Starting phenix.real_space_refine on Sun Aug 9 13:02:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u3j_41864/08_2026/8u3j_41864_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u3j_41864/08_2026/8u3j_41864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u3j_41864/08_2026/8u3j_41864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u3j_41864/08_2026/8u3j_41864.map" model { file = "/net/cci-nas-00/data/ceres_data/8u3j_41864/08_2026/8u3j_41864_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u3j_41864/08_2026/8u3j_41864_trim.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 100 5.16 5 Na 1 4.78 5 C 11452 2.51 5 N 2804 2.21 5 O 3100 1.98 5 H 17500 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34961 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8703 Classifications: {'peptide': 533} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 518} Chain: "D" Number of atoms: 8703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8703 Classifications: {'peptide': 533} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 518} Chain: "B" Number of atoms: 8703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8703 Classifications: {'peptide': 533} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 518} Chain: "C" Number of atoms: 8703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8703 Classifications: {'peptide': 533} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 518} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {' NA': 1, '3PH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 5.66, per 1000 atoms: 0.16 Number of scatterers: 34961 At special positions: 0 Unit cell: (124.44, 124.44, 116.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 100 16.00 P 4 15.00 Na 1 11.00 O 3100 8.00 N 2804 7.00 C 11452 6.00 H 17500 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 930.9 milliseconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4032 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 4 sheets defined 64.4% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 203 through 211 removed outlier: 3.597A pdb=" N ILE A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 223 removed outlier: 3.687A pdb=" N ASN A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 250 through 257 Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.751A pdb=" N ALA A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 335 through 343 Processing helix chain 'A' and resid 345 through 354 removed outlier: 3.622A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 409 through 414 removed outlier: 3.559A pdb=" N MET A 412 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU A 413 " --> pdb=" O HIS A 410 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 414 " --> pdb=" O ASP A 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 409 through 414' Processing helix chain 'A' and resid 415 through 454 removed outlier: 3.789A pdb=" N ASN A 419 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LYS A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 500 removed outlier: 3.582A pdb=" N TYR A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 removed outlier: 4.338A pdb=" N VAL A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 531 Processing helix chain 'A' and resid 536 through 551 Processing helix chain 'A' and resid 552 through 557 removed outlier: 3.511A pdb=" N TYR A 555 " --> pdb=" O MET A 552 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 599 removed outlier: 3.618A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR A 584 " --> pdb=" O PHE A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 640 removed outlier: 3.957A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 643 No H-bonds generated for 'chain 'A' and resid 641 through 643' Processing helix chain 'A' and resid 655 through 684 removed outlier: 3.699A pdb=" N GLU A 684 " --> pdb=" O ALA A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 711 Processing helix chain 'D' and resid 203 through 211 removed outlier: 3.596A pdb=" N ILE D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 223 removed outlier: 3.687A pdb=" N ASN D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 250 through 257 Processing helix chain 'D' and resid 261 through 269 Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.751A pdb=" N ALA D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 335 through 343 Processing helix chain 'D' and resid 345 through 354 removed outlier: 3.622A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 409 through 414 removed outlier: 3.559A pdb=" N MET D 412 " --> pdb=" O ARG D 409 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU D 413 " --> pdb=" O HIS D 410 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 414 " --> pdb=" O ASP D 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 409 through 414' Processing helix chain 'D' and resid 415 through 454 removed outlier: 3.789A pdb=" N ASN D 419 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LYS D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR D 454 " --> pdb=" O ALA D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 500 removed outlier: 3.582A pdb=" N TYR D 472 " --> pdb=" O THR D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 509 removed outlier: 4.337A pdb=" N VAL D 508 " --> pdb=" O LYS D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'D' and resid 536 through 551 Processing helix chain 'D' and resid 552 through 557 