 0.045 0.147 1896 Planarity : 0.004 0.041 2440 Dihedral : 4.762 20.396 1805 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.01 % Allowed : 7.89 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.19), residues: 1630 helix: -2.11 (0.62), residues: 66 sheet: -0.29 (0.24), residues: 418 loop : -0.42 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 725 TYR 0.018 0.002 TYR L 31 PHE 0.011 0.002 PHE B 534 TRP 0.014 0.001 TRP A 509 HIS 0.006 0.001 HIS C 423 Details of bonding type rmsd covalent geometry : bond 0.00494 (13621) covalent geometry : angle 0.55359 (18534) SS BOND : bond 0.00186 ( 3) SS BOND : angle 0.47308 ( 6) hydrogen bonds : bond 0.03320 ( 293) hydrogen bonds : angle 5.71453 ( 846) *********************** 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 171 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 238 ARG cc_start: 0.7718 (mtm110) cc_final: 0.6925 (mtp85) REVERT: A 312 ARG cc_start: 0.8198 (mtt90) cc_final: 0.7890 (mtm-85) REVERT: A 419 ASN cc_start: 0.8124 (t0) cc_final: 0.7692 (m-40) REVERT: A 691 ASN cc_start: 0.7275 (t0) cc_final: 0.6925 (t0) REVERT: A 707 LYS cc_start: 0.8190 (pttt) cc_final: 0.7651 (ptmm) REVERT: A 710 ASN cc_start: 0.7656 (m-40) cc_final: 0.7179 (m-40) REVERT: B 233 GLN cc_start: 0.8270 (mt0) cc_final: 0.7411 (mm110) REVERT: B 238 ARG cc_start: 0.7828 (mtm110) cc_final: 0.7052 (mtt90) REVERT: B 312 ARG cc_start: 0.8300 (mtt90) cc_final: 0.7882 (mtp85) REVERT: B 485 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8587 (ttt180) REVERT: B 613 TYR cc_start: 0.8791 (m-80) cc_final: 0.8505 (m-80) REVERT: B 698 GLU cc_start: 0.8577 (mm-30) cc_final: 0.7524 (mp0) REVERT: C 233 GLN cc_start: 0.8399 (mt0) cc_final: 0.8081 (mt0) REVERT: C 316 LYS cc_start: 0.8089 (mttt) cc_final: 0.7567 (tttt) REVERT: C 384 ASP cc_start: 0.7664 (t70) cc_final: 0.7405 (t0) REVERT: C 588 GLN cc_start: 0.7986 (mp10) cc_final: 0.7577 (mm-40) REVERT: C 640 MET cc_start: 0.9345 (mtt) cc_final: 0.9112 (mtt) REVERT: C 641 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8314 (mmtt) REVERT: H 73 SER cc_start: 0.8804 (t) cc_final: 0.8502 (p) REVERT: H 93 THR cc_start: 0.8566 (t) cc_final: 0.8254 (m) REVERT: H 101 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8071 (tm-30) REVERT: H 106 CYS cc_start: 0.7096 (m) cc_final: 0.6867 (m) outliers start: 29 outliers final: 25 residues processed: 163 average time/residue: 0.1172 time to fit residues: 27.7675 Evaluate side-chains 163 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 485 ARG Chi-restraints excluded: chain B residue 569 THR 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 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 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 131 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 9 optimal weight: 0.2980 chunk 85 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- 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 592 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.089571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.077712 restraints weight = 18865.390| |-----------------------------------------------------------------------------| r_work (start): 0.2596 rms_B_bonded: 1.00 r_work: 0.2504 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2408 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13624 Z= 0.169 Angle : 0.523 7.739 18540 Z= 0.273 Chirality : 0.043 0.139 1896 Planarity : 0.004 0.043 2440 Dihedral : 4.669 20.181 1805 