Starting phenix.real_space_refine on Tue Aug 26 08:50:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u3j_41864/08_2025/8u3j_41864_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u3j_41864/08_2025/8u3j_41864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u3j_41864/08_2025/8u3j_41864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u3j_41864/08_2025/8u3j_41864.map" model { file = "/net/cci-nas-00/data/ceres_data/8u3j_41864/08_2025/8u3j_41864_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u3j_41864/08_2025/8u3j_41864_trim.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 100 5.16 5 Na 1 4.78 5 C 11452 2.51 5 N 2804 2.21 5 O 3100 1.98 5 H 17500 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34961 Number of models: 1 Model: "" Number of chains: 6 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: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {' NA': 1, '3PH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "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} Restraints were copied for chains: B, C, D Time building chain proxies: 11.64, per 1000 atoms: 0.33 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: 3.23 Conformation dependent library (CDL) restraints added in 997.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.87 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: 8.38 Time building geometry restraints manager: 4.43 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: 63384 2.82 - 5.65: 292 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 - 27.99: 15972 27.99 - 55.98: 644 55.98 - 83.97: 44 83.97 - 111.96: 16 111.96 - 139.95: 4 Dihedral angle restraints: 16680 sinusoidal: 8864 harmonic: 7816 Sorted by residual: dihedral pdb=" C21 3PH C 801 " pdb=" C2 3PH C 801 " pdb=" O21 3PH C 801 " pdb=" C3 3PH C 801 " ideal model delta sinusoidal sigma weight residual 147.58 -72.47 -139.95 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" C21 3PH B 801 " pdb=" C2 3PH B 801 " pdb=" O21 3PH B 801 " pdb=" C3 3PH B 801 " ideal model delta sinusoidal sigma weight residual 147.58 -72.52 -139.90 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" C21 3PH A 801 " pdb=" C2 3PH A 801 " pdb=" O21 3PH A 801 " pdb=" C3 3PH A 801 " ideal model delta sinusoidal sigma weight residual 147.58 -72.52 -139.90 1 3.00e+01 1.11e-03 1.88e+01 ... (remaining 16677 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: 7.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.220 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 38.580 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 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:9.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 : 14.562 139.945 6528 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 aren 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 covalent geometry : bond 0.00450 (17872) covalent geometry : angle 0.72015 (24172) hydrogen bonds : bond 0.13334 ( 952) hydrogen bonds : angle 4.93057 ( 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 : 0.931 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: 1.0491 time to fit residues: 332.2962 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 : 0.544 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 223 ASN D 202 GLN D 223 ASN B 202 GLN B 223 ASN C 202 GLN C 223 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.186107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.116499 restraints weight = 60128.723| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.66 r_work: 0.3285 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17872 Z= 0.125 Angle : 0.485 4.770 24172 Z= 0.268 Chirality : 0.036 0.131 2704 Planarity : 0.004 0.056 2984 Dihedral : 7.846 119.667 2480 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.53 % Allowed : 8.39 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.20), residues: 2124 helix: 2.79 (0.15), residues: 1280 sheet: -0.79 (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 0.007 0.001 TYR D 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 covalent geometry : bond 0.00256 (17872) covalent geometry : angle 0.48487 (24172) hydrogen bonds : bond 0.07009 ( 952) hydrogen bonds : angle 3.79323 ( 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: 10 poor density : 249 time to evaluate : 1.028 Fit side-chains REVERT: A 445 MET cc_start: 0.9085 (tpt) cc_final: 0.8347 (tpt) REVERT: A 580 PHE cc_start: 0.8101 (m-10) cc_final: 0.7459 (t80) REVERT: A 746 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.5272 (tm-30) REVERT: D 445 MET cc_start: 0.9084 (tpt) cc_final: 0.8342 (tpt) REVERT: D 580 PHE cc_start: 0.8100 (m-10) cc_final: 0.7465 (t80) REVERT: D 746 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.5271 (tm-30) REVERT: B 445 MET cc_start: 0.9087 (tpt) cc_final: 0.8351 (tpt) REVERT: B 580 PHE cc_start: 0.8119 (m-10) cc_final: 0.7474 (t80) REVERT: B 746 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.5273 (tm-30) REVERT: C 445 MET cc_start: 0.9083 (tpt) cc_final: 0.8350 (tpt) REVERT: C 580 PHE cc_start: 0.8108 (m-10) cc_final: 0.7466 (t80) REVERT: C 746 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.5274 (tm-30) outliers start: 10 outliers final: 8 residues processed: 255 average time/residue: 0.9992 time to fit residues: 291.5132 Evaluate side-chains 256 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 244 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 682 MET Chi-restraints excluded: chain C residue 746 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 52 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 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: 8.9990 chunk 158 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.179081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.110055 restraints weight = 60335.369| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.60 r_work: 0.3083 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 17872 Z= 0.275 Angle : 0.614 5.427 24172 Z= 0.344 Chirality : 0.042 0.210 2704 Planarity : 0.005 0.059 2984 Dihedral : 8.437 118.926 2472 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.12 % Allowed : 10.24 % Favored : 87.63 % 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 aren not related in a simple way. whole: 0.87 (0.19), residues: 2124 helix: 2.30 (0.15), residues: 1276 sheet: -1.89 (0.55), residues: 84 loop : -2.29 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 721 TYR 0.015 0.002 TYR C 530 PHE 0.023 0.002 PHE A 649 TRP 0.008 0.001 TRP C 697 HIS 0.003 0.001 HIS D 289 Details of bonding type rmsd covalent geometry : bond 0.00667 (17872) covalent geometry : angle 0.61415 (24172) hydrogen bonds : bond 0.10967 ( 952) hydrogen bonds : angle 4.17690 ( 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 301 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 261 time to evaluate : 0.704 Fit side-chains REVERT: A 331 ARG cc_start: 0.7263 (mtp180) cc_final: 0.7002 (mtp85) REVERT: A 445 MET cc_start: 0.9183 (tpt) cc_final: 0.8707 (tpt) REVERT: A 580 PHE cc_start: 0.8201 (m-10) cc_final: 0.7634 (t80) REVERT: D 331 ARG cc_start: 0.7246 (mtp180) cc_final: 0.6988 (mtp85) REVERT: D 445 MET cc_start: 0.9179 (tpt) cc_final: 0.8702 (tpt) REVERT: D 580 PHE cc_start: 0.8207 (m-10) cc_final: 0.7646 (t80) REVERT: D 653 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.8591 (p90) REVERT: B 331 ARG cc_start: 0.7253 (mtp180) cc_final: 0.6991 (mtp85) REVERT: B 445 MET cc_start: 0.9187 (tpt) cc_final: 0.8713 (tpt) REVERT: B 580 PHE cc_start: 0.8204 (m-10) cc_final: 0.7640 (t80) REVERT: B 653 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.8554 (p90) REVERT: C 331 ARG cc_start: 0.7267 (mtp180) cc_final: 0.7008 (mtp85) REVERT: C 445 MET cc_start: 0.9183 (tpt) cc_final: 0.8708 (tpt) REVERT: C 580 PHE cc_start: 0.8193 (m-10) cc_final: 0.7632 (t80) outliers start: 40 outliers final: 19 residues processed: 276 average time/residue: 1.0576 time to fit residues: 331.4094 Evaluate side-chains 266 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 245 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 653 TYR Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 716 MET Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 653 TYR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 