removed outlier: 3.511A pdb=" N TYR D 555 " --> pdb=" O MET D 552 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 599 removed outlier: 3.618A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR D 584 " --> pdb=" O PHE D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 640 removed outlier: 3.957A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 643 No H-bonds generated for 'chain 'D' and resid 641 through 643' Processing helix chain 'D' and resid 655 through 684 removed outlier: 3.700A pdb=" N GLU D 684 " --> pdb=" O ALA D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 711 Processing helix chain 'B' and resid 203 through 211 removed outlier: 3.597A pdb=" N ILE B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 223 removed outlier: 3.687A pdb=" N ASN B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 261 through 269 Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.751A pdb=" N ALA B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 345 through 354 removed outlier: 3.622A pdb=" N GLN B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 409 through 414 removed outlier: 3.560A pdb=" N MET B 412 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU B 413 " --> pdb=" O HIS B 410 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 414 " --> pdb=" O ASP B 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 409 through 414' Processing helix chain 'B' and resid 415 through 454 removed outlier: 3.789A pdb=" N ASN B 419 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LYS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 500 removed outlier: 3.582A pdb=" N TYR B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 509 removed outlier: 4.338A pdb=" N VAL B 508 " --> pdb=" O LYS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 531 Processing helix chain 'B' and resid 536 through 551 Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.511A pdb=" N TYR B 555 " --> pdb=" O MET B 552 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 599 removed outlier: 3.618A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR B 584 " --> pdb=" O PHE B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 640 removed outlier: 3.957A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 643 No H-bonds generated for 'chain 'B' and resid 641 through 643' Processing helix chain 'B' and resid 655 through 684 removed outlier: 3.699A pdb=" N GLU B 684 " --> pdb=" O ALA B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 711 Processing helix chain 'C' and resid 203 through 211 removed outlier: 3.597A pdb=" N ILE C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 223 removed outlier: 3.687A pdb=" N ASN C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 250 through 257 Processing helix chain 'C' and resid 261 through 269 Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.751A pdb=" N ALA C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 335 through 343 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.622A pdb=" N GLN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 394 through 402 Processing helix chain 'C' and resid 409 through 414 removed outlier: 3.559A pdb=" N MET C 412 " --> pdb=" O ARG C 409 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU C 413 " --> pdb=" O HIS C 410 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU C 414 " --> pdb=" O ASP C 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 409 through 414' Processing helix chain 'C' and resid 415 through 454 removed outlier: 3.790A pdb=" N ASN C 419 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LYS C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR C 454 " --> pdb=" O ALA C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 500 removed outlier: 3.582A pdb=" N TYR C 472 " --> pdb=" O THR C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 509 removed outlier: 4.339A pdb=" N VAL C 508 " --> pdb=" O LYS C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 531 Processing helix chain 'C' and resid 536 through 551 Processing helix chain 'C' and resid 552 through 557 removed outlier: 3.511A pdb=" N TYR C 555 " --> pdb=" O MET C 552 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 599 removed outlier: 3.619A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR C 584 " --> pdb=" O PHE C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 640 removed outlier: 3.957A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 643 No H-bonds generated for 'chain 'C' and resid 641 through 643' Processing helix chain 'C' and resid 655 through 684 removed outlier: 3.699A pdb=" N GLU C 684 " --> pdb=" O ALA C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 711 Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 374 removed outlier: 5.714A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 746 " --> pdb=" O HIS A 378 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 368 through 374 removed outlier: 5.714A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU D 746 " --> pdb=" O HIS D 378 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 368 through 374 removed outlier: 5.714A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 746 " --> pdb=" O HIS B 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 368 through 374 removed outlier: 5.714A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 746 " --> pdb=" O HIS C 378 " (cutoff:3.500A) 952 hydrogen bonds defined for protein. 