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.08 % Allowed : 8.17 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.19), residues: 1630 helix: -2.04 (0.63), residues: 66 sheet: -0.16 (0.25), residues: 415 loop : -0.44 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 725 TYR 0.013 0.002 TYR B 350 PHE 0.011 0.002 PHE C 629 TRP 0.012 0.001 TRP A 509 HIS 0.005 0.001 HIS C 423 Details of bonding type rmsd covalent geometry : bond 0.00408 (13621) covalent geometry : angle 0.52310 (18534) SS BOND : bond 0.00201 ( 3) SS BOND : angle 0.46125 ( 6) hydrogen bonds : bond 0.03133 ( 293) hydrogen bonds : angle 5.60260 ( 846) *********************** 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 172 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 238 ARG cc_start: 0.7719 (mtm110) cc_final: 0.7013 (mtp85) REVERT: A 312 ARG cc_start: 0.8182 (mtt90) cc_final: 0.7865 (mtm-85) REVERT: A 419 ASN cc_start: 0.8112 (t0) cc_final: 0.7664 (m-40) REVERT: A 579 GLN cc_start: 0.8367 (mt0) cc_final: 0.8055 (mt0) REVERT: A 691 ASN cc_start: 0.7346 (t0) cc_final: 0.6978 (t0) REVERT: A 707 LYS cc_start: 0.8194 (pttt) cc_final: 0.7666 (ptmm) REVERT: A 710 ASN cc_start: 0.7679 (m-40) cc_final: 0.7264 (m-40) REVERT: B 233 GLN cc_start: 0.8227 (mt0) cc_final: 0.7364 (mm110) REVERT: B 238 ARG cc_start: 0.7882 (mtm110) cc_final: 0.7078 (mtt90) REVERT: B 312 ARG cc_start: 0.8296 (mtt90) cc_final: 0.7894 (mtp85) REVERT: B 613 TYR cc_start: 0.8775 (m-80) cc_final: 0.8490 (m-80) REVERT: B 698 GLU cc_start: 0.8602 (mm-30) cc_final: 0.7562 (mp0) REVERT: C 233 GLN cc_start: 0.8409 (mt0) cc_final: 0.7976 (mt0) REVERT: C 316 LYS cc_start: 0.8095 (mttt) cc_final: 0.7581 (tttt) REVERT: C 384 ASP cc_start: 0.7598 (t70) cc_final: 0.7323 (t0) REVERT: C 470 ASN cc_start: 0.8704 (t0) cc_final: 0.8499 (t0) REVERT: C 588 GLN cc_start: 0.7987 (mp10) cc_final: 0.7595 (mm-40) REVERT: C 640 MET cc_start: 0.9326 (mtt) cc_final: 0.9078 (mtt) REVERT: C 641 LYS cc_start: 0.8725 (mtmt) cc_final: 0.8303 (mmtt) REVERT: H 73 SER cc_start: 0.8796 (t) cc_final: 0.8501 (p) REVERT: H 101 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8088 (tm-30) REVERT: H 106 CYS cc_start: 0.7080 (m) cc_final: 0.6853 (m) outliers start: 30 outliers final: 25 residues processed: 161 average time/residue: 0.1167 time to fit residues: 27.4546 Evaluate side-chains 164 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 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 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 69 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 chunk 154 optimal weight: 30.0000 chunk 46 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.089285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.077489 restraints weight = 18961.747| |-----------------------------------------------------------------------------| r_work (start): 0.2591 rms_B_bonded: 1.00 r_work: 0.2498 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2403 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2381 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= 0.173 Angle : 0.524 7.205 18540 Z= 0.274 Chirality : 0.044 0.173 1896 Planarity : 0.004 0.043 2440 Dihedral : 4.643 20.102 1805 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.15 % Allowed : 8.