Starting phenix.real_space_refine on Fri Mar 6 04:32:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q5p_13843/03_2026/7q5p_13843.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q5p_13843/03_2026/7q5p_13843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7q5p_13843/03_2026/7q5p_13843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q5p_13843/03_2026/7q5p_13843.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q5p_13843/03_2026/7q5p_13843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q5p_13843/03_2026/7q5p_13843.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 9276 2.51 5 N 2691 2.21 5 O 2853 1.98 5 H 14244 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29112 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 9704 Classifications: {'peptide': 627} Link IDs: {'PTRANS': 28, 'TRANS': 598} Chain breaks: 1 Restraints were copied for chains: B, C Time building chain proxies: 12.49, per 1000 atoms: 0.43 Number of scatterers: 29112 At special positions: 0 Unit cell: (90.2, 94.6, 184.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 O 2853 8.00 N 2691 7.00 C 9276 6.00 H 14244 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 780.2 milliseconds 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3426 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 22 sheets defined 14.8% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.689A pdb=" N LEU A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 151 through 163 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 264 through 283 removed outlier: 4.375A pdb=" N HIS A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 625 through 635 Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.689A pdb=" N LEU B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 86 Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 114 through 125 Processing helix chain 'B' and resid 151 through 163 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 264 through 283 removed outlier: 4.374A pdb=" N HIS B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 279 " --> pdb=" O ARG B 275 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 459 through 464 Processing helix chain 'B' and resid 625 through 635 Processing helix chain 'B' and resid 636 through 638 No H-bonds generated for 'chain 'B' and resid 636 through 638' Processing helix chain 'C' and resid 47 through 52 removed outlier: 3.689A pdb=" N LEU C 51 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 86 Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 114 through 125 Processing helix chain 'C' and resid 151 through 163 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 264 through 283 removed outlier: 4.374A pdb=" N HIS C 270 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU C 279 " --> pdb=" O ARG C 275 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 459 through 464 Processing helix chain 'C' and resid 625 through 635 Processing helix chain 'C' and resid 636 through 638 No H-bonds generated for 'chain 'C' and resid 636 through 638' Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 10 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 8 through 10 current: chain 'A' and resid 31 through 41 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 31 through 41 current: chain 'A' and resid 67 through 69 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 67 through 69 current: chain 'A' and resid 87 through 89 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 87 through 89 current: chain 'A' and resid 284 through 290 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 290 current: chain 'A' and resid 314 through 325 removed outlier: 5.338A pdb=" N ILE A 317 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 347 " --> pdb=" O ILE A 317 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 339 through 348 current: chain 'B' and resid 31 through 41 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 31 through 41 current: chain 'B' and resid 67 through 69 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 67 through 69 current: chain 'B' and resid 87 through 89 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 87 through 89 current: chain 'B' and resid 284 through 290 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 284 through 290 current: chain 'B' and resid 314 through 325 removed outlier: 5.337A pdb=" N ILE B 317 " --> pdb=" O ILE B 347 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 347 " --> pdb=" O ILE B 317 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 339 through 348 current: chain 'C' and resid 31 through 41 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 31 through 41 current: chain 'C' and resid 67 through 69 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 67 through 69 current: chain 'C' and resid 87 through 89 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 87 through 89 current: chain 'C' and resid 284 through 290 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 290 current: chain 'C' and resid 314 through 325 removed outlier: 5.337A pdb=" N ILE C 317 " --> pdb=" O ILE C 347 