2772 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: 7.41 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 17205 1.04 - 1.23: 599 1.23 - 1.43: 7336 1.43 - 1.63: 10060 1.63 - 1.82: 172 Bond restraints: 35372 Sorted by residual: bond pdb=" N MET B 682 " pdb=" H MET B 682 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.83e+01 bond pdb=" N MET C 644 " pdb=" H MET C 644 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.82e+01 bond pdb=" N GLU D 371 " pdb=" H GLU D 371 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.82e+01 bond pdb=" N SER D 278 " pdb=" H SER D 278 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N LEU B 678 " pdb=" H LEU B 678 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.80e+01 ... (remaining 35367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 63381 2.82 - 5.65: 295 5.65 - 8.47: 24 8.47 - 11.29: 12 11.29 - 14.12: 4 Bond angle restraints: 63716 Sorted by residual: angle pdb=" O LEU D 681 " pdb=" C LEU D 681 " pdb=" N MET D 682 " ideal model delta sigma weight residual 122.12 116.11 6.01 1.06e+00 8.90e-01 3.21e+01 angle pdb=" O LEU C 681 " pdb=" C LEU C 681 " pdb=" N MET C 682 " ideal model delta sigma weight residual 122.12 116.13 5.99 1.06e+00 8.90e-01 3.19e+01 angle pdb=" O LEU A 681 " pdb=" C LEU A 681 " pdb=" N MET A 682 " ideal model delta sigma weight residual 122.12 116.13 5.99 1.06e+00 8.90e-01 3.19e+01 angle pdb=" O LEU B 681 " pdb=" C LEU B 681 " pdb=" N MET B 682 " ideal model delta sigma weight residual 122.12 116.15 5.97 1.06e+00 8.90e-01 3.17e+01 angle pdb=" CA LEU D 681 " pdb=" C LEU D 681 " pdb=" N MET D 682 " ideal model delta sigma weight residual 117.30 123.30 -6.00 1.16e+00 7.43e-01 2.68e+01 ... (remaining 63711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 15075 17.89 - 35.78: 1193 35.78 - 53.67: 264 53.67 - 71.56: 72 71.56 - 89.44: 40 Dihedral angle restraints: 16644 sinusoidal: 8828 harmonic: 7816 Sorted by residual: dihedral pdb=" CA VAL D 415 " pdb=" C VAL D 415 " pdb=" N GLU D 416 " pdb=" CA GLU D 416 " ideal model delta harmonic sigma weight residual -180.00 -162.34 -17.66 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA VAL A 415 " pdb=" C VAL A 415 " pdb=" N GLU A 416 " pdb=" CA GLU A 416 " ideal model delta harmonic sigma weight residual -180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA VAL B 415 " pdb=" C VAL B 415 " pdb=" N GLU B 416 " pdb=" CA GLU B 416 " ideal model delta harmonic sigma weight residual -180.00 -162.41 -17.59 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 16641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1969 0.037 - 0.073: 594 0.073 - 0.110: 105 0.110 - 0.147: 31 0.147 - 0.183: 5 Chirality restraints: 2704 Sorted by residual: chirality pdb=" CA VAL D 457 " pdb=" N VAL D 457 " pdb=" C VAL D 457 " pdb=" CB VAL D 457 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" CA VAL C 457 " pdb=" N VAL C 457 " pdb=" C VAL C 457 " pdb=" CB VAL C 457 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.36e-01 chirality pdb=" CA VAL A 457 " pdb=" N VAL A 457 " pdb=" C VAL A 457 " pdb=" CB VAL A 457 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.14e-01 ... (remaining 2701 not shown) Planarity restraints: 5056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 223 " 0.130 2.00e-02 2.50e+03 1.26e-01 2.37e+02 pdb=" CG ASN D 223 " -0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN D 223 " -0.125 2.00e-02 2.50e+03 pdb=" ND2 ASN D 223 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN D 223 " -0.175 2.00e-02 2.50e+03 pdb="HD22 ASN D 223 " 0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 223 " -0.130 2.00e-02 2.50e+03 1.26e-01 2.37e+02 pdb=" CG ASN B 223 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN B 223 " 0.125 2.00e-02 2.50e+03 pdb=" ND2 ASN B 223 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN B 223 " 0.175 2.00e-02 2.50e+03 pdb="HD22 ASN B 223 " -0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 223 " -0.130 2.00e-02 2.50e+03 1.25e-01 2.36e+02 pdb=" CG ASN A 223 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN A 223 " 0.125 2.00e-02 2.50e+03 pdb=" ND2 ASN A 223 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 223 " 0.174 2.00e-02 2.50e+03 pdb="HD22 ASN A 223 " -0.178 2.00e-02 2.50e+03 ... (remaining 5053 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 2867 2.23 - 2.82: 74004 2.82 - 3.42: 84127 3.42 - 4.01: 109077 4.01 - 4.60: 170951 Nonbonded interactions: 441026 Sorted by model distance: nonbonded pdb=" HZ3 LYS A 238 " pdb=" OE2 GLU A 293 " model vdw 1.641 2.450 nonbonded pdb=" HZ3 LYS C 238 " pdb=" OE2 GLU C 293 " model vdw 1.641 2.450 nonbonded pdb=" HZ3 LYS B 238 " pdb=" OE2 GLU B 293 " model vdw 1.641 2.450 nonbonded pdb=" HZ3 LYS D 238 " pdb=" OE2 GLU D 293 " model vdw 1.641 2.450 nonbonded pdb=" OD1 ASP D 296 " pdb="HD21 ASN D 301 " model vdw 1.696 2.450 ... (remaining 441021 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' and resid 197 through 801) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 6.040 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: 0.220 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 29.160 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 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:7.