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.19), residues: 1630 helix: -2.04 (0.63), residues: 66 sheet: -0.12 (0.25), residues: 415 loop : -0.47 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 725 TYR 0.013 0.002 TYR B 350 PHE 0.011 0.002 PHE C 629 TRP 0.012 0.001 TRP A 509 HIS 0.005 0.001 HIS C 423 Details of bonding type rmsd covalent geometry : bond 0.00418 (13621) covalent geometry : angle 0.52378 (18534) SS BOND : bond 0.00189 ( 3) SS BOND : angle 0.47820 ( 6) hydrogen bonds : bond 0.03141 ( 293) hydrogen bonds : angle 5.57910 ( 846) *********************** 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: 31 poor density : 138 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 238 ARG cc_start: 0.7717 (mtm110) cc_final: 0.6991 (mtp85) REVERT: A 312 ARG cc_start: 0.8204 (mtt90) cc_final: 0.7895 (mtm-85) REVERT: A 419 ASN cc_start: 0.8107 (t0) cc_final: 0.7660 (m-40) REVERT: A 579 GLN cc_start: 0.8378 (mt0) cc_final: 0.8048 (mt0) REVERT: A 586 SER cc_start: 0.8863 (p) cc_final: 0.8337 (m) REVERT: A 691 ASN cc_start: 0.7445 (t0) cc_final: 0.7068 (t0) REVERT: A 707 LYS cc_start: 0.8185 (pttt) cc_final: 0.7647 (ptmm) REVERT: A 710 ASN cc_start: 0.7686 (m-40) cc_final: 0.7264 (m-40) REVERT: B 233 GLN cc_start: 0.8214 (mt0) cc_final: 0.7350 (mm110) REVERT: B 238 ARG cc_start: 0.7868 (mtm110) cc_final: 0.7041 (mtt90) REVERT: B 312 ARG cc_start: 0.8299 (mtt90) cc_final: 0.7898 (mtp85) REVERT: B 613 TYR cc_start: 0.8773 (m-80) cc_final: 0.8485 (m-80) REVERT: B 698 GLU cc_start: 0.8597 (mm-30) cc_final: 0.7553 (mp0) REVERT: C 233 GLN cc_start: 0.8403 (mt0) cc_final: 0.7972 (mt0) REVERT: C 316 LYS cc_start: 0.8098 (mttt) cc_final: 0.7541 (tttt) REVERT: C 384 ASP cc_start: 0.7605 (t70) cc_final: 0.7313 (t0) REVERT: C 470 ASN cc_start: 0.8700 (t0) cc_final: 0.8497 (t0) REVERT: C 588 GLN cc_start: 0.7968 (mp10) cc_final: 0.7578 (mm-40) REVERT: C 640 MET cc_start: 0.9326 (mtt) cc_final: 0.9084 (mtt) REVERT: C 641 LYS cc_start: 0.8727 (mtmt) cc_final: 0.8298 (mmtt) REVERT: H 73 SER cc_start: 0.8810 (t) cc_final: 0.8518 (p) REVERT: H 101 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8083 (tm-30) REVERT: H 106 CYS cc_start: 0.7077 (m) cc_final: 0.6843 (m) outliers start: 31 outliers final: 27 residues processed: 158 average time/residue: 0.1128 time to fit residues: 26.0599 Evaluate side-chains 166 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 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 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 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 3 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 30 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 112 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 150 optimal weight: 20.0000 chunk 157 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 63 optimal weight: 0.5980 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.089565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.077463 restraints weight = 18879.647| |-----------------------------------------------------------------------------| r_work (start): 0.2590 rms_B_bonded: 1.03 r_work: 0.2497 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2400 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13624 Z= 0.156 Angle : 0.507 7.010 18540 Z= 0.265 Chirality : 0.043 0.139 1896 Planarity : 0.004 0.043 2440 Dihedral : 4.559 20.051 1805 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.01 % Allowed : 8.