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE C 347 " --> pdb=" O ILE C 317 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 113 removed outlier: 7.635A pdb=" N ASP A 105 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG A 148 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLU A 142 " --> pdb=" O ASN A 111 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N SER A 113 " --> pdb=" O GLU A 140 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLU A 140 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 132 removed outlier: 6.809A pdb=" N GLU A 131 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 243 removed outlier: 6.292A pdb=" N SER A 223 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ASP A 257 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLU A 225 " --> pdb=" O ASP A 257 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ASN A 227 " --> pdb=" O PRO A 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 392 removed outlier: 4.308A pdb=" N LYS A 389 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU A 430 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N SER A 434 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE A 445 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 466 through 467 removed outlier: 5.724A pdb=" N LEU A 496 " --> pdb=" O ASP C 505 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL C 507 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE A 498 " --> pdb=" O VAL C 507 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 503 through 508 Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 516 removed outlier: 3.629A pdb=" N ASN C 521 " --> pdb=" O GLU A 512 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS A 535 " --> pdb=" O GLU B 528 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N VAL B 530 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR A 537 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE B 532 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE A 539 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LYS B 551 " --> pdb=" O ASP C 544 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU C 546 " --> pdb=" O LYS B 551 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU B 553 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL C 548 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER B 555 " --> pdb=" O VAL C 548 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TYR A 560 " --> pdb=" O ARG C 569 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL C 571 " --> pdb=" O TYR A 560 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN C 584 " --> pdb=" O ASN C 580 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN B 591 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 512 through 516 removed outlier: 6.054A pdb=" N ASN A 521 " --> pdb=" O HIS B 514 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL B 516 " --> pdb=" O ASN A 521 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER A 523 " --> pdb=" O VAL B 516 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG A 520 " --> pdb=" O TYR C 529 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N THR C 531 " --> pdb=" O ARG A 520 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS A 522 " --> pdb=" O THR C 531 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS B 535 " --> pdb=" O GLU C 528 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N VAL C 530 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N THR B 537 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE C 532 " --> pdb=" O THR B 537 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE B 539 " --> pdb=" O ILE C 532 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 543 " --> pdb=" O ARG B 536 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ARG B 538 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU A 545 " --> pdb=" O ARG B 538 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VAL B 540 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG A 547 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN A 584 " --> pdb=" O ASN A 580 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 591 through 592 removed outlier: 6.421A pdb=" N ASN A 591 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN B 584 " --> pdb=" O ASN B 580 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS A 552 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LYS A 551 " --> pdb=" O ASP B 544 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LEU B 546 " --> pdb=" O LYS A 551 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU A 553 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL B 548 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N SER A 555 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL B 543 " --> pdb=" O ARG C 536 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ARG C 538 " --> pdb=" O VAL B 543 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLU B 545 " --> pdb=" O ARG C 538 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N VAL C 540 " --> pdb=" O GLU B 545 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG B 547 