Starting phenix.real_space_refine on Mon Jul 6 11:49:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u3j_41864/07_2026/8u3j_41864_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u3j_41864/07_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_41864/07_2026/8u3j_41864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u3j_41864/07_2026/8u3j_41864.map" model { file = "/net/cci-nas-00/data/ceres_data/8u3j_41864/07_2026/8u3j_41864_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u3j_41864/07_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-dev-6108/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, 34 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 6.44, per 1000 atoms: 0.18 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: 3.58 Conformation dependent library (CDL) restraints added in 989.8 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: 0.76 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: 7.61 Time building geometry restraints manager: 4.83 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: 5.130 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: 0.250 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 32.500 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:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.660 ------------------------------------------------------------------------------- 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 : 0.958 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: 1.1049 time to fit residues: 353.4605 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 : 0.940 ------------------------------------------------------------------------------- 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 C 652 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.186225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.116357 restraints weight = 60216.565| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.67 r_work: 0.3288 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17872 Z= 0.125 Angle : 0.484 4.760 24172 Z= 0.268 Chirality : 0.036 0.132 2704 Planarity : 0.004 0.056 2984 Dihedral : 6.080 61.372 2444 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.58 % Allowed : 8.39 % Favored : 91.03 % 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: 1.50 (0.20), residues: 2124 helix: 2.78 (0.15), residues: 1280 sheet: -0.86 (0.58), residues: 64 loop : -2.13 (0.22), residues: 780 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 0.010 0.001 PHE C 659 TRP 0.007 0.001 TRP D 372 HIS 0.003 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (17872) covalent geometry : angle 0.48419 / 0.27 (24172) hydrogen bonds : bond 0.06977 / 4.64 ( 952) hydrogen bonds : angle 3.77904 / 2.72 ( 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 259 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 248 time to evaluate : 0.990 Fit side-chains REVERT: A 445 MET cc_start: 0.9085 (tpt) cc_final: 0.8355 (tpt) REVERT: A 580 PHE cc_start: 0.8106 (m-10) cc_final: 0.7457 (t80) REVERT: A 746 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.5247 (tm-30) REVERT: D 445 MET cc_start: 0.9083 (tpt) cc_final: 0.8353 (tpt) REVERT: D 580 PHE cc_start: 0.8066 (m-10) cc_final: 0.7464 (t80) REVERT: D 652 ASN cc_start: 0.7920 (p0) cc_final: 0.7647 (p0) REVERT: D 746 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.5245 (tm-30) REVERT: B 445 MET cc_start: 0.9085 (tpt) cc_final: 0.8356 (tpt) REVERT: B 580 PHE cc_start: 0.8077 (m-10) cc_final: 0.7467 (t80) REVERT: B 652 ASN cc_start: 0.7933 (p0) cc_final: 0.7662 (p0) REVERT: B 746 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.5245 (tm-30) REVERT: C 445 MET cc_start: 0.9084 (tpt) cc_final: 0.8352 (tpt) REVERT: C 580 PHE cc_start: 0.8108 (m-10) cc_final: 0.7463 (t80) outliers start: 11 outliers final: 9 residues processed: 254 average time/residue: 1.1201 time to fit residues: 327.6186 Evaluate side-chains 255 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 243 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 493 ILE Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 682 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 52 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 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: 