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.20), residues: 1630 helix: -2.06 (0.63), residues: 66 sheet: -0.12 (0.25), residues: 418 loop : -0.45 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 725 TYR 0.012 0.001 TYR C 257 PHE 0.011 0.001 PHE C 629 TRP 0.011 0.001 TRP A 509 HIS 0.005 0.001 HIS C 423 Details of bonding type rmsd covalent geometry : bond 0.00375 (13621) covalent geometry : angle 0.50752 (18534) SS BOND : bond 0.00204 ( 3) SS BOND : angle 0.45251 ( 6) hydrogen bonds : bond 0.03037 ( 293) hydrogen bonds : angle 5.49925 ( 846) *********************** 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 167 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 238 ARG cc_start: 0.7706 (mtm110) cc_final: 0.6962 (mtp85) REVERT: A 312 ARG cc_start: 0.8185 (mtt90) cc_final: 0.7869 (mtm-85) REVERT: A 419 ASN cc_start: 0.8126 (t0) cc_final: 0.7675 (m-40) REVERT: A 579 GLN cc_start: 0.8384 (mt0) cc_final: 0.8056 (mt0) REVERT: A 586 SER cc_start: 0.8868 (p) cc_final: 0.8356 (m) REVERT: A 691 ASN cc_start: 0.7536 (t0) cc_final: 0.7110 (t0) REVERT: A 707 LYS cc_start: 0.8191 (pttt) cc_final: 0.7653 (ptmm) REVERT: A 710 ASN cc_start: 0.7693 (m-40) cc_final: 0.7267 (m-40) REVERT: B 233 GLN cc_start: 0.8215 (mt0) cc_final: 0.7324 (mm110) REVERT: B 238 ARG cc_start: 0.7947 (mtm110) cc_final: 0.7118 (mtt90) REVERT: B 312 ARG cc_start: 0.8317 (mtt90) cc_final: 0.7899 (mtp85) REVERT: B 613 TYR cc_start: 0.8768 (m-80) cc_final: 0.8474 (m-80) REVERT: B 698 GLU cc_start: 0.8606 (mm-30) cc_final: 0.7567 (mp0) REVERT: C 233 GLN cc_start: 0.8437 (mt0) cc_final: 0.8010 (mt0) REVERT: C 316 LYS cc_start: 0.8090 (mttt) cc_final: 0.7538 (tttt) REVERT: C 384 ASP cc_start: 0.7598 (t70) cc_final: 0.7309 (t0) REVERT: C 588 GLN cc_start: 0.7946 (mp10) cc_final: 0.7552 (mm-40) REVERT: C 640 MET cc_start: 0.9329 (mtt) cc_final: 0.9090 (mtt) REVERT: C 641 LYS cc_start: 0.8726 (mtmt) cc_final: 0.8288 (mmtt) REVERT: H 73 SER cc_start: 0.8847 (t) cc_final: 0.8550 (p) REVERT: H 101 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8107 (tm-30) REVERT: H 106 CYS cc_start: 0.7095 (m) cc_final: 0.6850 (m) REVERT: L 93 GLU cc_start: 0.8359 (tt0) cc_final: 0.8156 (tt0) outliers start: 29 outliers final: 27 residues processed: 157 average time/residue: 0.1169 time to fit residues: 26.9132 Evaluate side-chains 165 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain L residue 30 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 126 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.087752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.075965 restraints weight = 19184.735| |-----------------------------------------------------------------------------| r_work (start): 0.2567 rms_B_bonded: 1.00 r_work: 0.2475 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.2380 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13624 Z= 0.252 Angle : 0.580 7.381 18540 Z= 0.302 Chirality : 0.046 0.137 1896 Planarity : 0.005 0.043 2440 Dihedral : 4.837 20.438 1805 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.28 % Allowed : 8.79 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.19), residues: 1630 helix: -2.12 (0.64), residues: 66 sheet: -0.19 (0.25), residues: 418 loop : -0.59 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 725 TYR 0.017 0.002 TYR L 31 PHE 0.012 0.002 PHE B 534 TRP 0.016 0.002 TRP B 509 HIS 0.007 0.001 HIS C 423 Details of bonding type rmsd covalent geometry : bond 0.00612 (13621) covalent geometry : angle 0.58021 (18534) SS BOND : bond 0.00217 ( 3) SS BOND : angle 0.56171 ( 6) hydrogen bonds : bond 0.03496 ( 293) hydrogen bonds : angle 5.75910 ( 846) *********************** 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 171 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 