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 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 : 0.005 0.122 17872 Z= 0.248 Angle : 0.720 14.116 24172 Z= 0.413 Chirality : 0.037 0.183 2704 Planarity : 0.004 0.060 2984 Dihedral : 14.138 89.444 6492 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.21 % Allowed : 0.48 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.19), residues: 2124 helix: 2.48 (0.15), residues: 1264 sheet: None (None), residues: 0 loop : -2.21 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 721 TYR 0.015 0.001 TYR D 653 PHE 0.012 0.001 PHE C 649 TRP 0.007 0.001 TRP B 740 HIS 0.003 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.25 (17872) covalent geometry : angle 0.72016 / 0.41 (24172) hydrogen bonds : bond 0.13334 / 8.92 ( 952) hydrogen bonds : angle 4.93057 / 3.61 ( 2772) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 278 time to evaluate : 0.859 Fit side-chains REVERT: A 445 MET cc_start: 0.9197 (tpt) cc_final: 0.8141 (tpt) REVERT: D 445 MET cc_start: 0.9194 (tpt) cc_final: 0.8140 (tpt) REVERT: B 445 MET cc_start: 0.9197 (tpt) cc_final: 0.8140 (tpt) REVERT: C 445 MET cc_start: 0.9184 (tpt) cc_final: 0.8133 (tpt) outliers start: 4 outliers final: 4 residues processed: 278 average time/residue: 0.9425 time to fit residues: 302.4880 Evaluate side-chains 252 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 248 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain D residue 652 ASN Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain C residue 652 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 GLN A 223 ASN D 202 GLN D 223 ASN B 202 GLN B 223 ASN C 202 GLN C 223 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.186129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.116524 restraints weight = 60140.494| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.66 r_work: 0.3272 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17872 Z= 0.125 Angle : 0.484 4.778 24172 Z= 0.268 Chirality : 0.036 0.131 2704 Planarity : 0.004 0.056 2984 Dihedral : 5.962 59.363 2444 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.69 % Allowed : 8.23 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.20), residues: 2124 helix: 2.79 (0.15), residues: 1280 sheet: -0.74 (0.59), residues: 64 loop : -2.13 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 721 TYR 0.007 0.001 TYR C 555 PHE 0.011 0.001 PHE A 649 TRP 0.006 0.001 TRP D 372 HIS 0.003 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (17872) covalent geometry : angle 0.48419 / 0.27 (24172) hydrogen bonds : bond 0.07033 / 4.67 ( 952) hydrogen bonds : angle 3.80645 / 2.74 ( 2772) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 250 time to evaluate : 0.985 Fit side-chains REVERT: A 445 MET cc_start: 0.9092 (tpt) cc_final: 0.8349 (tpt) REVERT: A 580 PHE cc_start: 0.8094 (m-10) cc_final: 0.7462 (t80) REVERT: A 746 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.5314 (tm-30) REVERT: D 445 MET cc_start: 0.9090 (tpt) cc_final: 0.8340 (tpt) REVERT: D 580 PHE cc_start: 0.8093 (m-10) cc_final: 0.7467 (t80) REVERT: D 746 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.5314 (tm-30) REVERT: B 445 MET cc_start: 0.9096 (tpt) cc_final: 0.8348 (tpt) REVERT: B 580 PHE cc_start: 0.8109 (m-10) cc_final: 0.7477 (t80) REVERT: B 746 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.5314 (tm-30) REVERT: C 445 MET cc_start: 0.9091 (tpt) cc_final: 0.8345 (tpt) REVERT: C 580 PHE cc_start: 0.8098 (m-10) cc_final: 0.7468 (t80) REVERT: C 746 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.5309 (tm-30) outliers start: 13 outliers final: 11 residues processed: 259 average time/residue: 0.9309 time to fit residues: 278.6219 Evaluate side-chains 259 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 244 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 682 MET Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 682 MET Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 682 MET Chi-restraints excluded: chain C residue 746 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 52 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 189 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.180359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.111350 restraints weight = 60129.727| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.61 r_work: 0.3102 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 17872 Z= 0.240 Angle : 0.582 4.994 24172 Z= 0.326 Chirality : 0.040 0.175 2704 Planarity : 0.004 0.059 2984 Dihedral : 6.676 59.175 2436 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.43 % Allowed : 10.99 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.19), residues: 2124 helix: 2.42 (0.15), residues: 1276 sheet: -1.90 (0.55), residues: 84 loop : -2.25 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 721 TYR 0.013 0.002 TYR C 530 PHE 0.021 0.002 PHE C 649 TRP 0.008 0.001 TRP A 697 HIS 0.003 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.24 (17872) covalent geometry : angle 0.58165 / 0.33 (24172) hydrogen bonds : bond 0.10256 / 6.80 ( 952) hydrogen bonds : angle 4.09223 / 2.95 ( 2772) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 243 time to evaluate : 0.823 Fit side-chains REVERT: A 331 ARG cc_start: 0.7215 (mtp180) cc_final: 0.6951 (mtp85) REVERT: A 445 MET cc_start: 0.9194 (tpt) cc_final: 0.8679 (tpt) REVERT: A 580 PHE cc_start: 0.8195 (m-10) cc_final: 0.7634 (t80) REVERT: D 331 ARG cc_start: 0.7229 (mtp180) cc_final: 0.6969 (mtp85) REVERT: D 445 MET cc_start: 0.9194 (tpt) cc_final: 0.8679 (tpt) REVERT: D 580 PHE cc_start: 0.8203 (m-10) cc_final: 0.7640 (t80) REVERT: B 331 ARG cc_start: 0.7221 (mtp180) cc_final: 