5.9990 chunk 158 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 652 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.181428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.112456 restraints weight = 60138.272| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.60 r_work: 0.3121 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1471 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 : 0.557 4.890 24172 Z= 0.312 Chirality : 0.039 0.164 2704 Planarity : 0.004 0.057 2984 Dihedral : 6.523 59.977 2438 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.27 % Allowed : 10.99 % Favored : 87.74 % 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: 2.56 (0.15), residues: 1280 sheet: -1.85 (0.55), residues: 84 loop : -2.20 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 721 TYR 0.011 0.002 TYR C 555 PHE 0.019 0.002 PHE A 649 TRP 0.007 0.001 TRP C 740 HIS 0.002 0.001 HIS C 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (17872) covalent geometry : angle 0.55742 / 0.31 (24172) hydrogen bonds : bond 0.09625 / 6.38 ( 952) hydrogen bonds : angle 3.99543 / 2.88 ( 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 271 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 247 time to evaluate : 0.995 Fit side-chains REVERT: A 331 ARG cc_start: 0.7218 (mtp180) cc_final: 0.6958 (mtp85) REVERT: A 445 MET cc_start: 0.9212 (tpt) cc_final: 0.8660 (tpt) REVERT: A 580 PHE cc_start: 0.8177 (m-10) cc_final: 0.7621 (t80) REVERT: D 331 ARG cc_start: 0.7222 (mtp180) cc_final: 0.6961 (mtp85) REVERT: D 445 MET cc_start: 0.9212 (tpt) cc_final: 0.8662 (tpt) REVERT: D 580 PHE cc_start: 0.8184 (m-10) cc_final: 0.7628 (t80) REVERT: B 331 ARG cc_start: 0.7220 (mtp180) cc_final: 0.6960 (mtp85) REVERT: B 445 MET cc_start: 0.9216 (tpt) cc_final: 0.8665 (tpt) REVERT: B 580 PHE cc_start: 0.8185 (m-10) cc_final: 0.7628 (t80) REVERT: C 331 ARG cc_start: 0.7219 (mtp180) cc_final: 0.6958 (mtp85) REVERT: C 445 MET cc_start: 0.9206 (tpt) cc_final: 0.8656 (tpt) REVERT: C 580 PHE cc_start: 0.8175 (m-10) cc_final: 0.7626 (t80) outliers start: 24 outliers final: 8 residues processed: 258 average time/residue: 1.1652 time to fit residues: 343.8539 Evaluate side-chains 250 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 242 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 122 optimal weight: 0.0270 chunk 92 optimal weight: 0.8980 chunk 127 optimal weight: 0.5980 chunk 143 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- 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 = 0.4163 r_free = 0.4163 target = 0.186065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.115899 restraints weight = 59355.883| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.70 r_work: 0.3231 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1458 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= 0.118 Angle : 0.464 4.535 24172 Z= 0.257 Chirality : 0.035 0.130 2704 Planarity : 0.003 0.055 2984 Dihedral : 5.790 59.059 2438 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.69 % Allowed : 12.47 % Favored : 86.84 % 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: 1.59 (0.20), residues: 2124 helix: 2.94 (0.15), residues: 1276 sheet: -1.75 (0.56), residues: 84 loop : -2.10 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 721 TYR 0.008 0.001 TYR D 511 PHE 0.010 0.001 PHE B 649 TRP 0.006 0.001 TRP D 740 HIS 0.002 0.000 HIS C 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (17872) covalent geometry : angle 0.46407 / 0.26 (24172) hydrogen bonds : bond 0.06660 / 4.42 ( 952) hydrogen bonds : angle 3.61841 / 2.59 ( 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 256 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 243 time to evaluate : 0.950 Fit side-chains REVERT: A 331 ARG cc_start: 0.7168 (mtp180) cc_final: 0.6910 (mtp85) REVERT: A 445 MET cc_start: 0.9050 (tpt) cc_final: 0.8515 (tpt) REVERT: A 580 PHE cc_start: 0.8115 (m-10) cc_final: 0.7530 (t80) REVERT: A 743 ARG cc_start: 0.7987 (ptp90) cc_final: 0.7608 (ttp-110) REVERT: D 331 ARG cc_start: 0.7173 (mtp180) cc_final: 0.6915 (mtp85) REVERT: D 445 MET cc_start: 0.9042 (tpt) cc_final: 0.8510 (tpt) REVERT: D 580 PHE cc_start: 0.8107 (m-10) cc_final: 0.7522 (t80) REVERT: D 743 ARG