716 MET 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: 1.9990 chunk 122 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.184608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.115662 restraints weight = 59480.591| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.65 r_work: 0.3212 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1598 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= 0.146 Angle : 0.495 4.735 24172 Z= 0.276 Chirality : 0.036 0.134 2704 Planarity : 0.004 0.056 2984 Dihedral : 7.968 112.673 2472 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.49 % Allowed : 12.15 % Favored : 86.36 % 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 aren not related in a simple way. whole: 1.32 (0.20), residues: 2124 helix: 2.73 (0.15), residues: 1272 sheet: -1.69 (0.56), residues: 84 loop : -2.23 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 721 TYR 0.009 0.001 TYR A 511 PHE 0.012 0.001 PHE D 649 TRP 0.007 0.001 TRP B 740 HIS 0.002 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00315 (17872) covalent geometry : angle 0.49514 (24172) hydrogen bonds : bond 0.07811 ( 952) hydrogen bonds : angle 3.77613 ( 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 288 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 260 time to evaluate : 0.923 Fit side-chains REVERT: A 331 ARG cc_start: 0.7219 (mtp180) cc_final: 0.6960 (mtp85) REVERT: A 445 MET cc_start: 0.9049 (tpt) cc_final: 0.8654 (tpt) REVERT: A 580 PHE cc_start: 0.8140 (m-10) cc_final: 0.7564 (t80) REVERT: A 743 ARG cc_start: 0.8036 (ptp90) cc_final: 0.7646 (ttp-110) REVERT: D 331 ARG cc_start: 0.7200 (mtp180) cc_final: 0.6941 (mtp85) REVERT: D 445 MET cc_start: 0.9048 (tpt) cc_final: 0.8652 (tpt) REVERT: D 580 PHE cc_start: 0.8129 (m-10) cc_final: 0.7553 (t80) REVERT: D 743 ARG cc_start: 0.8031 (ptp90) cc_final: 0.7638 (ttp-110) REVERT: B 331 ARG cc_start: 0.7239 (mtp180) cc_final: 0.6982 (mtp85) REVERT: B 445 MET cc_start: 0.9045 (tpt) cc_final: 0.8653 (tpt) REVERT: B 580 PHE cc_start: 0.8149 (m-10) cc_final: 0.7567 (t80) REVERT: B 743 ARG cc_start: 0.8033 (ptp90) cc_final: 0.7644 (ttp-110) REVERT: C 331 ARG cc_start: 0.7240 (mtp180) cc_final: 0.6982 (mtp85) REVERT: C 445 MET cc_start: 0.9054 (tpt) cc_final: 0.8659 (tpt) REVERT: C 580 PHE cc_start: 0.8139 (m-10) cc_final: 0.7554 (t80) REVERT: C 743 ARG cc_start: 0.8060 (ptp90) cc_final: 0.7665 (ttp-110) outliers start: 28 outliers final: 7 residues processed: 268 average time/residue: 1.0444 time to fit residues: 319.9024 Evaluate side-chains 257 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 250 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 570 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 13 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 184 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 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: 1.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.183569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.114241 restraints weight = 59569.458| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.65 r_work: 0.3126 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17872 Z= 0.156 Angle : 0.502 4.610 24172 Z= 0.280 Chirality : 0.036 0.134 2704 Planarity : 0.004 0.055 2984 Dihedral : 7.451 108.326 2472 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.96 % Allowed : 12.31 % 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 aren not related in a simple way. whole: 1.33 (0.19), residues: 2124 helix: 2.73 (0.15), residues: 1276 sheet: -1.62 (0.57), residues: 84 loop : -2.27 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 721 TYR 0.009 0.001 TYR A 511 PHE 0.014 0.001 PHE A 649 TRP 0.007 0.001 TRP C 740 HIS 0.002 0.001 HIS D 289 Details of bonding type rmsd covalent geometry : bond 0.00346 (17872) covalent geometry : angle 0.50222 (24172) hydrogen bonds : bond 0.08154 ( 952) hydrogen bonds : angle 3.75269 ( 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 288 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 251 time to evaluate : 0.624 Fit side-chains REVERT: A 331 ARG cc_start: 