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ASN B 521 " --> pdb=" O HIS C 514 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL C 516 " --> pdb=" O ASN B 521 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER B 523 " --> pdb=" O VAL C 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 601 through 602 removed outlier: 3.788A pdb=" N ILE A 602 " --> pdb=" O HIS C 609 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 609 through 610 removed outlier: 6.621A pdb=" N HIS A 609 " --> pdb=" O ILE B 602 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 104 through 113 removed outlier: 7.636A pdb=" N ASP B 105 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG B 148 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLU B 142 " --> pdb=" O ASN B 111 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N SER B 113 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLU B 140 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 130 through 132 removed outlier: 6.808A pdb=" N GLU B 131 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.292A pdb=" N SER B 223 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ASP B 257 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLU B 225 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ASN B 227 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 389 through 392 removed outlier: 4.308A pdb=" N LYS B 389 " --> pdb=" O VAL B 373 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU B 430 " --> pdb=" O VAL B 449 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER B 434 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE B 445 " --> pdb=" O SER B 434 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 503 through 508 Processing sheet with id=AB9, first strand: chain 'B' and resid 609 through 610 removed outlier: 6.651A pdb=" N HIS B 609 " --> pdb=" O ILE C 602 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 104 through 113 removed outlier: 7.635A pdb=" N ASP C 105 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG C 148 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU C 142 " --> pdb=" O ASN C 111 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N SER C 113 " --> pdb=" O GLU C 140 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLU C 140 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 130 through 132 removed outlier: 6.809A pdb=" N GLU C 131 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 240 through 243 removed outlier: 6.293A pdb=" N SER C 223 " --> pdb=" O LEU C 255 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ASP C 257 " --> pdb=" O SER C 223 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLU C 225 " --> pdb=" O ASP C 257 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ASN C 227 " --> pdb=" O PRO C 259 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 389 through 392 removed outlier: 4.308A pdb=" N LYS C 389 " --> pdb=" O VAL C 373 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU C 430 " --> pdb=" O VAL C 449 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER C 434 " --> pdb=" O ILE C 445 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE C 445 " --> pdb=" O SER C 434 " (cutoff:3.500A) 349 hydrogen bonds defined for protein. 888 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: 6.88 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 14220 1.03 - 1.22: 24 1.22 - 1.42: 6687 1.42 - 1.61: 8445 1.61 - 1.81: 72 Bond restraints: 29448 Sorted by residual: bond pdb=" N LEU A 6 " pdb=" H LEU A 6 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.81e+00 bond pdb=" N LEU C 6 " pdb=" H LEU C 6 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.56e+00 bond pdb=" N LEU B 6 " pdb=" H LEU B 6 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.55e+00 bond pdb=" N ARG A 5 " pdb=" CA ARG A 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N ARG C 5 " pdb=" CA ARG C 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 ... (remaining 29443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.95: 52832 5.95 - 11.89: 7 11.89 - 17.84: 0 17.84 - 23.78: 6 23.78 - 29.73: 12 Bond angle restraints: 52857 Sorted by residual: angle pdb=" CG1 ILE A 562 " pdb=" CD1 ILE A 562 " pdb="HD12 ILE A 562 " ideal model delta sigma weight residual 109.00 79.27 29.73 3.00e+00 1.11e-01 9.82e+01 angle pdb=" CG1 ILE C 562 " pdb=" CD1 ILE C 562 " pdb="HD12 ILE C 562 " ideal model delta sigma weight residual 109.00 79.28 29.72 3.00e+00 1.11e-01 9.81e+01 angle pdb=" CG1 ILE B 562 " pdb=" CD1 ILE B 562 " pdb="HD12 ILE B 562 " ideal model delta sigma weight residual 109.00 79.34 29.66 3.00e+00 1.11e-01 9.78e+01 angle pdb=" CG1 ILE C 562 " pdb=" CD1 ILE C 562 " pdb="HD13 ILE C 562 " ideal model delta sigma weight residual 109.00 79.66 29.34 3.00e+00 1.11e-01 9.57e+01 angle pdb=" CG1 ILE A 562 " pdb=" CD1 ILE A 562 " pdb="HD13 ILE A 562 " ideal model delta sigma weight residual 109.00 79.66 29.34 3.00e+00 1.11e-01 9.56e+01 ... (remaining 52852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 12460 17.87 - 35.74: 884 35.74 - 53.60: 319 53.60 - 71.47: 242 71.47 - 89.34: 30 Dihedral angle restraints: 13935 sinusoidal: 