Starting phenix.real_space_refine on Thu Mar 5 02:26:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xj2_33217/03_2026/7xj2_33217.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xj2_33217/03_2026/7xj2_33217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xj2_33217/03_2026/7xj2_33217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xj2_33217/03_2026/7xj2_33217.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xj2_33217/03_2026/7xj2_33217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xj2_33217/03_2026/7xj2_33217.map" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.068 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 112 5.16 5 C 12123 2.51 5 N 3074 2.21 5 O 3117 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.03s 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: 18438 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4585 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 13, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 299 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 27, 'GLN:plan1': 3, 'ASN:plan1': 7, 'ASP:plan': 11, 'TYR:plan': 1, 'HIS:plan': 2, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 248 Chain: "C" Number of atoms: 4575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4575 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 13, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 376 Unresolved non-hydrogen angles: 464 Unresolved non-hydrogen dihedrals: 306 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 28, 'GLN:plan1': 3, 'ASN:plan1': 8, 'ASP:plan': 12, 'TYR:plan': 1, 'HIS:plan': 2, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 258 Chain: "A" Number of atoms: 4571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4571 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 13, 'TRANS': 593} Chain breaks: 4 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 28, 'GLN:plan1': 3, 'ASN:plan1': 7, 'ASP:plan': 12, 'TYR:plan': 2, 'HIS:plan': 2, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 262 Chain: "D" Number of atoms: 4575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4575 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 13, 'TRANS': 593} Chain breaks: 4 Unresolved non-hydrogen bonds: 376 Unresolved non-hydrogen angles: 464 Unresolved non-hydrogen dihedrals: 306 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 28, 'GLN:plan1': 3, 'ASN:plan1': 8, 'ASP:plan': 12, 'TYR:plan': 1, 'HIS:plan': 2, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 258 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'EQK': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'EQK': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'EQK': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'EQK': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.30, per 1000 atoms: 0.23 Number of scatterers: 18438 At special positions: 0 Unit cell: (117.52, 117.52, 123.76, 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 112 16.00 F 12 9.00 O 3117 8.00 N 3074 7.00 C 12123 6.00 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: 1.61 Conformation dependent library (CDL) restraints added in 805.7 milliseconds 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4640 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 4 sheets defined 69.0% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 133 through 149 removed outlier: 3.537A pdb=" N ARG B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.644A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 4.154A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 331 through 336 removed outlier: 3.600A pdb=" N THR B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.612A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 402 through 410 Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.540A pdb=" N HIS B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 Processing helix chain 'B' and resid 483 through 506 Processing helix chain 'B' and resid 521 through 542 Processing helix chain 'B' and resid 546 through 566 removed outlier: 4.313A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 586 Processing helix chain 'B' and resid 586 through 609 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.928A pdb=" N SER B 620 " --> pdb=" O LYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 Processing helix chain 'B' and resid 650 through 679 removed outlier: 3.728A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 707 removed outlier: 4.277A pdb=" N ASN B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N SER B 685 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 716 Processing helix chain 'C' and resid 119 through 130 Processing helix chain 'C' and resid 133 through 149 removed outlier: 3.984A pdb=" N ARG C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.663A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 4.101A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 227 through 237 Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 331 through 336 Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.516A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 374 removed outlier: 5.463A pdb=" N SER C 372 " --> pdb=" O ARG C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 410 Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.547A pdb=" N HIS C 426 " --> pdb=" O LEU C 422 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 