cc_start: 0.7982 (ptp90) cc_final: 0.7599 (ttp-110) REVERT: B 331 ARG cc_start: 0.7172 (mtp180) cc_final: 0.6911 (mtp85) REVERT: B 445 MET cc_start: 0.9044 (tpt) cc_final: 0.8510 (tpt) REVERT: B 580 PHE cc_start: 0.8125 (m-10) cc_final: 0.7536 (t80) REVERT: B 743 ARG cc_start: 0.7994 (ptp90) cc_final: 0.7619 (ttp-110) REVERT: C 331 ARG cc_start: 0.7170 (mtp180) cc_final: 0.6910 (mtp85) REVERT: C 445 MET cc_start: 0.9043 (tpt) cc_final: 0.8511 (tpt) REVERT: C 580 PHE cc_start: 0.8113 (m-10) cc_final: 0.7523 (t80) REVERT: C 743 ARG cc_start: 0.7991 (ptp90) cc_final: 0.7616 (ttp-110) outliers start: 13 outliers final: 5 residues processed: 243 average time/residue: 1.0044 time to fit residues: 281.3748 Evaluate side-chains 238 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 233 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 652 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 13 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 0.0170 overall best weight: 1.3824 ------------------------------------------------------------------------------- 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 = 0.4148 r_free = 0.4148 target = 0.184272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.114321 restraints weight = 59474.708| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.68 r_work: 0.3183 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1654 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= 0.136 Angle : 0.478 4.387 24172 Z= 0.265 Chirality : 0.036 0.130 2704 Planarity : 0.004 0.054 2984 Dihedral : 5.590 55.814 2438 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.17 % Allowed : 12.58 % Favored : 86.25 % 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: 1.57 (0.20), residues: 2124 helix: 2.91 (0.15), residues: 1276 sheet: -1.75 (0.55), residues: 84 loop : -2.10 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 428 TYR 0.007 0.001 TYR B 555 PHE 0.012 0.001 PHE D 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 0.00295 / 0.14 (17872) covalent geometry : angle 0.47754 / 0.26 (24172) hydrogen bonds : bond 0.07321 / 4.85 ( 952) hydrogen bonds : angle 3.62380 / 2.60 ( 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 269 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 247 time to evaluate : 0.996 Fit side-chains REVERT: A 331 ARG cc_start: 0.7197 (mtp180) cc_final: 0.6930 (mtp85) REVERT: A 445 MET cc_start: 0.9027 (tpt) cc_final: 0.8521 (tpt) REVERT: A 580 PHE cc_start: 0.8117 (m-10) cc_final: 0.7541 (t80) REVERT: A 743 ARG cc_start: 0.8001 (ptp90) cc_final: 0.7609 (ttp-110) REVERT: D 331 ARG cc_start: 0.7197 (mtp180) cc_final: 0.6927 (mtp85) REVERT: D 445 MET cc_start: 0.9023 (tpt) cc_final: 0.8519 (tpt) REVERT: D 580 PHE cc_start: 0.8102 (m-10) cc_final: 0.7523 (t80) REVERT: D 600 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7638 (mt-10) REVERT: D 743 ARG cc_start: 0.8002 (ptp90) cc_final: 0.7606 (ttp-110) REVERT: B 331 ARG cc_start: 0.7197 (mtp180) cc_final: 0.6929 (mtp85) REVERT: B 445 MET cc_start: 0.9021 (tpt) cc_final: 0.8519 (tpt) REVERT: B 580 PHE cc_start: 0.8118 (m-10) cc_final: 0.7540 (t80) REVERT: B 743 ARG cc_start: 0.8017 (ptp90) cc_final: 0.7626 (ttp-110) REVERT: C 331 ARG cc_start: 0.7201 (mtp180) cc_final: 0.6934 (mtp85) REVERT: C 445 MET cc_start: 0.9026 (tpt) cc_final: 0.8520 (tpt) REVERT: C 580 PHE cc_start: 0.8118 (m-10) cc_final: 0.7537 (t80) REVERT: C 743 ARG cc_start: 0.8015 (ptp90) cc_final: 0.7619 (ttp-110) outliers start: 22 outliers final: 8 residues processed: 253 average time/residue: 1.0453 time to fit residues: 307.0135 Evaluate side-chains 250 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 242 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 601 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 55 optimal weight: 9.9990 chunk 202 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 203 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4177 r_free = 0.4177 target = 0.187338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.118252 restraints weight = 59406.268| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.66 r_work: 0.3176 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1773 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= 0.111 