0.7252 (mtp180) cc_final: 0.6956 (mtp85) REVERT: A 445 MET cc_start: 0.9087 (tpt) cc_final: 0.8733 (tpt) REVERT: A 580 PHE cc_start: 0.8170 (m-10) cc_final: 0.7611 (t80) REVERT: A 636 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8595 (tp30) REVERT: A 743 ARG cc_start: 0.8134 (ptp90) cc_final: 0.7751 (ttp-110) REVERT: D 331 ARG cc_start: 0.7244 (mtp180) cc_final: 0.6945 (mtp85) REVERT: D 445 MET cc_start: 0.9081 (tpt) cc_final: 0.8729 (tpt) REVERT: D 580 PHE cc_start: 0.8165 (m-10) cc_final: 0.7602 (t80) REVERT: D 743 ARG cc_start: 0.8130 (ptp90) cc_final: 0.7744 (ttp-110) REVERT: B 331 ARG cc_start: 0.7268 (mtp180) cc_final: 0.6974 (mtp85) REVERT: B 445 MET cc_start: 0.9080 (tpt) cc_final: 0.8728 (tpt) REVERT: B 580 PHE cc_start: 0.8171 (m-10) cc_final: 0.7607 (t80) REVERT: B 743 ARG cc_start: 0.8129 (ptp90) cc_final: 0.7746 (ttp-110) REVERT: C 331 ARG cc_start: 0.7251 (mtp180) cc_final: 0.6955 (mtp85) REVERT: C 445 MET cc_start: 0.9089 (tpt) cc_final: 0.8731 (tpt) REVERT: C 580 PHE cc_start: 0.8167 (m-10) cc_final: 0.7607 (t80) REVERT: C 636 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8626 (tp30) REVERT: C 743 ARG cc_start: 0.8131 (ptp90) cc_final: 0.7751 (ttp-110) outliers start: 37 outliers final: 21 residues processed: 270 average time/residue: 0.9536 time to fit residues: 295.2959 Evaluate side-chains 272 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 251 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE 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 682 MET Chi-restraints excluded: chain D residue 277 ILE 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 682 MET Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 394 SER 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 277 ILE Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 682 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 55 optimal weight: 9.9990 chunk 202 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 0.0060 chunk 203 optimal weight: 0.9980 chunk 47 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 overall best weight: 0.5974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.188663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.119832 restraints weight = 59427.369| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.71 r_work: 0.3283 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1908 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= 0.105 Angle : 0.447 4.480 24172 Z= 0.245 Chirality : 0.034 0.127 2704 Planarity : 0.003 0.052 2984 Dihedral : 6.806 105.690 2472 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.64 % Allowed : 13.64 % 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 aren not related in a simple way. whole: 1.81 (0.20), residues: 2124 helix: 3.18 (0.15), residues: 1264 sheet: -1.48 (0.55), residues: 84 loop : -2.08 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 500 TYR 0.007 0.001 TYR B 511 PHE 0.007 0.001 PHE D 659 TRP 0.006 0.001 TRP C 740 HIS 0.002 0.000 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00207 (17872) covalent geometry : angle 0.44738 (24172) hydrogen bonds : bond 0.05516 ( 952) hydrogen bonds : angle 3.42370 ( 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 257 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 245 time to evaluate : 0.929 Fit side-chains REVERT: A 331 ARG cc_start: 0.7185 (mtp180) cc_final: 0.6875 (mtp85) REVERT: A 445 MET cc_start: 0.8984 (tpt) cc_final: 0.8586 (tpt) REVERT: A 580 PHE cc_start: 0.8063 (m-10) cc_final: 0.7520 (t80) REVERT: A 636 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8480 (tp30) REVERT: A 743 ARG cc_start: 0.7974 (ptp90) cc_final: 0.7491 (ttp-110) REVERT: D 331 ARG cc_start: 0.7184 (mtp180) cc_final: 0.6873 (mtp85) REVERT: D 445 MET cc_start: 0.8982 (tpt) cc_final: 0.8579 (tpt) REVERT: D 580 PHE cc_start: 0.8051 (m-10) cc_final: 0.7510 (t80) REVERT: D 743 ARG cc_start: 0.7972 (ptp90) cc_final: 0.7488 (ttp-110) REVERT: B 331 ARG cc_start: 0.7188 (mtp180) cc_final: 0.6880 (mtp85) REVERT: B 445 MET cc_start: 0.8976 (tpt) cc_final: 0.8578 (tpt) REVERT: B 580 PHE cc_start: 0.8060 (m-10) cc_final: 0.7515 (t80) REVERT: B 743 ARG cc_start: 0.7977 (ptp90) cc_final: 0.7496 (ttp-110) REVERT: C 331 ARG cc_start: 0.7191 (mtp180) cc_final: 0.6885 (mtp85) REVERT: C 445 MET cc_start: 0.8992 (tpt) cc_final: 0.8588 (tpt) REVERT: C 580 PHE cc_start: 0.8062 (m-10) cc_final: 0.7528 (t80) REVERT: C 636 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8474 (tp30) REVERT: C 743 ARG cc_start: 0.7977 (ptp90) cc_final: 0.7493 (ttp-110) outliers start: 12 outliers final: 13 residues processed: 249 average time/residue: 1.0121 time to fit residues: 291.7281 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 : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain D residue 277 ILE 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 B residue 547 MET Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 573 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 110 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 162 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 ASN D 676 ASN B 676 ASN C 676 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.180063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111397 restraints weight = 59516.241| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.61 r_work: 0.3115 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.004 0.024 17872 Z= 0.180 Angle : 0.519 4.512 24172 Z= 0.289 Chirality : 0.037 0.134 2704 Planarity : 0.004 0.053 2984 Dihedral : 7.304 103.548 2472 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.43 % Allowed : 13.85 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.19), residues: 2124 helix: 2.74 (0.15), residues: 1280 sheet: -1.56 (0.56), residues: 84 loop : -2.20 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 721 TYR 0.010 0.001 TYR A 453 PHE 0.017 0.002 PHE C 649 TRP 0.006 0.001 TRP C 740 HIS 0.002 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00414 (17872) covalent geometry : angle 0.51947 (24172) hydrogen bonds : bond 0.08560 ( 952) hydrogen bonds : angle 3.74256 ( 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 298 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 271 time to evaluate : 0.973 Fit side-chains REVERT: A 331 ARG cc_start: 0.7220 (mtp180) cc_final: 0.6899 (mtp85) REVERT: A 445 MET cc_start: 0.9099 (tpt) cc_final: 0.8778 (tpt) REVERT: A 580 PHE cc_start: 0.8145 (m-10) cc_final: 0.7600 (t80) REVERT: A 743 ARG cc_start: 0.8180 (ptp90) cc_final: 0.7664 (ttp-110) REVERT: A 746 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.5308 (tm-30) REVERT: D 331 ARG cc_start: 0.7218 (mtp180) cc_final: 0.6894 (mtp85) REVERT: D 445 MET cc_start: 0.9093 (tpt) cc_final: 0.8774 (tpt) REVERT: D 580 PHE cc_start: 0.8146 (m-10) cc_final: 0.7593 (t80) REVERT: D 743 ARG cc_start: 0.8176 (ptp90) cc_final: 0.7661 (ttp-110) REVERT: D 746 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.5327 (tm-30) REVERT: B 331 ARG cc_start: 0.7221 (mtp180) cc_final: 0.6903 (mtp85) REVERT: B 445 MET cc_start: 0.9098 (tpt) cc_final: 0.8780 (tpt) REVERT: B 547 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8494 (ttp) REVERT: B 580 PHE cc_start: 0.8150 (m-10) cc_final: 0.7604 (t80) REVERT: B 743 ARG cc_start: 0.8170 (ptp90) cc_final: 0.7660 (ttp-110) REVERT: B 746 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.5289 (tm-30) REVERT: C 331 ARG cc_start: 0.7221 (mtp180) cc_final: 0.6899 (mtp85) REVERT: C 445 MET cc_start: 0.9097 (tpt) cc_final: 0.8776 (tpt) REVERT: C 580 PHE cc_start: 0.8154 (m-10) cc_final: 0.7607 (t80) REVERT: C 743 ARG cc_start: 0.8185 (ptp90) cc_final: 0.7674 (ttp-110) REVERT: C 746 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.5308 (tm-30) outliers start: 27 outliers final: 12 residues processed: 279 average time/residue: 1.2006 time to fit residues: 381.6255 Evaluate side-chains 268 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 251 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE 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 746 GLU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain B residue 277 ILE 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 547 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 