7572 harmonic: 6363 Sorted by residual: dihedral pdb=" CA TYR A 258 " pdb=" C TYR A 258 " pdb=" N PRO A 259 " pdb=" CA PRO A 259 " ideal model delta harmonic sigma weight residual -180.00 -149.92 -30.08 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA TYR C 258 " pdb=" C TYR C 258 " pdb=" N PRO C 259 " pdb=" CA PRO C 259 " ideal model delta harmonic sigma weight residual 180.00 -149.92 -30.08 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA TYR B 258 " pdb=" C TYR B 258 " pdb=" N PRO B 259 " pdb=" CA PRO B 259 " ideal model delta harmonic sigma weight residual -180.00 -149.96 -30.04 0 5.00e+00 4.00e-02 3.61e+01 ... (remaining 13932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1315 0.038 - 0.076: 619 0.076 - 0.114: 200 0.114 - 0.153: 20 0.153 - 0.191: 6 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA HIS B 609 " pdb=" N HIS B 609 " pdb=" C HIS B 609 " pdb=" CB HIS B 609 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.09e-01 chirality pdb=" CA HIS A 609 " pdb=" N HIS A 609 " pdb=" C HIS A 609 " pdb=" CB HIS A 609 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.93e-01 chirality pdb=" CA HIS C 609 " pdb=" N HIS C 609 " pdb=" C HIS C 609 " pdb=" CB HIS C 609 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.80e-01 ... (remaining 2157 not shown) Planarity restraints: 4557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 107 " -0.069 9.50e-02 1.11e+02 4.36e-02 3.14e+01 pdb=" NE ARG B 107 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG B 107 " 0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG B 107 " 0.061 2.00e-02 2.50e+03 pdb=" NH2 ARG B 107 " 0.021 2.00e-02 2.50e+03 pdb="HH11 ARG B 107 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 107 " -0.060 2.00e-02 2.50e+03 pdb="HH21 ARG B 107 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 107 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 107 " 0.068 9.50e-02 1.11e+02 4.33e-02 3.11e+01 pdb=" NE ARG A 107 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG A 107 " -0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG A 107 " -0.061 2.00e-02 2.50e+03 pdb=" NH2 ARG A 107 " -0.021 2.00e-02 2.50e+03 pdb="HH11 ARG A 107 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 107 " 0.060 2.00e-02 2.50e+03 pdb="HH21 ARG A 107 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 107 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 107 " -0.069 9.50e-02 1.11e+02 4.34e-02 3.09e+01 pdb=" NE ARG C 107 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG C 107 " 0.044 2.00e-02 2.50e+03 pdb=" NH1 ARG C 107 " 0.061 2.00e-02 2.50e+03 pdb=" NH2 ARG C 107 " 0.021 2.00e-02 2.50e+03 pdb="HH11 ARG C 107 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG C 107 " -0.060 2.00e-02 2.50e+03 pdb="HH21 ARG C 107 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG C 107 " -0.021 2.00e-02 2.50e+03 ... (remaining 4554 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1640 2.16 - 2.77: 60254 2.77 - 3.38: 84782 3.38 - 3.99: 116021 3.99 - 4.60: 179456 Nonbonded interactions: 442153 Sorted by model distance: nonbonded pdb=" O LEU A 553 " pdb=" H LEU B 546 " model vdw 1.550 2.450 nonbonded pdb=" O LEU B 553 " pdb=" H LEU C 546 " model vdw 1.566 2.450 nonbonded pdb=" OE1 GLU A 563 " pdb=" HG SER B 555 " model vdw 1.567 2.450 nonbonded pdb=" OD1 ASN C 10 " pdb=" HG SER C 59 " model vdw 1.585 2.450 nonbonded pdb=" OD1 ASN B 10 " pdb=" HG SER B 59 " model vdw 1.586 2.450 ... (remaining 442148 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.170 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 35.450 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 15204 Z= 0.321 Angle : 0.730 7.063 20601 Z= 0.402 Chirality : 0.047 0.191 2160 Planarity : 0.009 0.098 2766 Dihedral : 14.112 89.339 5622 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.22 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.18), residues: 1869 helix: -2.30 (0.28), residues: 183 sheet: -1.55 (0.21), residues: 522 loop : -1.08 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.003 ARG B 107 TYR 0.032 0.004 TYR B 143 PHE 0.023 0.003 PHE C 435 TRP 0.014 0.004 TRP A 414 HIS 0.009 0.003 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00751 (15204) covalent geometry : angle 0.73042 (20601) hydrogen bonds : bond 0.22201 ( 349) hydrogen bonds : angle 10.07518 ( 888) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 ASN cc_start: 0.8446 (m-40) cc_final: 0.8244 (m110) REVERT: A 481 ASN cc_start: 0.8505 (m110) cc_final: 0.8295 (m-40) REVERT: B 316 LEU cc_start: 0.8460 (tp) cc_final: 0.8211 (tp) REVERT: B 384 GLN cc_start: 0.8075 (pm20) cc_final: 0.7691 (mp10) REVERT: B 463 ASN cc_start: 0.8513 (m-40) cc_final: 0.8257 (m110) REVERT: C 181 ASP cc_start: 0.7094 (p0) cc_final: 0.6813 (p0) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.3490 time to fit residues: 125.2953 Evaluate side-chains 117 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 0.2980 chunk 149 optimal weight: 0.0570 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 GLN B 339 GLN B 626 GLN ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN C 360 HIS C 626 