Angle : 0.451 4.205 24172 Z= 0.247 Chirality : 0.035 0.125 2704 Planarity : 0.003 0.051 2984 Dihedral : 5.209 55.506 2436 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.69 % Allowed : 13.59 % Favored : 85.72 % 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: 1.82 (0.20), residues: 2124 helix: 3.10 (0.15), residues: 1272 sheet: -1.56 (0.55), residues: 84 loop : -1.97 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 428 TYR 0.007 0.001 TYR A 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 0.00226 / 0.11 (17872) covalent geometry : angle 0.45089 / 0.25 (24172) hydrogen bonds : bond 0.06101 / 4.04 ( 952) hydrogen bonds : angle 3.46829 / 2.48 ( 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: 13 poor density : 246 time to evaluate : 0.892 Fit side-chains REVERT: A 331 ARG cc_start: 0.7203 (mtp180) cc_final: 0.6906 (mtp85) REVERT: A 445 MET cc_start: 0.9060 (tpt) cc_final: 0.8621 (tpt) REVERT: A 580 PHE cc_start: 0.8143 (m-10) cc_final: 0.7590 (t80) REVERT: A 601 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7175 (p0) REVERT: A 743 ARG cc_start: 0.8024 (ptp90) cc_final: 0.7555 (ttp-110) REVERT: D 331 ARG cc_start: 0.7201 (mtp180) cc_final: 0.6902 (mtp85) REVERT: D 445 MET cc_start: 0.9062 (tpt) cc_final: 0.8625 (tpt) REVERT: D 580 PHE cc_start: 0.8133 (m-10) cc_final: 0.7575 (t80) REVERT: D 743 ARG cc_start: 0.8016 (ptp90) cc_final: 0.7544 (ttp-110) REVERT: B 331 ARG cc_start: 0.7205 (mtp180) cc_final: 0.6907 (mtp85) REVERT: B 445 MET cc_start: 0.9063 (tpt) cc_final: 0.8623 (tpt) REVERT: B 580 PHE cc_start: 0.8144 (m-10) cc_final: 0.7586 (t80) REVERT: B 743 ARG cc_start: 0.8025 (ptp90) cc_final: 0.7560 (ttp-110) REVERT: C 331 ARG cc_start: 0.7213 (mtp180) cc_final: 0.6918 (mtp85) REVERT: C 445 MET cc_start: 0.9062 (tpt) cc_final: 0.8625 (tpt) REVERT: C 580 PHE cc_start: 0.8141 (m-10) cc_final: 0.7586 (t80) REVERT: C 601 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.7063 (p0) REVERT: C 743 ARG cc_start: 0.8022 (ptp90) cc_final: 0.7554 (ttp-110) outliers start: 13 outliers final: 11 residues processed: 250 average time/residue: 0.9199 time to fit residues: 271.5678 Evaluate side-chains 247 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 234 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 682 MET Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 682 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 601 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 110 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 112 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.4151 r_free = 0.4151 target = 0.184358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114844 restraints weight = 59459.052| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.66 r_work: 0.3189 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1848 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= 0.140 Angle : 0.482 4.267 24172 Z= 0.266 Chirality : 0.036 0.130 2704 Planarity : 0.003 0.053 2984 Dihedral : 5.372 46.710 2436 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.54 % Allowed : 13.59 % Favored : 84.87 % 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: 1.60 (0.20), residues: 2124 helix: 2.88 (0.15), residues: 1284 sheet: -1.58 (0.56), residues: 84 loop : -2.08 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 721 TYR 0.008 0.001 TYR A 453 PHE 0.013 0.001 PHE D 649 TRP 0.006 0.001 TRP C 740 HIS 0.002 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (17872) covalent geometry : angle 0.48176 / 0.27 (24172) hydrogen bonds : bond 0.07391 / 4.90 ( 952) hydrogen bonds : angle 3.59453 / 2.58 ( 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 270 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ARG cc_start: 0.7191 (mtp180) cc_final: 0.6886 (mtp85) REVERT: A 445 MET cc_start: 0.8982 (tpt) cc_final: 0.8584 (tpt) REVERT: A 580 PHE cc_start: 0.8120 (m-10) cc_final: 0.7537 (t80) REVERT: A 743 ARG cc_start: 0.8027 (ptp90) cc_final: 0.7508 (ttp-110) REVERT: A 746 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.5162 (tm-30) REVERT: D 331 ARG cc_start: 0.7187 (mtp180) cc_final: 0.6879 (mtp85) REVERT: D 445 MET cc_start: 0.8979 (tpt) cc_final: 0.8581 (tpt) REVERT: D 580 PHE cc_start: 0.8107 (m-10) cc_final: 