238 ARG cc_start: 0.7766 (mtm110) cc_final: 0.7006 (mtp85) REVERT: A 312 ARG cc_start: 0.8237 (mtt90) cc_final: 0.7916 (mtm-85) REVERT: A 419 ASN cc_start: 0.8123 (t0) cc_final: 0.7682 (m-40) REVERT: A 586 SER cc_start: 0.8896 (p) cc_final: 0.8362 (m) REVERT: A 690 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6624 (tt0) REVERT: A 691 ASN cc_start: 0.7683 (t0) cc_final: 0.7244 (t0) REVERT: A 707 LYS cc_start: 0.8217 (pttt) cc_final: 0.7666 (ptmm) REVERT: A 710 ASN cc_start: 0.7683 (m-40) cc_final: 0.7271 (m-40) REVERT: B 233 GLN cc_start: 0.8253 (mt0) cc_final: 0.7408 (mm110) REVERT: B 238 ARG cc_start: 0.7964 (mtm110) cc_final: 0.7177 (mtt90) REVERT: B 312 ARG cc_start: 0.8300 (mtt90) cc_final: 0.7895 (mtp85) REVERT: B 613 TYR cc_start: 0.8811 (m-80) cc_final: 0.8531 (m-80) REVERT: B 698 GLU cc_start: 0.8600 (mm-30) cc_final: 0.7511 (mp0) REVERT: C 233 GLN cc_start: 0.8448 (mt0) cc_final: 0.8015 (mt0) REVERT: C 316 LYS cc_start: 0.8060 (mttt) cc_final: 0.7490 (tttt) REVERT: C 384 ASP cc_start: 0.7675 (t70) cc_final: 0.7412 (t0) REVERT: C 588 GLN cc_start: 0.7978 (mp10) cc_final: 0.7536 (mm-40) REVERT: C 640 MET cc_start: 0.9340 (mtt) cc_final: 0.9129 (mtt) REVERT: C 641 LYS cc_start: 0.8739 (mtmt) cc_final: 0.8313 (mmtt) REVERT: H 73 SER cc_start: 0.8806 (t) cc_final: 0.8504 (p) REVERT: H 101 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8087 (tm-30) REVERT: H 106 CYS cc_start: 0.7061 (m) cc_final: 0.6811 (m) REVERT: L 93 GLU cc_start: 0.8420 (tt0) cc_final: 0.8201 (tt0) outliers start: 33 outliers final: 28 residues processed: 160 average time/residue: 0.1208 time to fit residues: 27.9290 Evaluate side-chains 166 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 A residue 690 GLU 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 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 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 3 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 11 optimal weight: 8.9990 chunk 20 optimal weight: 0.0980 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 69 optimal weight: 0.0980 chunk 149 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 592 GLN B 585 GLN B 688 GLN C 290 HIS ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.091481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.080456 restraints weight = 18829.793| |-----------------------------------------------------------------------------| r_work (start): 0.2637 rms_B_bonded: 0.89 r_work: 0.2549 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2459 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13624 Z= 0.097 Angle : 0.470 7.313 18540 Z= 0.246 Chirality : 0.041 0.243 1896 Planarity : 0.004 0.044 2440 Dihedral : 4.280 19.510 1805 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.31 % Allowed : 9.76 % Favored : 88.93 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.20), residues: 1630 helix: -1.97 (0.63), residues: 66 sheet: -0.01 (0.25), residues: 418 loop : -0.43 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 725 TYR 0.012 0.001 TYR C 257 PHE 0.010 0.001 PHE B 535 TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS C 423 Details of bonding type rmsd covalent geometry : bond 0.00221 (13621) covalent geometry : angle 0.47000 (18534) SS BOND : bond 0.00274 ( 3) SS BOND : angle 0.42677 ( 6) hydrogen bonds : bond 0.02659 ( 293) hydrogen bonds : angle 5.19483 ( 846) ********************** 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 165 