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.105406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.091195 restraints weight = 74108.675| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.70 r_work: 0.3706 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15204 Z= 0.153 Angle : 0.669 7.641 20601 Z= 0.362 Chirality : 0.046 0.144 2160 Planarity : 0.005 0.047 2766 Dihedral : 7.114 26.752 2088 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.05 % Favored : 93.79 % Rotamer: Outliers : 1.44 % Allowed : 8.29 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.19), residues: 1869 helix: -1.22 (0.32), residues: 216 sheet: -1.94 (0.21), residues: 531 loop : -0.62 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 233 TYR 0.013 0.001 TYR A 143 PHE 0.013 0.002 PHE A 435 TRP 0.010 0.001 TRP C 394 HIS 0.006 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00334 (15204) covalent geometry : angle 0.66862 (20601) hydrogen bonds : bond 0.04483 ( 349) hydrogen bonds : angle 7.29286 ( 888) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 VAL cc_start: 0.8959 (t) cc_final: 0.8553 (p) REVERT: A 210 MET cc_start: 0.8513 (mmm) cc_final: 0.8127 (mmm) REVERT: A 463 ASN cc_start: 0.8575 (m-40) cc_final: 0.8292 (m110) REVERT: B 153 ASP cc_start: 0.8761 (m-30) cc_final: 0.8530 (m-30) REVERT: B 270 HIS cc_start: 0.7000 (OUTLIER) cc_final: 0.6313 (t-90) REVERT: B 487 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7768 (ttm) REVERT: C 181 ASP cc_start: 0.7163 (p0) cc_final: 0.6861 (p0) outliers start: 23 outliers final: 13 residues processed: 155 average time/residue: 0.3380 time to fit residues: 73.3762 Evaluate side-chains 122 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 503 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 130 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 180 optimal weight: 0.0170 chunk 77 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.098587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.084719 restraints weight = 78758.701| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.69 r_work: 0.3595 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15204 Z= 0.249 Angle : 0.665 7.098 20601 Z= 0.363 Chirality : 0.045 0.142 2160 Planarity : 0.005 0.050 2766 Dihedral : 6.866 26.616 2088 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 2.26 % Allowed : 9.10 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.19), residues: 1869 helix: -0.81 (0.35), residues: 216 sheet: -2.23 (0.20), residues: 531 loop : -0.82 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 233 TYR 0.016 0.002 TYR A 143 PHE 0.016 0.002 PHE A 306 TRP 0.014 0.002 TRP C 213 HIS 0.011 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00536 (15204) covalent geometry : angle 0.66523 (20601) hydrogen bonds : bond 0.04141 ( 349) hydrogen bonds : angle 6.90430 ( 888) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 VAL cc_start: 0.8939 (t) cc_final: 0.8462 (p) REVERT: A 321 ARG cc_start: 0.7207 (mmm160) cc_final: 0.6953 (mmm160) REVERT: A 481 ASN cc_start: 0.8473 (m110) cc_final: 0.8131 (m-40) REVERT: A 558 GLN cc_start: 0.7887 (mt0) cc_final: 0.7582 (mm-40) REVERT: B 153 ASP cc_start: 0.8773 (m-30) cc_final: 0.8505 (m-30) REVERT: B 316 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8508 (tp) REVERT: B 558 GLN cc_start: 0.8044 (mt0) cc_final: 0.7746 (mm-40) REVERT: C 384 GLN cc_start: 0.8243 (pm20) cc_final: 0.7966 (mp10) REVERT: C 558 GLN cc_start: 0.8178 (mt0) cc_final: 0.7830 (mm-40) outliers start: 36 outliers final: 23 residues processed: 131 average time/residue: 0.2973 time to fit residues: 56.8400 Evaluate side-chains 123 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 487 MET Chi-restraints excluded: chain C residue 503 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 79 optimal weight: 0.9990 chunk 149 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 169 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.099960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.086313 restraints weight = 77924.794| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.63 r_work: 0.3595 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15204 Z= 0.167 Angle : 0.612 7.466 20601 Z= 0.326 Chirality : 0.044 0.137 2160 Planarity : 0.004 0.039 2766 Dihedral : 6.367 25.733 2088 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.32 % Allowed : 9.79 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.19), residues: 1869 helix: -0.25 (0.37), residues: 207 sheet: -2.16 (0.21), residues: 522 loop : -0.70 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 205 TYR 0.015 0.001 TYR A 143 PHE 0.010 0.001 PHE C 306 TRP 0.013 0.001 TRP C 213 HIS 0.007 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00351 (15204) covalent geometry : angle 0.61173 (20601) hydrogen bonds : bond 0.03504 ( 349) hydrogen bonds : angle 6.56857 ( 888) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 VAL cc_start: 0.8832 (t) cc_final: 0.8352 (p) REVERT: A 321 ARG cc_start: 0.7222 (mmm160) cc_final: 0.6968 (mmm160) REVERT: A 481 ASN cc_start: 0.8448 (m110) cc_final: 0.8112 (m-40) REVERT: A 558 GLN cc_start: 