746 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 161 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.185074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.116148 restraints weight = 59321.916| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.66 r_work: 0.3210 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2080 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= 0.131 Angle : 0.486 5.069 24172 Z= 0.266 Chirality : 0.036 0.132 2704 Planarity : 0.003 0.053 2984 Dihedral : 7.036 102.267 2472 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.75 % Allowed : 14.01 % Favored : 84.24 % 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 aren not related in a simple way. whole: 1.51 (0.20), residues: 2124 helix: 2.88 (0.15), residues: 1276 sheet: -1.49 (0.56), residues: 84 loop : -2.21 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 721 TYR 0.009 0.001 TYR D 511 PHE 0.011 0.001 PHE B 649 TRP 0.007 0.001 TRP B 740 HIS 0.002 0.000 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00280 (17872) covalent geometry : angle 0.48609 (24172) hydrogen bonds : bond 0.07150 ( 952) hydrogen bonds : angle 3.60530 ( 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 290 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 257 time to evaluate : 0.992 Fit side-chains REVERT: A 331 ARG cc_start: 0.7170 (mtp180) cc_final: 0.6857 (mtp85) REVERT: A 445 MET cc_start: 0.8929 (tpt) cc_final: 0.8587 (tpt) REVERT: A 580 PHE cc_start: 0.8089 (m-10) cc_final: 0.7512 (t80) REVERT: A 601 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7192 (p0) REVERT: A 636 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8519 (tp30) REVERT: A 743 ARG cc_start: 0.8006 (ptp90) cc_final: 0.7507 (ttp-110) REVERT: A 746 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.5112 (tm-30) REVERT: D 331 ARG cc_start: 0.7162 (mtp180) cc_final: 0.6829 (mtp85) REVERT: D 445 MET cc_start: 0.8925 (tpt) cc_final: 0.8585 (tpt) REVERT: D 580 PHE cc_start: 0.8077 (m-10) cc_final: 0.7502 (t80) REVERT: D 601 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7174 (p0) REVERT: D 636 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8530 (tp30) REVERT: D 743 ARG cc_start: 0.7999 (ptp90) cc_final: 0.7496 (ttp-110) REVERT: D 746 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.5122 (tm-30) REVERT: B 331 ARG cc_start: 0.7173 (mtp180) cc_final: 0.6847 (mtp85) REVERT: B 445 MET cc_start: 0.8928 (tpt) cc_final: 0.8586 (tpt) REVERT: B 580 PHE cc_start: 0.8097 (m-10) cc_final: 0.7517 (t80) REVERT: B 601 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7175 (p0) REVERT: B 636 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8524 (tp30) REVERT: B 743 ARG cc_start: 0.8006 (ptp90) cc_final: 0.7505 (ttp-110) REVERT: B 746 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.5115 (tm-30) REVERT: C 331 ARG cc_start: 0.7172 (mtp180) cc_final: 0.6844 (mtp85) REVERT: C 445 MET cc_start: 0.8944 (tpt) cc_final: 0.8599 (tpt) REVERT: C 580 PHE cc_start: 0.8101 (m-10) cc_final: 0.7523 (t80) REVERT: C 601 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.7143 (p0) REVERT: C 636 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8373 (tp30) REVERT: C 743 ARG cc_start: 0.8018 (ptp90) cc_final: 0.7517 (ttp-110) REVERT: C 746 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.5132 (tm-30) outliers start: 33 outliers final: 12 residues processed: 270 average time/residue: 1.1305 time to fit residues: 351.9045 Evaluate side-chains 272 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 252 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 601 ASP Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 277 ILE 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 601 ASP Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 746 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 191 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 93 optimal weight: 0.0970 chunk 1 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.185509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.116229 restraints weight = 59208.852| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.68 