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 238 ARG cc_start: 0.7680 (mtm110) cc_final: 0.7020 (mtp85) REVERT: A 419 ASN cc_start: 0.8086 (t0) cc_final: 0.7642 (m-40) REVERT: A 579 GLN cc_start: 0.8247 (mt0) cc_final: 0.7935 (mt0) REVERT: A 586 SER cc_start: 0.8844 (p) cc_final: 0.8322 (m) REVERT: A 707 LYS cc_start: 0.8213 (pttt) cc_final: 0.7711 (ptmm) REVERT: A 710 ASN cc_start: 0.7643 (m-40) cc_final: 0.7244 (m-40) REVERT: B 233 GLN cc_start: 0.8200 (mt0) cc_final: 0.7369 (mm110) REVERT: B 238 ARG cc_start: 0.7920 (mtm110) cc_final: 0.7273 (mtt90) REVERT: B 312 ARG cc_start: 0.8296 (mtt90) cc_final: 0.7929 (mtp85) REVERT: B 419 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8270 (m-40) REVERT: B 613 TYR cc_start: 0.8701 (m-80) cc_final: 0.8438 (m-80) REVERT: B 698 GLU cc_start: 0.8534 (mm-30) cc_final: 0.7592 (mp0) REVERT: C 233 GLN cc_start: 0.8482 (mt0) cc_final: 0.8089 (mt0) REVERT: C 237 ASP cc_start: 0.8108 (p0) cc_final: 0.7789 (p0) REVERT: C 316 LYS cc_start: 0.8136 (mttt) cc_final: 0.7683 (tttt) REVERT: C 384 ASP cc_start: 0.7579 (t70) cc_final: 0.7289 (t0) REVERT: C 588 GLN cc_start: 0.7937 (mp10) cc_final: 0.7545 (mm-40) REVERT: C 640 MET cc_start: 0.9284 (mtt) cc_final: 0.9026 (mtt) REVERT: C 641 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8363 (mmtt) REVERT: H 73 SER cc_start: 0.8858 (t) cc_final: 0.8614 (p) REVERT: H 106 CYS cc_start: 0.6964 (m) cc_final: 0.6721 (m) outliers start: 19 outliers final: 15 residues processed: 156 average time/residue: 0.1118 time to fit residues: 25.3570 Evaluate side-chains 155 residues out of total 1445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 THR 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 448 SER Chi-restraints excluded: chain C residue 593 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 L residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 79 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 93 optimal weight: 0.0020 chunk 42 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 overall best weight: 3.7994 ------------------------------------------------------------------------------- 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 = 0.2771 r_free = 0.2771 target = 0.089374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.077280 restraints weight = 19031.137| |-----------------------------------------------------------------------------| r_work (start): 0.2589 rms_B_bonded: 1.05 r_work: 0.2497 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2400 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13624 Z= 0.166 Angle : 0.518 7.114 18540 Z= 0.270 Chirality : 0.043 0.218 1896 Planarity : 0.004 0.042 2440 Dihedral : 4.484 19.889 1805 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.31 % Allowed : 9.83 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.20), residues: 1630 helix: -1.99 (0.64), residues: 66 sheet: -0.02 (0.25), residues: 418 loop : -0.47 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 312 TYR 0.012 0.002 TYR B 350 PHE 0.011 0.001 PHE C 629 TRP 0.013 0.001 TRP A 509 HIS 0.006 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00399 (13621) covalent geometry : angle 0.51823 (18534) SS BOND : bond 0.00188 ( 3) SS BOND : angle 0.39448 ( 6) hydrogen bonds : bond 0.03081 ( 293) hydrogen bonds : angle 5.39086 ( 846) =============================================================================== Job complete usr+sys time: 3022.34 seconds wall clock time: 52 minutes 40.49 seconds (3160.49 seconds total)