0.7831 (mt0) cc_final: 0.7522 (mm-40) REVERT: B 36 GLN cc_start: 0.8115 (mp10) cc_final: 0.7819 (mp10) REVERT: B 153 ASP cc_start: 0.8773 (m-30) cc_final: 0.8565 (m-30) REVERT: C 541 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7694 (mt0) outliers start: 37 outliers final: 28 residues processed: 136 average time/residue: 0.3299 time to fit residues: 63.8245 Evaluate side-chains 123 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 541 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 113 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 168 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 147 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 182 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.099771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.086247 restraints weight = 78137.104| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.62 r_work: 0.3591 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15204 Z= 0.146 Angle : 0.580 6.503 20601 Z= 0.307 Chirality : 0.044 0.131 2160 Planarity : 0.004 0.096 2766 Dihedral : 6.047 24.740 2088 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.57 % Allowed : 9.98 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.20), residues: 1869 helix: 0.06 (0.38), residues: 207 sheet: -2.13 (0.21), residues: 522 loop : -0.65 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 205 TYR 0.013 0.001 TYR A 143 PHE 0.010 0.001 PHE C 33 TRP 0.011 0.001 TRP C 213 HIS 0.007 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00313 (15204) covalent geometry : angle 0.57987 (20601) hydrogen bonds : bond 0.03269 ( 349) hydrogen bonds : angle 6.39127 ( 888) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 VAL cc_start: 0.8819 (t) cc_final: 0.8397 (p) REVERT: A 321 ARG cc_start: 0.7241 (mmm160) cc_final: 0.7013 (mmm160) REVERT: A 481 ASN cc_start: 0.8433 (m110) cc_final: 0.7881 (m110) REVERT: B 36 GLN cc_start: 0.8028 (mp10) cc_final: 0.7814 (mp10) REVERT: B 153 ASP cc_start: 0.8787 (m-30) cc_final: 0.8477 (m-30) REVERT: B 541 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7997 (mt0) REVERT: C 541 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7620 (mt0) outliers start: 41 outliers final: 33 residues processed: 128 average time/residue: 0.2775 time to fit residues: 52.9596 Evaluate side-chains 128 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 487 MET Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 570 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 174 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.096905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.083414 restraints weight = 79945.634| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.65 r_work: 0.3559 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 15204 Z= 0.215 Angle : 0.615 6.312 20601 Z= 0.330 Chirality : 0.044 0.136 2160 Planarity : 0.004 0.046 2766 Dihedral : 6.184 25.280 2088 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 2.76 % Allowed : 10.23 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.19), residues: 1869 helix: -0.02 (0.38), residues: 207 sheet: -2.37 (0.20), residues: 522 loop : -0.88 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 31 TYR 0.011 0.001 TYR A 143 PHE 0.014 0.002 PHE C 33 TRP 0.015 0.002 TRP C 213 HIS 0.008 0.001 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00458 (15204) covalent geometry : angle 0.61518 (20601) hydrogen bonds : bond 0.03361 ( 349) hydrogen bonds : angle 6.53695 ( 888) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 92 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7520 (pt0) REVERT: A 195 VAL cc_start: 0.8803 (t) cc_final: 0.8424 (p) REVERT: A 204 GLN cc_start: 0.6519 (OUTLIER) cc_final: 0.5740 (pp30) REVERT: A 406 CYS cc_start: 0.8496 (t) cc_final: 0.8186 (p) REVERT: A 481 ASN cc_start: 0.8444 (m110) cc_final: 0.8092 (m-40) REVERT: A 558 GLN cc_start: 0.7981 (mt0) cc_final: 0.7653 (mm-40) REVERT: B 541 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7926 (mt0) REVERT: B 558 GLN cc_start: 0.7875 (mt0) cc_final: 0.7643 (mm-40) REVERT: C 143 TYR cc_start: 0.8238 (t80) cc_final: 0.7850 (t80) REVERT: C 541 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7687 (mt0) REVERT: C 558 GLN cc_start: 0.8069 (mt0) cc_final: 0.7723 (mm-40) outliers start: 44 outliers final: 31 residues processed: 120 average time/residue: 0.3105 time to fit residues: 53.4371 Evaluate side-chains 121 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 406 CYS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 487 MET Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 541 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 113 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 163 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.096624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.083183 restraints weight = 80122.284| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.66 r_work: 0.3559 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15204 Z= 0.212 Angle : 0.612 7.195 20601 Z= 0.327 Chirality : 0.044 0.136 2160 Planarity : 0.004 0.052 2766 Dihedral : 6.107 24.948 