0.6959 (mtp85) REVERT: B 445 MET cc_start: 0.9200 (tpt) cc_final: 0.8688 (tpt) REVERT: B 580 PHE cc_start: 0.8196 (m-10) cc_final: 0.7637 (t80) REVERT: C 331 ARG cc_start: 0.7223 (mtp180) cc_final: 0.6962 (mtp85) REVERT: C 445 MET cc_start: 0.9191 (tpt) cc_final: 0.8678 (tpt) REVERT: C 580 PHE cc_start: 0.8190 (m-10) cc_final: 0.7632 (t80) outliers start: 27 outliers final: 11 residues processed: 254 average time/residue: 0.9708 time to fit residues: 283.6528 Evaluate side-chains 253 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 242 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 652 ASN Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 652 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 135 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.183572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113536 restraints weight = 59714.744| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.70 r_work: 0.3216 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 17872 Z= 0.143 Angle : 0.491 4.706 24172 Z= 0.274 Chirality : 0.036 0.133 2704 Planarity : 0.004 0.056 2984 Dihedral : 6.184 54.788 2436 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.11 % Allowed : 12.10 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.20), residues: 2124 helix: 2.72 (0.15), residues: 1276 sheet: -1.76 (0.56), residues: 84 loop : -2.19 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 721 TYR 0.008 0.001 TYR C 555 PHE 0.012 0.001 PHE A 649 TRP 0.007 0.001 TRP C 740 HIS 0.002 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (17872) covalent geometry : angle 0.49115 / 0.27 (24172) hydrogen bonds : bond 0.07786 / 5.16 ( 952) hydrogen bonds : angle 3.76520 / 2.70 ( 2772) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 248 time to evaluate : 0.817 Fit side-chains REVERT: A 331 ARG cc_start: 0.7203 (mtp180) cc_final: 0.6944 (mtp85) REVERT: A 445 MET cc_start: 0.9057 (tpt) cc_final: 0.8629 (tpt) REVERT: A 580 PHE cc_start: 0.8122 (m-10) cc_final: 0.7545 (t80) REVERT: A 743 ARG cc_start: 0.8060 (ptp90) cc_final: 0.7666 (ttp-110) REVERT: D 331 ARG cc_start: 0.7212 (mtp180) cc_final: 0.6952 (mtp85) REVERT: D 445 MET cc_start: 0.9055 (tpt) cc_final: 0.8626 (tpt) REVERT: D 580 PHE cc_start: 0.8117 (m-10) cc_final: 0.7544 (t80) REVERT: D 743 ARG cc_start: 0.8049 (ptp90) cc_final: 0.7654 (ttp-110) REVERT: B 331 ARG cc_start: 0.7208 (mtp180) cc_final: 0.6949 (mtp85) REVERT: B 445 MET cc_start: 0.9052 (tpt) cc_final: 0.8625 (tpt) REVERT: B 580 PHE cc_start: 0.8128 (m-10) cc_final: 0.7553 (t80) REVERT: B 743 ARG cc_start: 0.8045 (ptp90) cc_final: 0.7652 (ttp-110) REVERT: C 331 ARG cc_start: 0.7211 (mtp180) cc_final: 0.6953 (mtp85) REVERT: C 445 MET cc_start: 0.9057 (tpt) cc_final: 0.8627 (tpt) REVERT: C 580 PHE cc_start: 0.8118 (m-10) cc_final: 0.7538 (t80) REVERT: C 743 ARG cc_start: 0.8059 (ptp90) cc_final: 0.7662 (ttp-110) outliers start: 21 outliers final: 7 residues processed: 251 average time/residue: 0.9320 time to fit residues: 271.0593 Evaluate side-chains 244 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 237 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 570 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 13 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.185426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.115669 restraints weight = 59512.812| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.69 r_work: 0.3164 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 17872 Z= 0.125 Angle : 0.466 4.437 24172 Z= 0.258 Chirality : 0.035 0.131 2704 Planarity : 0.003 0.053 2984 Dihedral : 5.656 55.892 2436 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.54 % Allowed : 12.63 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.20), residues: 2124 helix: 2.94 (0.15), residues: 1272 sheet: -1.72 (0.56), residues: 84 loop : -2.18 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 721 TYR 0.008 0.001 TYR D 511 PHE 0.010 0.001 PHE C 649 TRP 0.007 0.001 TRP C 740 HIS 0.002 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (17872) covalent geometry : angle 0.46626 / 0.26 (24172) hydrogen bonds : bond 0.06880 / 4.56 ( 952) hydrogen bonds : angle 3.58190 / 2.57 ( 2772) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 0.918 Fit side-chains REVERT: A 331 ARG cc_start: 0.7221 (mtp180) cc_final: 0.6924 (mtp85) REVERT: A 445 MET cc_start: 0.9085 (tpt) cc_final: 0.8670 (tpt) REVERT: A 580 PHE cc_start: 0.8162 (m-10) cc_final: 0.7591 (t80) REVERT: A 743 ARG cc_start: 0.8062 (ptp90) cc_final: 0.7536 (ttp-110) REVERT: D 331 ARG cc_start: 0.7211 (mtp180) cc_final: 0.6914 (mtp85) REVERT: D 445 MET cc_start: 0.9074 (tpt) cc_final: 0.8664 (tpt) REVERT: D 580 PHE cc_start: 0.8151 (m-10) cc_final: 0.7574 (t80) REVERT: D 743 ARG cc_start: 0.8053 (ptp90) cc_final: 0.7523 (ttp-110) REVERT: B 331 ARG cc_start: 0.7213 (mtp180) cc_final: 0.6919 (mtp85) REVERT: B 445 MET cc_start: 0.9077 (tpt) cc_final: 0.8665 (tpt) REVERT: B 580 PHE cc_start: 0.8174 (m-10) cc_final: 0.7601 (t80) REVERT: B 743 ARG cc_start: 0.8065 (ptp90) cc_final: 0.7539 (ttp-110) REVERT: C 331 ARG cc_start: 0.7218 (mtp180) cc_final: 0.6921 (mtp85) REVERT: C 445 MET cc_start: 0.9081 (tpt) cc_final: 0.8669 (tpt) REVERT: C 580 PHE cc_start: 0.8160 (m-10) cc_final: 0.7583 (t80) REVERT: C 743 ARG cc_start: 0.8057 (ptp90) cc_final: 0.7534 (ttp-110) outliers start: 29 outliers final: 15 residues processed: 250 average time/residue: 0.8202 time