Processing helix chain 'C' and resid 481 through 506 Processing helix chain 'C' and resid 521 through 542 Processing helix chain 'C' and resid 547 through 562 Processing helix chain 'C' and resid 569 through 586 Processing helix chain 'C' and resid 586 through 609 Processing helix chain 'C' and resid 616 through 620 removed outlier: 4.045A pdb=" N SER C 620 " --> pdb=" O LYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 Processing helix chain 'C' and resid 650 through 678 Processing helix chain 'C' and resid 679 through 707 removed outlier: 4.252A pdb=" N ASN C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N SER C 685 " --> pdb=" O VAL C 681 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'A' and resid 119 through 130 Processing helix chain 'A' and resid 133 through 149 Processing helix chain 'A' and resid 155 through 163 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.602A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 4.149A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.645A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 331 through 336 removed outlier: 3.574A pdb=" N THR A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.600A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 374 removed outlier: 5.438A pdb=" N SER A 372 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 410 Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.537A pdb=" N HIS A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 Processing helix chain 'A' and resid 482 through 506 Processing helix chain 'A' and resid 521 through 542 Processing helix chain 'A' and resid 546 through 566 removed outlier: 4.515A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 586 Processing helix chain 'A' and resid 586 through 609 Processing helix chain 'A' and resid 624 through 638 Processing helix chain 'A' and resid 650 through 678 Processing helix chain 'A' and resid 679 through 707 removed outlier: 4.165A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N SER A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'D' and resid 119 through 130 Processing helix chain 'D' and resid 133 through 149 removed outlier: 3.987A pdb=" N ARG D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.653A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 4.120A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 227 through 237 Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'D' and resid 309 through 314 Processing helix chain 'D' and resid 316 through 328 Processing helix chain 'D' and resid 331 through 336 removed outlier: 3.575A pdb=" N THR D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.605A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 374 removed outlier: 3.513A pdb=" N ARG D 371 " --> pdb=" O LYS D 368 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N SER D 372 " --> pdb=" O ARG D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 410 Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.542A pdb=" N HIS D 426 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 Processing helix chain 'D' and resid 481 through 506 removed outlier: 4.059A pdb=" N GLY D 486 " --> pdb=" O LEU D 482 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 542 Processing helix chain 'D' and resid 546 through 562 removed outlier: 4.631A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 565 No H-bonds generated for 'chain 'D' and resid 563 through 565' Processing helix chain 'D' and resid 569 through 609 removed outlier: 3.920A pdb=" N VAL D 587 " --> pdb=" O ILE D 583 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS D 589 " --> pdb=" O HIS D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 Processing helix chain 'D' and resid 650 through 678 Processing helix chain 'D' and resid 679 through 707 removed outlier: 4.022A pdb=" N ASN D 683 " --> pdb=" O GLU D 679 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N SER D 685 " --> pdb=" O VAL D 681 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 716 Processing sheet with id=AA1, first strand: chain 'B' and resid 376 through 378 Processing sheet with id=AA2, first strand: chain 'C' and resid 376 through 378 Processing sheet with id=AA3, first strand: chain 'A' and resid 376 through 378 Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 378 1173 hydrogen bonds defined for protein. 3462 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.48: 10625 1.48 - 1.84: 8212 1.84 - 2.19: 0 2.19 - 2.54: 0 2.54 - 2.89: 2 Bond restraints: 18839 Sorted by residual: bond pdb=" C PRO B 613 " pdb=" N ASN B 616 " ideal model delta sigma weight residual 1.332 2.895 -1.562 1.40e-02 5.10e+03 1.25e+04 bond pdb=" C PRO C 613 " pdb=" N ASN C 616 " ideal model delta sigma weight residual 1.334 2.894 -1.560 1.42e-02 4.96e+03 1.21e+04 bond pdb=" C20 EQK D1101 " pdb=" S01 EQK D1101 " ideal model delta sigma weight residual 1.732 1.509 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C20 EQK B1101 " pdb=" S01 EQK B1101 " ideal model delta sigma weight residual 1.732 1.511 0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C20 EQK C1101 " pdb=" S01 EQK C1101 " ideal model delta sigma weight residual 1.732 1.511 0.221 2.00e-02 2.50e+03 1.22e+02 ... (remaining 18834 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.84: 25650 9.84 - 19.68: 6 19.68 - 29.52: 2 29.52 - 39.36: 0 39.36 - 49.20: 2 Bond angle restraints: 25660 Sorted by residual: angle pdb=" O