r_work: 0.3201 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2150 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= 0.128 Angle : 0.481 4.858 24172 Z= 0.263 Chirality : 0.035 0.128 2704 Planarity : 0.003 0.053 2984 Dihedral : 6.987 100.119 2472 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.59 % Allowed : 13.96 % Favored : 84.45 % 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 aren not related in a simple way. whole: 1.53 (0.20), residues: 2124 helix: 2.91 (0.15), residues: 1276 sheet: -1.41 (0.57), residues: 84 loop : -2.22 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 428 TYR 0.008 0.001 TYR B 511 PHE 0.011 0.001 PHE B 649 TRP 0.006 0.001 TRP C 740 HIS 0.002 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00270 (17872) covalent geometry : angle 0.48148 (24172) hydrogen bonds : bond 0.06957 ( 952) hydrogen bonds : angle 3.55496 ( 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 284 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 254 time to evaluate : 0.983 Fit side-chains REVERT: A 331 ARG cc_start: 0.7184 (mtp180) cc_final: 0.6847 (mtp85) REVERT: A 445 MET cc_start: 0.9017 (tpt) cc_final: 0.8666 (tpt) REVERT: A 580 PHE cc_start: 0.8119 (m-10) cc_final: 0.7564 (t80) REVERT: A 601 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7240 (p0) REVERT: A 636 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8565 (tp30) REVERT: A 743 ARG cc_start: 0.8069 (ptp90) cc_final: 0.7593 (ttp-110) REVERT: A 746 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.5181 (tm-30) REVERT: D 445 MET cc_start: 0.9014 (tpt) cc_final: 0.8667 (tpt) REVERT: D 580 PHE cc_start: 0.8119 (m-10) cc_final: 0.7560 (t80) REVERT: D 601 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.7219 (p0) REVERT: D 636 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8569 (tp30) REVERT: D 743 ARG cc_start: 0.8063 (ptp90) cc_final: 0.7587 (ttp-110) REVERT: D 746 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.5194 (tm-30) REVERT: B 445 MET cc_start: 0.9013 (tpt) cc_final: 0.8665 (tpt) REVERT: B 580 PHE cc_start: 0.8126 (m-10) cc_final: 0.7569 (t80) REVERT: B 601 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7232 (p0) REVERT: B 636 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8559 (tp30) REVERT: B 743 ARG cc_start: 0.8075 (ptp90) cc_final: 0.7603 (ttp-110) REVERT: B 746 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.5189 (tm-30) REVERT: C 331 ARG cc_start: 0.7183 (mtp180) cc_final: 0.6850 (mtp85) REVERT: C 445 MET cc_start: 0.9024 (tpt) cc_final: 0.8673 (tpt) REVERT: C 580 PHE cc_start: 0.8115 (m-10) cc_final: 0.7564 (t80) REVERT: C 601 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7179 (p0) REVERT: C 636 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8417 (tp30) REVERT: C 743 ARG cc_start: 0.8077 (ptp90) cc_final: 0.7605 (ttp-110) REVERT: C 746 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.5197 (tm-30) outliers start: 30 outliers final: 22 residues processed: 268 average time/residue: 1.1443 time to fit residues: 352.0804 Evaluate side-chains 285 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 255 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 500 ARG Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 500 ARG Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 746 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 113 optimal weight: 0.5980 chunk 163 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 178 optimal weight: 0.3980 chunk 45 optimal weight: 0.2980 chunk 115 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.185630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.118457 restraints weight = 59503.117| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.63 r_work: 0.3193 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17872 Z= 0.111 Angle : 0.465 4.726 24172 Z= 0.251 Chirality : 0.035 0.126 2704 Planarity : 0.003 0.052 2984 Dihedral : 6.795 97.989 2472 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.27 % Allowed : 14.70 % Favored : 84.02 % 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 aren not related in a simple