to fit residues: 242.0938 Evaluate side-chains 249 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 234 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 682 MET Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 682 MET Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 682 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 55 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 203 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.187888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118201 restraints weight = 59492.971| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.71 r_work: 0.3208 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 17872 Z= 0.107 Angle : 0.444 4.258 24172 Z= 0.243 Chirality : 0.035 0.128 2704 Planarity : 0.003 0.051 2984 Dihedral : 5.264 53.372 2436 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.11 % Allowed : 13.22 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.20), residues: 2124 helix: 3.11 (0.15), residues: 1272 sheet: -1.56 (0.55), residues: 84 loop : -2.01 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 721 TYR 0.007 0.001 TYR C 511 PHE 0.009 0.001 PHE A 659 TRP 0.006 0.001 TRP B 740 HIS 0.002 0.000 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 (17872) covalent geometry : angle 0.44411 / 0.24 (24172) hydrogen bonds : bond 0.05839 / 3.87 ( 952) hydrogen bonds : angle 3.42539 / 2.45 ( 2772) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 238 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ARG cc_start: 0.7187 (mtp180) cc_final: 0.6877 (mtp85) REVERT: A 445 MET cc_start: 0.9006 (tpt) cc_final: 0.8565 (tpt) REVERT: A 580 PHE cc_start: 0.8141 (m-10) cc_final: 0.7554 (t80) REVERT: A 677 MET cc_start: 0.7489 (tmm) cc_final: 0.7177 (tmm) REVERT: A 743 ARG cc_start: 0.8006 (ptp90) cc_final: 0.7497 (ttp-110) REVERT: D 331 ARG cc_start: 0.7196 (mtp180) cc_final: 0.6886 (mtp85) REVERT: D 445 MET cc_start: 0.9001 (tpt) cc_final: 0.8559 (tpt) REVERT: D 580 PHE cc_start: 0.8118 (m-10) cc_final: 0.7521 (t80) REVERT: D 743 ARG cc_start: 0.7997 (ptp90) cc_final: 0.7485 (ttp-110) REVERT: B 331 ARG cc_start: 0.7189 (mtp180) cc_final: 0.6882 (mtp85) REVERT: B 445 MET cc_start: 0.9005 (tpt) cc_final: 0.8560 (tpt) REVERT: B 580 PHE cc_start: 0.8123 (m-10) cc_final: 0.7536 (t80) REVERT: B 677 MET cc_start: 0.7489 (tmm) cc_final: 0.7175 (tmm) REVERT: B 743 ARG cc_start: 0.8002 (ptp90) cc_final: 0.7494 (ttp-110) REVERT: C 331 ARG cc_start: 0.7191 (mtp180) cc_final: 0.6882 (mtp85) REVERT: C 445 MET cc_start: 0.9007 (tpt) cc_final: 0.8561 (tpt) REVERT: C 580 PHE cc_start: 0.8128 (m-10) cc_final: 0.7548 (t80) REVERT: C 743 ARG cc_start: 0.8001 (ptp90) cc_final: 0.7494 (ttp-110) outliers start: 21 outliers final: 17 residues processed: 243 average time/residue: 0.7712 time to fit residues: 222.7511 Evaluate side-chains 248 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 231 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 574 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 110 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 162 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 676 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.180175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.110376 restraints weight = 59525.562| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.66 r_work: 0.3107 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 17872 Z= 0.216 Angle : 0.551 5.101 24172 Z= 0.307 Chirality : 0.039 0.197 2704 Planarity : 0.004 0.055 2984 Dihedral : 5.703 42.885 2436 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.65 % Allowed : 13.64 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.19), residues: 2124 helix: 2.58 (0.15), residues: 1276 sheet: -1.65 (0.56), residues: 84 loop : -2.26 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 721 TYR 0.012 0.002 TYR A 453 PHE 0.020 0.002 PHE C 649 TRP 0.006 0.001 TRP C 740 HIS 0.003 0.001 HIS C 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (17872) covalent geometry : angle 0.55065 / 0.31 (24172) hydrogen bonds : bond 0.09528 / 6.31 ( 952) hydrogen bonds : angle 3.87796 / 2.79 ( 2772) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 253 time to evaluate : 0.764 Fit side-chains REVERT: A 331 ARG cc_start: 0.7233 (mtp180) cc_final: 0.6909 (mtp85) REVERT: A 445 MET cc_start: 0.9130 (tpt) cc_final: 0.8815 (tpt) REVERT: A 580 PHE cc_start: 0.8179 (m-10) cc_final: 0.7627 (t80) REVERT: A 743 ARG cc_start: 0.8231 (ptp90) cc_final: 0.7696 (ttp-110) REVERT: A 746 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.5363 (tm-30) REVERT: D 331 ARG cc_start: 0.7242 (mtp180) cc_final: 0.6918 (mtp85) REVERT: D 445 MET cc_start: 0.9129 (tpt) cc_final: 0.8811 (tpt) REVERT: D 580 PHE cc_start: 0.8193 (m-10) cc_final: 0.7638 (t80) REVERT: D 743 ARG cc_start: 0.8227 (ptp90) cc_final: 0.7695 (ttp-110) REVERT: D 746 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.5364 (tm-30) REVERT: B 331 ARG cc_start: 0.7236 (mtp180) cc_final: 0.6916 (mtp85) REVERT: B 445 MET cc_start: 0.9129 (tpt) cc_final: 0.8814 (tpt) REVERT: B 580 PHE cc_start: 0.8202 (m-10) cc_final: 0.7648 (t80) REVERT: B 743 ARG cc_start: 0.8229 (ptp90) cc_final: 0.7697 (ttp-110) REVERT: B 746 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.5340 (tm-30) REVERT: C 331 ARG cc_start: 0.7232 (mtp180) cc_final: 0.6906 (mtp85) REVERT: C 445 MET cc_start: 0.9129 (tpt) cc_final: 0.8813 (tpt) REVERT: C 580 PHE cc_start: 