2088 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 2.45 % Allowed : 11.17 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.19), residues: 1869 helix: 0.12 (0.38), residues: 207 sheet: -2.47 (0.21), residues: 510 loop : -0.99 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 205 TYR 0.012 0.001 TYR A 143 PHE 0.013 0.002 PHE B 33 TRP 0.014 0.002 TRP C 213 HIS 0.007 0.001 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00448 (15204) covalent geometry : angle 0.61180 (20601) hydrogen bonds : bond 0.03284 ( 349) hydrogen bonds : angle 6.54253 ( 888) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 90 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 VAL cc_start: 0.8781 (t) cc_final: 0.8420 (p) REVERT: A 204 GLN cc_start: 0.6470 (OUTLIER) cc_final: 0.5752 (pp30) REVERT: A 406 CYS cc_start: 0.8753 (t) cc_final: 0.8187 (p) REVERT: A 481 ASN cc_start: 0.8458 (m110) cc_final: 0.8105 (m-40) REVERT: A 558 GLN cc_start: 0.7980 (mt0) cc_final: 0.7690 (mm-40) REVERT: A 610 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8335 (mt) REVERT: B 153 ASP cc_start: 0.8749 (m-30) cc_final: 0.8425 (m-30) REVERT: B 541 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7931 (mt0) REVERT: C 143 TYR cc_start: 0.8208 (t80) cc_final: 0.7815 (t80) REVERT: C 541 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7660 (mt0) outliers start: 39 outliers final: 31 residues processed: 113 average time/residue: 0.2702 time to fit residues: 45.6208 Evaluate side-chains 123 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 88 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 487 MET Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 570 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 131 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 52 optimal weight: 0.0970 chunk 54 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.098446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.084754 restraints weight = 78742.979| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.70 r_work: 0.3587 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15204 Z= 0.132 Angle : 0.568 9.726 20601 Z= 0.299 Chirality : 0.044 0.135 2160 Planarity : 0.004 0.044 2766 Dihedral : 5.822 23.992 2088 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.07 % Allowed : 11.68 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.20), residues: 1869 helix: 0.46 (0.40), residues: 207 sheet: -2.31 (0.21), residues: 510 loop : -0.85 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 31 TYR 0.013 0.001 TYR B 143 PHE 0.010 0.001 PHE C 33 TRP 0.011 0.001 TRP C 213 HIS 0.006 0.001 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00280 (15204) covalent geometry : angle 0.56766 (20601) hydrogen bonds : bond 0.03082 ( 349) hydrogen bonds : angle 6.36833 ( 888) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 VAL cc_start: 0.8761 (t) cc_final: 0.8421 (p) REVERT: A 406 CYS cc_start: 0.8699 (t) cc_final: 0.8123 (p) REVERT: A 481 ASN cc_start: 0.8390 (m110) cc_final: 0.7849 (m110) REVERT: A 610 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8241 (mt) REVERT: B 153 ASP cc_start: 0.8745 (m-30) cc_final: 0.8436 (m-30) REVERT: B 204 GLN cc_start: 0.5563 (OUTLIER) cc_final: 0.5326 (pp30) REVERT: B 541 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7947 (mt0) REVERT: C 143 TYR cc_start: 0.8136 (t80) cc_final: 0.7739 (t80) REVERT: C 555 SER cc_start: 0.7945 (OUTLIER) cc_final: 0.7604 (t) REVERT: C 610 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8160 (mt) outliers start: 33 outliers final: 24 residues processed: 113 average time/residue: 0.2908 time to fit residues: 47.8496 Evaluate side-chains 117 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 209 HIS Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 610 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 63 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 168 optimal weight: 0.0370 chunk 103 optimal weight: 1.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.096467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.082901 restraints weight = 80515.917| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.72 r_work: 0.3549 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15204 Z= 0.198 Angle : 0.596 10.563 20601 Z= 0.317 Chirality : 0.044 0.140 2160 Planarity : 0.004 0.039 2766 Dihedral : 5.908 24.324 2088 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 2.51 % Allowed : 11.24 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.20), residues: 1869 helix: 0.48 (0.40), residues: 207 sheet: -2.49 (0.21), residues: 510 loop : -0.93 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 31 TYR 0.011 0.001 TYR B 143 PHE 0.011 0.001 PHE A 33 TRP 0.013 0.002 TRP C 213 HIS 0.007 0.001 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00422 (15204) covalent geometry : angle 0.59629 (20601) hydrogen bonds : bond 0.03149 ( 349) hydrogen bonds : angle 6.49202 ( 888) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 90 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 VAL cc_start: 0.8811 (t) cc_final: 0.8489 (p) REVERT: A 204 GLN cc_start: 