way. whole: 1.67 (0.20), residues: 2124 helix: 3.03 (0.15), residues: 1272 sheet: -1.28 (0.58), residues: 84 loop : -2.18 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 428 TYR 0.007 0.001 TYR A 511 PHE 0.009 0.001 PHE B 659 TRP 0.006 0.001 TRP C 740 HIS 0.002 0.000 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00229 (17872) covalent geometry : angle 0.46461 (24172) hydrogen bonds : bond 0.06025 ( 952) hydrogen bonds : angle 3.43178 ( 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 289 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 265 time to evaluate : 0.847 Fit side-chains REVERT: A 445 MET cc_start: 0.8987 (tpt) cc_final: 0.8621 (tpt) REVERT: A 580 PHE cc_start: 0.8120 (m-10) cc_final: 0.7558 (t80) REVERT: A 601 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.7088 (p0) REVERT: A 636 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8554 (tp30) REVERT: A 743 ARG cc_start: 0.8037 (ptp90) cc_final: 0.7588 (ttp-110) REVERT: A 746 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.5073 (tm-30) REVERT: D 445 MET cc_start: 0.8985 (tpt) cc_final: 0.8616 (tpt) REVERT: D 580 PHE cc_start: 0.8124 (m-10) cc_final: 0.7554 (t80) REVERT: D 601 ASP cc_start: 0.7323 (OUTLIER) cc_final: 0.7059 (p0) REVERT: D 636 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8561 (tp30) REVERT: D 743 ARG cc_start: 0.8026 (ptp90) cc_final: 0.7579 (ttp-110) REVERT: D 746 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.5074 (tm-30) REVERT: B 445 MET cc_start: 0.8987 (tpt) cc_final: 0.8619 (tpt) REVERT: B 580 PHE cc_start: 0.8128 (m-10) cc_final: 0.7558 (t80) REVERT: B 601 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.7074 (p0) REVERT: B 636 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8559 (tp30) REVERT: B 743 ARG cc_start: 0.8041 (ptp90) cc_final: 0.7595 (ttp-110) REVERT: B 746 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.5074 (tm-30) REVERT: C 445 MET cc_start: 0.8988 (tpt) cc_final: 0.8617 (tpt) REVERT: C 580 PHE cc_start: 0.8117 (m-10) cc_final: 0.7554 (t80) REVERT: C 601 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.7035 (p0) REVERT: C 636 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8531 (tp30) REVERT: C 743 ARG cc_start: 0.8049 (ptp90) cc_final: 0.7603 (ttp-110) REVERT: C 746 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.5092 (tm-30) outliers start: 24 outliers final: 16 residues processed: 275 average time/residue: 1.0923 time to fit residues: 344.9595 Evaluate side-chains 275 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 251 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 500 ARG 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 601 ASP Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 500 ARG Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 746 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 101 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 196 optimal weight: 0.5980 chunk 169 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.186890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.117899 restraints weight = 59473.515| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.67 r_work: 0.3178 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17872 Z= 0.120 Angle : 0.474 4.650 24172 Z= 0.257 Chirality : 0.035 0.125 2704 Planarity : 0.003 0.052 2984 Dihedral : 6.850 96.870 2472 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.27 % Allowed : 14.76 % Favored : 83.97 % 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 aren not related in a simple way. whole: 1.60 (0.20), residues: 2124 helix: 2.95 (0.15), residues: 1280 sheet: -1.25 (0.58), residues: 84 loop : -2.24 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 428 TYR 0.006 0.001 TYR B 511 PHE 0.010 0.001 PHE C 649 TRP 0.006 0.001 TRP C 740 HIS 0.002 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00255 (17872) covalent geometry : angle 0.47438 (24172) hydrogen bonds : bond 0.06484 ( 952) hydrogen bonds : angle 3.45691 ( 2772) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12555.35 seconds wall clock time: 212 minutes 46.90 seconds (12766.90 seconds total)