0.7516 (t80) REVERT: D 743 ARG cc_start: 0.8020 (ptp90) cc_final: 0.7500 (ttp-110) REVERT: D 746 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.5159 (tm-30) REVERT: B 331 ARG cc_start: 0.7189 (mtp180) cc_final: 0.6883 (mtp85) REVERT: B 445 MET cc_start: 0.8970 (tpt) cc_final: 0.8578 (tpt) REVERT: B 580 PHE cc_start: 0.8120 (m-10) cc_final: 0.7531 (t80) REVERT: B 743 ARG cc_start: 0.8022 (ptp90) cc_final: 0.7505 (ttp-110) REVERT: B 746 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.5176 (tm-30) REVERT: C 331 ARG cc_start: 0.7188 (mtp180) cc_final: 0.6884 (mtp85) REVERT: C 445 MET cc_start: 0.8980 (tpt) cc_final: 0.8584 (tpt) REVERT: C 580 PHE cc_start: 0.8106 (m-10) cc_final: 0.7525 (t80) REVERT: C 601 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7153 (p0) REVERT: C 743 ARG cc_start: 0.8030 (ptp90) cc_final: 0.7509 (ttp-110) outliers start: 29 outliers final: 13 residues processed: 251 average time/residue: 0.9690 time to fit residues: 284.1103 Evaluate side-chains 255 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 238 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 573 ILE 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 570 GLU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 746 GLU 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 570 GLU Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 682 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 161 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 182 optimal weight: 0.0030 chunk 68 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.182619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.114799 restraints weight = 59506.132| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.61 r_work: 0.3203 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1941 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= 0.144 Angle : 0.483 4.292 24172 Z= 0.268 Chirality : 0.036 0.134 2704 Planarity : 0.004 0.055 2984 Dihedral : 5.556 49.550 2436 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.22 % Allowed : 13.85 % Favored : 84.93 % 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: 2.84 (0.15), residues: 1284 sheet: -1.50 (0.56), residues: 84 loop : -2.18 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 721 TYR 0.008 0.001 TYR C 511 PHE 0.013 0.001 PHE B 649 TRP 0.006 0.001 TRP A 740 HIS 0.002 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (17872) covalent geometry : angle 0.48311 / 0.27 (24172) hydrogen bonds : bond 0.07508 / 4.97 ( 952) hydrogen bonds : angle 3.62454 / 2.60 ( 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 269 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 246 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ARG cc_start: 0.7213 (mtp180) cc_final: 0.6901 (mtp85) REVERT: A 445 MET cc_start: 0.9049 (tpt) cc_final: 0.8678 (tpt) REVERT: A 580 PHE cc_start: 0.8141 (m-10) cc_final: 0.7584 (t80) REVERT: A 743 ARG cc_start: 0.8113 (ptp90) cc_final: 0.7619 (ttp-110) REVERT: A 746 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.5205 (tm-30) REVERT: D 331 ARG cc_start: 0.7211 (mtp180) cc_final: 0.6895 (mtp85) REVERT: D 445 MET cc_start: 0.9046 (tpt) cc_final: 0.8677 (tpt) REVERT: D 580 PHE cc_start: 0.8120 (m-10) cc_final: 0.7554 (t80) REVERT: D 743 ARG cc_start: 0.8101 (ptp90) cc_final: 0.7604 (ttp-110) REVERT: D 746 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.5204 (tm-30) REVERT: B 331 ARG cc_start: 0.7214 (mtp180) cc_final: 0.6902 (mtp85) REVERT: B 445 MET cc_start: 0.9042 (tpt) cc_final: 0.8675 (tpt) REVERT: B 580 PHE cc_start: 0.8131 (m-10) cc_final: 0.7564 (t80) REVERT: B 600 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7643 (mt-10) REVERT: B 743 ARG cc_start: 0.8113 (ptp90) cc_final: 0.7622 (ttp-110) REVERT: B 746 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.5217 (tm-30) REVERT: C 331 ARG cc_start: 0.7216 (mtp180) cc_final: 0.6903 (mtp85) REVERT: C 445 MET cc_start: 0.9050 (tpt) cc_final: 0.8678 (tpt) REVERT: C 580 PHE cc_start: 0.8135 (m-10) cc_final: 0.7574 (t80) REVERT: C 743 ARG cc_start: 0.8116 (ptp90) cc_final: 0.7624 (ttp-110) outliers start: 23 outliers final: 13 residues processed: 254 average time/residue: 0.9107 time to fit residues: 272.8551 Evaluate side-chains 255 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 239 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 573 ILE 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 547 MET Chi-restraints excluded: chain B residue 570 GLU 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 573 ILE 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: 1.