0.6387 (OUTLIER) cc_final: 0.5646 (pp30) REVERT: A 481 ASN cc_start: 0.8448 (m110) cc_final: 0.8089 (m-40) REVERT: A 558 GLN cc_start: 0.7954 (mt0) cc_final: 0.7675 (mm-40) REVERT: A 610 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8341 (mt) REVERT: B 153 ASP cc_start: 0.8758 (m-30) cc_final: 0.8453 (m-30) REVERT: B 204 GLN cc_start: 0.5591 (OUTLIER) cc_final: 0.4475 (pp30) REVERT: B 541 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8002 (mt0) REVERT: B 610 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8206 (mt) REVERT: C 143 TYR cc_start: 0.8166 (t80) cc_final: 0.7761 (t80) REVERT: C 541 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7617 (mt0) REVERT: C 555 SER cc_start: 0.8136 (OUTLIER) cc_final: 0.7730 (t) REVERT: C 610 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8173 (mt) outliers start: 40 outliers final: 27 residues processed: 117 average time/residue: 0.2924 time to fit residues: 50.1027 Evaluate side-chains 121 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 406 CYS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 610 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 171 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.096667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.083164 restraints weight = 80081.406| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.71 r_work: 0.3539 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15204 Z= 0.187 Angle : 0.591 9.355 20601 Z= 0.314 Chirality : 0.044 0.140 2160 Planarity : 0.004 0.040 2766 Dihedral : 5.895 23.935 2088 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 2.32 % Allowed : 11.42 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.20), residues: 1869 helix: 0.57 (0.40), residues: 207 sheet: -2.57 (0.21), residues: 510 loop : -0.95 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 31 TYR 0.012 0.001 TYR A 143 PHE 0.011 0.001 PHE C 33 TRP 0.013 0.002 TRP C 213 HIS 0.007 0.001 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00396 (15204) covalent geometry : angle 0.59090 (20601) hydrogen bonds : bond 0.03115 ( 349) hydrogen bonds : angle 6.48179 ( 888) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue ALA 7 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLN cc_start: 0.6377 (OUTLIER) cc_final: 0.5631 (pp30) REVERT: A 321 ARG cc_start: 0.7248 (mmm160) cc_final: 0.7014 (mmp-170) REVERT: A 481 ASN cc_start: 0.8432 (m110) cc_final: 0.8070 (m-40) REVERT: A 558 GLN cc_start: 0.7945 (mt0) cc_final: 0.7696 (mm-40) REVERT: A 610 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8215 (mt) REVERT: B 153 ASP cc_start: 0.8761 (m-30) cc_final: 0.8459 (m-30) REVERT: B 204 GLN cc_start: 0.5581 (OUTLIER) cc_final: 0.4536 (pp30) REVERT: B 541 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8005 (mt0) REVERT: B 555 SER cc_start: 0.7915 (m) cc_final: 0.7501 (t) REVERT: B 610 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8172 (mt) REVERT: C 143 TYR cc_start: 0.8158 (t80) cc_final: 0.7754 (t80) REVERT: C 541 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7615 (mt0) REVERT: C 610 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8224 (mt) outliers start: 37 outliers final: 25 residues processed: 116 average time/residue: 0.2876 time to fit residues: 49.5875 Evaluate side-chains 119 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 174 ARG Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 270 HIS Chi-restraints excluded: chain B residue 406 CYS Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 541 GLN Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 360 HIS Chi-restraints excluded: chain C residue 406 CYS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 610 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 53 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 145 optimal weight: 0.0980 chunk 128 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 168 optimal weight: 0.0870 chunk 75 optimal weight: 0.6980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.102668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.089235 restraints weight = 76268.766| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.52 r_work: 0.3673 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15204 Z= 0.116 Angle : 0.553 9.319 20601 Z= 0.289 Chirality : 0.044 0.138 2160 Planarity : 0.003 0.041 2766 Dihedral : 5.562 23.458 2088 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.01 % Allowed : 11.86 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.20), residues: 1869 helix: 0.83 (0.41), residues: 207 sheet: -2.34 (0.21), residues: 510 loop : -0.76 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 31 TYR 0.015 0.001 TYR A 143 PHE 0.010 0.001 PHE B 167 TRP 0.013 0.001 TRP A 394 HIS 0.005 0.001 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00250 (15204) covalent geometry : angle 0.55276 (20601) hydrogen bonds : bond 0.02935 ( 349) hydrogen bonds : angle 6.26048 ( 888) =============================================================================== Job complete usr+sys time: 7036.88 seconds wall clock time: 119 minutes 55.03 seconds (7195.03 seconds total)