0.8202 (m-10) cc_final: 0.7649 (t80) REVERT: C 743 ARG cc_start: 0.8232 (ptp90) cc_final: 0.7700 (ttp-110) REVERT: C 746 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.5361 (tm-30) outliers start: 31 outliers final: 15 residues processed: 261 average time/residue: 0.8834 time to fit residues: 267.2834 Evaluate side-chains 257 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 238 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 746 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 161 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 203 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.183618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.114264 restraints weight = 59267.554| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.67 r_work: 0.3133 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 17872 Z= 0.142 Angle : 0.494 5.024 24172 Z= 0.273 Chirality : 0.036 0.135 2704 Planarity : 0.004 0.055 2984 Dihedral : 5.207 34.315 2436 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.65 % Allowed : 14.70 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.20), residues: 2124 helix: 2.82 (0.15), residues: 1272 sheet: -1.54 (0.56), residues: 84 loop : -2.28 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 721 TYR 0.010 0.001 TYR A 511 PHE 0.012 0.001 PHE A 649 TRP 0.007 0.001 TRP A 740 HIS 0.002 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (17872) covalent geometry : angle 0.49370 / 0.27 (24172) hydrogen bonds : bond 0.07649 / 5.07 ( 952) hydrogen bonds : angle 3.67765 / 2.64 ( 2772) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 251 time to evaluate : 0.635 Fit side-chains REVERT: A 331 ARG cc_start: 0.7202 (mtp180) cc_final: 0.6891 (mtp85) REVERT: A 445 MET cc_start: 0.9057 (tpt) cc_final: 0.8712 (tpt) REVERT: A 580 PHE cc_start: 0.8144 (m-10) cc_final: 0.7578 (t80) REVERT: A 636 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8564 (tp30) REVERT: A 743 ARG cc_start: 0.8113 (ptp90) cc_final: 0.7649 (ttp-110) REVERT: A 746 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.5234 (tm-30) REVERT: D 331 ARG cc_start: 0.7204 (mtp180) cc_final: 0.6890 (mtp85) REVERT: D 445 MET cc_start: 0.9052 (tpt) cc_final: 0.8710 (tpt) REVERT: D 580 PHE cc_start: 0.8155 (m-10) cc_final: 0.7578 (t80) REVERT: D 636 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8575 (tp30) REVERT: D 743 ARG cc_start: 0.8101 (ptp90) cc_final: 0.7633 (ttp-110) REVERT: D 746 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.5235 (tm-30) REVERT: B 331 ARG cc_start: 0.7198 (mtp180) cc_final: 0.6891 (mtp85) REVERT: B 445 MET cc_start: 0.9050 (tpt) cc_final: 0.8709 (tpt) REVERT: B 580 PHE cc_start: 0.8176 (m-10) cc_final: 0.7601 (t80) REVERT: B 636 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8552 (tp30) REVERT: B 743 ARG cc_start: 0.8116 (ptp90) cc_final: 0.7654 (ttp-110) REVERT: B 746 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.5235 (tm-30) REVERT: C 331 ARG cc_start: 0.7201 (mtp180) cc_final: 0.6890 (mtp85) REVERT: C 445 MET cc_start: 0.9061 (tpt) cc_final: 0.8713 (tpt) REVERT: C 580 PHE cc_start: 0.8173 (m-10) cc_final: 0.7599 (t80) REVERT: C 636 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8562 (tp30) REVERT: C 743 ARG cc_start: 0.8113 (ptp90) cc_final: 0.7648 (ttp-110) REVERT: C 746 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.5236 (tm-30) outliers start: 31 outliers final: 18 residues processed: 259 average time/residue: 0.8372 time to fit residues: 252.9613 Evaluate side-chains 265 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 243 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 746 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 191 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.181648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.111777 restraints weight = 59323.951| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.67 r_work: 0.3111 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 17872 Z= 0.164 Angle : 0.515 4.668 24172 Z= 0.285 Chirality : 0.037 0.154 2704 Planarity : 0.004 0.055 2984 Dihedral : 5.266 36.702 2436 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.86 % Allowed : 14.65 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.19), residues: 2124 helix: 2.66 (0.15), residues: 1280 sheet: -1.53 (0.58), residues: 84 loop : -2.32 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 428 TYR 0.009 0.001 TYR C 511 PHE 0.015 0.001 PHE A 649 TRP 0.007 0.001 TRP B 740 HIS 0.002 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (17872) covalent geometry : angle 0.51501 / 0.29 (24172) hydrogen bonds : bond 0.08303 / 5.50 ( 952) hydrogen bonds : angle 3.73855 / 2.69 ( 2772) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 243 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 MET cc_start: 0.9061 (tpt) cc_final: 0.8709 (tpt) REVERT: A 580 PHE cc_start: 0.8130 (m-10) cc_final: 0.7574 (t80) REVERT: A 636 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8559 (tp30) REVERT: A 743 ARG cc_start: 0.8146 (ptp90) cc_final: 0.7679 (ttp-110) REVERT: A 746 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.5254 (tm-30) REVERT: D 331 ARG cc_start: 0.7205 (mtp180) cc_final: 0.6869 (mtp85) REVERT: D 445 MET cc_start: 0.9058 (tpt) cc_final: 0.8708 (tpt) REVERT: D 580 PHE cc_start: 0.8142 (m-10) cc_final: 0.7589 (t80) REVERT: D 636 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8583 (tp30) REVERT: D 743 ARG cc_start: 