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 166 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.186763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.117802 restraints weight = 59191.514| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.60 r_work: 0.3248 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17872 Z= 0.112 Angle : 0.459 4.202 24172 Z= 0.252 Chirality : 0.035 0.124 2704 Planarity : 0.003 0.053 2984 Dihedral : 5.343 51.885 2436 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.22 % Allowed : 14.28 % Favored : 84.50 % 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: 1.75 (0.20), residues: 2124 helix: 3.09 (0.15), residues: 1272 sheet: -1.35 (0.56), residues: 84 loop : -2.11 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 428 TYR 0.007 0.001 TYR C 511 PHE 0.009 0.001 PHE A 659 TRP 0.006 0.001 TRP C 740 HIS 0.002 0.000 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (17872) covalent geometry : angle 0.45905 / 0.25 (24172) hydrogen bonds : bond 0.06261 / 4.15 ( 952) hydrogen bonds : angle 3.46334 / 2.48 ( 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 266 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 243 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ARG cc_start: 0.7187 (mtp180) cc_final: 0.6888 (mtp85) REVERT: A 445 MET cc_start: 0.8998 (tpt) cc_final: 0.8591 (tpt) REVERT: A 574 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7441 (tm) REVERT: A 580 PHE cc_start: 0.8118 (m-10) cc_final: 0.7521 (t80) REVERT: A 601 ASP cc_start: 0.7371 (p0) cc_final: 0.7127 (p0) REVERT: A 743 ARG cc_start: 0.8035 (ptp90) cc_final: 0.7571 (ttp-110) REVERT: A 746 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.5109 (tm-30) REVERT: D 331 ARG cc_start: 0.7180 (mtp180) cc_final: 0.6878 (mtp85) REVERT: D 445 MET cc_start: 0.8992 (tpt) cc_final: 0.8586 (tpt) REVERT: D 574 LEU cc_start: 0.7665 (mt) cc_final: 0.7416 (tm) REVERT: D 580 PHE cc_start: 0.8119 (m-10) cc_final: 0.7514 (t80) REVERT: D 743 ARG cc_start: 0.8023 (ptp90) cc_final: 0.7555 (ttp-110) REVERT: D 746 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.5089 (tm-30) REVERT: B 331 ARG cc_start: 0.7188 (mtp180) cc_final: 0.6890 (mtp85) REVERT: B 445 MET cc_start: 0.8986 (tpt) cc_final: 0.8580 (tpt) REVERT: B 574 LEU cc_start: 0.7667 (mt) cc_final: 0.7415 (tm) REVERT: B 580 PHE cc_start: 0.8123 (m-10) cc_final: 0.7517 (t80) REVERT: B 743 ARG cc_start: 0.8036 (ptp90) cc_final: 0.7576 (ttp-110) REVERT: B 746 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.5151 (tm-30) REVERT: C 331 ARG cc_start: 0.7185 (mtp180) cc_final: 0.6887 (mtp85) REVERT: C 445 MET cc_start: 0.8993 (tpt) cc_final: 0.8585 (tpt) REVERT: C 574 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7438 (tm) REVERT: C 580 PHE cc_start: 0.8109 (m-10) cc_final: 0.7515 (t80) REVERT: C 601 ASP cc_start: 0.7287 (p0) cc_final: 0.7082 (p0) REVERT: C 743 ARG cc_start: 0.8040 (ptp90) cc_final: 0.7578 (ttp-110) outliers start: 23 outliers final: 12 residues processed: 252 average time/residue: 0.8916 time to fit residues: 265.1789 Evaluate side-chains 256 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 239 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 574 LEU 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 573 ILE 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 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 574 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 113 optimal weight: 0.0970 chunk 163 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.4165 r_free = 0.4165 target = 0.185745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.116488 restraints weight = 59433.809| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.67 r_work: 0.3214 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2039 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= 0.123 Angle : 0.467 4.144 24172 Z= 0.257 Chirality : 0.035 0.127 2704 Planarity : 0.003 0.053 2984 Dihedral : 5.477 54.983 2436 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.74 % Allowed : 14.65 % Favored : 84.61 % 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: 1.66 (0.20), residues: 2124 helix: 2.99 (0.15), residues: 1280 sheet: -1.41 (0.56), residues: 84 loop : -2.15 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 721 TYR 0.007 0.001 TYR D 511 PHE 0.011 0.001 PHE D 649 TRP 0.006 0.001 TRP D 740 HIS 0.002 0.001 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (17872) covalent geometry : angle 0.46660 / 0.26 (24172) hydrogen bonds : bond 0.06662 / 4.41 ( 952) hydrogen bonds : angle 3.48480 / 2.50 ( 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 254 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 240 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ARG cc_start: 0.7166 (mtp180) cc_final: 0.6863 (mtp85) REVERT: A 445 MET cc_start: 0.8945 (tpt) cc_final: 0.8530 (tpt) REVERT: A 574 LEU cc_start: 0.7683 (mt) cc_final: 0.7452 (tm) REVERT: A 580 PHE cc_start: 0.8106 (m-10) cc_final: 0.7492 (t80) REVERT: A 601 ASP cc_start: 0.7385 (p0) cc_final: 0.7160 (p0) REVERT: A 743 ARG cc_start: 0.8016 (ptp90) cc_final: 0.7532 (ttp-110) REVERT: A 746 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.5012 (tm-30) REVERT: D 331 ARG cc_start: 0.7152 (mtp180) cc_final: 0.6845 (mtp85) REVERT: D 445 MET cc_start: 0.8942 (tpt) cc_final: 0.8527 (tpt) REVERT: D 580 PHE cc_start: 0.8108 (m-10) cc_final: 0.7487 (t80) REVERT: D 743 ARG cc_start: 0.8013 (ptp90) cc_final: 0.7525 (ttp-110) REVERT: D 746 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.5024 (tm-30) REVERT: B 331 ARG cc_start: 0.7164 (mtp180) cc_final: 0.6863 (mtp85) REVERT: B 445 MET cc_start: 0.8933 (tpt) cc_final: 0.8525 (tpt) REVERT: B 580 PHE cc_start: 0.8114 (m-10) cc_final: 0.7495 (t80) REVERT: B 743 ARG cc_start: 0.8025 (ptp90) cc_final: 0.7541 (ttp-110) REVERT: B 746 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.5046 (tm-30) REVERT: C 331 ARG cc_start: 0.7161 (mtp180) cc_final: 0.6860 (mtp85) REVERT: C 445 MET cc_start: 0.8944 (tpt) cc_final: 0.8533 (tpt) REVERT: C 574 LEU cc_start: 0.7679 (mt) cc_final: 0.7447 (tm) REVERT: C 580 PHE cc_start: 0.8098 (m-10) cc_final: 0.7486 (t80) REVERT: C 601 ASP cc_start: 0.7305 (p0) cc_final: 0.7098 (p0) REVERT: C 743 ARG cc_start: 0.8022 (ptp90) cc_final: 0.7540 (ttp-110) outliers start: 14 outliers final: 11 residues processed: 245 average time/residue: 0.9645 time to fit residues: 278.1591 Evaluate side-chains 255 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 241 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 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 547 MET Chi-restraints excluded: chain B residue 570 GLU 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 682 MET 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: 0.8980 chunk 166 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 200 optimal weight: 0.2980 chunk 196 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.4163 r_free = 0.4163 target = 0.185654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.116329 restraints weight = 59491.109| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.67 r_work: 0.3242 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2095 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= 0.124 Angle : 0.469 4.162 24172 Z= 0.257 Chirality : 0.035 0.126 2704 Planarity : 0.003 0.053 2984 Dihedral : 5.573 59.981 2436 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.96 % Allowed : 14.76 % Favored : 84.29 % 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: 1.68 (0.20), residues: 2124 helix: 3.01 (0.15), residues: 1276 sheet: -1.21 (0.58), residues: 84 loop : -2.16 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 575 TYR 0.007 0.001 TYR A 511 PHE 0.011 0.001 PHE B 649 TRP 0.006 0.001 TRP C 740 HIS 0.002 0.000 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (17872) covalent geometry : angle 0.46919 / 0.26 (24172) hydrogen bonds : bond 0.06663 / 4.41 ( 952) hydrogen bonds : angle 3.48517 / 2.50 ( 2772) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12667.74 seconds wall clock time: 214 minutes 41.09 seconds (12881.09 seconds total)