0.8150 (ptp90) cc_final: 0.7685 (ttp-110) REVERT: D 746 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.5268 (tm-30) REVERT: B 445 MET cc_start: 0.9059 (tpt) cc_final: 0.8708 (tpt) REVERT: B 580 PHE cc_start: 0.8140 (m-10) cc_final: 0.7589 (t80) REVERT: B 636 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8568 (tp30) REVERT: B 743 ARG cc_start: 0.8137 (ptp90) cc_final: 0.7672 (ttp-110) REVERT: B 746 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.5242 (tm-30) REVERT: C 445 MET cc_start: 0.9064 (tpt) cc_final: 0.8710 (tpt) REVERT: C 580 PHE cc_start: 0.8142 (m-10) cc_final: 0.7592 (t80) REVERT: C 636 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8584 (tp30) REVERT: C 743 ARG cc_start: 0.8149 (ptp90) cc_final: 0.7684 (ttp-110) REVERT: C 746 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.5261 (tm-30) outliers start: 35 outliers final: 14 residues processed: 257 average time/residue: 0.9046 time to fit residues: 269.9522 Evaluate side-chains 257 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 239 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 746 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 113 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 94 optimal weight: 0.0980 chunk 59 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 180 optimal weight: 0.8980 chunk 178 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.184152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.114823 restraints weight = 59517.308| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.66 r_work: 0.3142 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 17872 Z= 0.137 Angle : 0.492 4.508 24172 Z= 0.271 Chirality : 0.036 0.132 2704 Planarity : 0.004 0.054 2984 Dihedral : 5.092 32.655 2436 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.38 % Allowed : 15.39 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.19), residues: 2124 helix: 2.83 (0.15), residues: 1276 sheet: -1.48 (0.58), residues: 84 loop : -2.30 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 428 TYR 0.009 0.001 TYR C 511 PHE 0.012 0.001 PHE A 649 TRP 0.007 0.001 TRP A 740 HIS 0.002 0.000 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (17872) covalent geometry : angle 0.49158 / 0.27 (24172) hydrogen bonds : bond 0.07422 / 4.92 ( 952) hydrogen bonds : angle 3.63199 / 2.61 ( 2772) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 249 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 MET cc_start: 0.9016 (tpt) cc_final: 0.8665 (tpt) REVERT: A 580 PHE cc_start: 0.8119 (m-10) cc_final: 0.7561 (t80) REVERT: A 636 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8563 (tp30) REVERT: A 743 ARG cc_start: 0.8118 (ptp90) cc_final: 0.7644 (ttp-110) REVERT: A 746 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.5185 (tm-30) REVERT: D 445 MET cc_start: 0.9009 (tpt) cc_final: 0.8664 (tpt) REVERT: D 580 PHE cc_start: 0.8138 (m-10) cc_final: 0.7554 (t80) REVERT: D 636 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8575 (tp30) REVERT: D 743 ARG cc_start: 0.8112 (ptp90) cc_final: 0.7632 (ttp-110) REVERT: D 746 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.5207 (tm-30) REVERT: B 445 MET cc_start: 0.9014 (tpt) cc_final: 0.8666 (tpt) REVERT: B 580 PHE cc_start: 0.8170 (m-10) cc_final: 0.7569 (t80) REVERT: B 636 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8565 (tp30) REVERT: B 743 ARG cc_start: 0.8119 (ptp90) cc_final: 0.7647 (ttp-110) REVERT: B 746 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.5194 (tm-30) REVERT: C 445 MET cc_start: 0.9031 (tpt) cc_final: 0.8683 (tpt) REVERT: C 580 PHE cc_start: 0.8138 (m-10) cc_final: 0.7560 (t80) REVERT: C 636 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8569 (tp30) REVERT: C 743 ARG cc_start: 0.8117 (ptp90) cc_final: 0.7643 (ttp-110) REVERT: C 746 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.5194 (tm-30) outliers start: 26 outliers final: 21 residues processed: 263 average time/residue: 0.8716 time to fit residues: 266.9883 Evaluate side-chains 269 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 500 ARG Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 500 ARG Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 746 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 101 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 128 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.182288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.114287 restraints weight = 59569.086| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.61 r_work: 0.3162 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17872 Z= 0.130 Angle : 0.482 4.718 24172 Z= 0.265 Chirality : 0.036 0.130 2704 Planarity : 0.003 0.053 2984 Dihedral : 4.950 32.159 2436 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.91 % Allowed : 14.86 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.20), residues: 2124 helix: 2.91 (0.15), residues: 1272 sheet: -1.47 (0.59), residues: 84 loop : -2.31 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 428 TYR 0.008 0.001 TYR C 511 PHE 0.011 0.001 PHE C 649 TRP 0.007 0.001 TRP B 740 HIS 0.002 0.000 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (17872) covalent geometry : angle 0.48220 / 0.26 (24172) hydrogen bonds : bond 0.07037 / 4.66 ( 952) hydrogen bonds : angle 3.55836 / 2.55 ( 2772) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10950.17 seconds wall clock time: 185 minutes 13.73 seconds (11113.73 seconds total)