PRO B 613 " pdb=" C PRO B 613 " pdb=" N ASN B 616 " ideal model delta sigma weight residual 122.64 73.44 49.20 1.35e+00 5.49e-01 1.33e+03 angle pdb=" O PRO C 613 " pdb=" C PRO C 613 " pdb=" N ASN C 616 " ideal model delta sigma weight residual 122.64 74.81 47.83 1.35e+00 5.49e-01 1.26e+03 angle pdb=" C PRO C 613 " pdb=" N ASN C 616 " pdb=" CA ASN C 616 " ideal model delta sigma weight residual 122.36 146.31 -23.95 1.47e+00 4.63e-01 2.65e+02 angle pdb=" C PRO B 613 " pdb=" N ASN B 616 " pdb=" CA ASN B 616 " ideal model delta sigma weight residual 121.54 145.84 -24.30 1.91e+00 2.74e-01 1.62e+02 angle pdb=" CA PRO B 613 " pdb=" C PRO B 613 " pdb=" N ASN B 616 " ideal model delta sigma weight residual 116.70 133.32 -16.62 2.07e+00 2.33e-01 6.45e+01 ... (remaining 25655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.87: 10353 24.87 - 49.74: 561 49.74 - 74.61: 81 74.61 - 99.49: 39 99.49 - 124.36: 2 Dihedral angle restraints: 11036 sinusoidal: 3899 harmonic: 7137 Sorted by residual: dihedral pdb=" CA PRO C 613 " pdb=" C PRO C 613 " pdb=" N ASN C 616 " pdb=" CA ASN C 616 " ideal model delta harmonic sigma weight residual -180.00 -55.64 -124.36 0 5.00e+00 4.00e-02 6.19e+02 dihedral pdb=" CA PRO B 613 " pdb=" C PRO B 613 " pdb=" N ASN B 616 " pdb=" CA ASN B 616 " ideal model delta harmonic sigma weight residual -180.00 -59.93 -120.07 0 5.00e+00 4.00e-02 5.77e+02 dihedral pdb=" CA HIS C 585 " pdb=" C HIS C 585 " pdb=" N ASP C 586 " pdb=" CA ASP C 586 " ideal model delta harmonic sigma weight residual 180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 11033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2848 0.074 - 0.147: 208 0.147 - 0.221: 7 0.221 - 0.295: 0 0.295 - 0.368: 1 Chirality restraints: 3064 Sorted by residual: chirality pdb=" CA GLU A 702 " pdb=" N GLU A 702 " pdb=" C GLU A 702 " pdb=" CB GLU A 702 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA ARG D 462 " pdb=" N ARG D 462 " pdb=" C ARG D 462 " pdb=" CB ARG D 462 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA GLU A 704 " pdb=" N GLU A 704 " pdb=" C GLU A 704 " pdb=" CB GLU A 704 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 3061 not shown) Planarity restraints: 3145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO C 613 " 0.176 2.00e-02 2.50e+03 2.19e-01 4.80e+02 pdb=" C PRO C 613 " -0.372 2.00e-02 2.50e+03 pdb=" O PRO C 613 " 0.139 2.00e-02 2.50e+03 pdb=" N ASN C 616 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 613 " -0.176 2.00e-02 2.50e+03 2.18e-01 4.76e+02 pdb=" C PRO B 613 " 0.370 2.00e-02 2.50e+03 pdb=" O PRO B 613 " -0.138 2.00e-02 2.50e+03 pdb=" N ASN B 616 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 566 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C THR D 566 " -0.033 2.00e-02 2.50e+03 pdb=" O THR D 566 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG D 567 " 0.011 2.00e-02 2.50e+03 ... (remaining 3142 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2101 2.74 - 3.28: 19966 3.28 - 3.82: 30814 3.82 - 4.36: 35365 4.36 - 4.90: 60012 Nonbonded interactions: 148258 Sorted by model distance: nonbonded pdb=" OH TYR A 260 " pdb=" ND2 ASN A 297 " model vdw 2.203 3.120 nonbonded pdb=" OG SER A 620 " pdb=" CA GLN A 646 " model vdw 2.213 3.470 nonbonded pdb=" OG1 THR D 636 " pdb=" OH TYR D 661 " model vdw 2.223 3.040 nonbonded pdb=" OE2 GLU C 334 " pdb=" NH2 ARG C 363 " model vdw 2.225 3.120 nonbonded pdb=" OG1 THR C 636 " pdb=" OH TYR C 661 " model vdw 2.226 3.040 ... (remaining 148253 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 118 through 749 or (resid 750 through 752 and (name N or n \ ame CA or name C or name O or name CB )) or resid 753 through 1101)) selection = (chain 'B' and (resid 118 through 621 or (resid 622 and (name N or name CA or na \ me C or name O or name CB )) or resid 623 through 749 or (resid 750 through 752 \ and (name N or name CA or name C or name O or name CB )) or resid 753 through 11 \ 01)) selection = (chain 'C' and (resid 118 through 621 or (resid 622 and (name N or name CA or na \ me C or name O or name CB )) or resid 623 through 1101)) selection = (chain 'D' and (resid 118 through 621 or (resid 622 and (name N or name CA or na \ me C or name O or name CB )) or resid 623 through 1101)) } 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 group one per residue 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.020 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 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 : 0.019 1.562 18839 Z= 1.250 Angle : 0.903 49.198 25660 Z= 0.536 Chirality : 0.040 0.368 3064 Planarity : 0.006 0.219 3145 Dihedral : 16.461 124.358 6396 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.75 % Allowed : 18.44 % Favored : 77.81 % 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: -3.17 (0.15), residues: 2388 helix: -1.29 (0.11), residues: 1524 sheet: -5.07 (0.32), residues: 84 loop : -3.21 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 696 TYR 0.020 0.002 TYR B 451 PHE 0.012 0.001 PHE D 601 TRP 0.020 0.001 TRP B 380 HIS 0.003 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.01904 (18839) covalent geometry : angle 0.90305 (25660) hydrogen bonds : bond 0.13580 ( 1173) hydrogen bonds : angle 6.29574 ( 3462) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 480 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 279 GLN cc_start: 0.8622 (mt0) cc_final: 0.8414 (mt0) REVERT: B 318 LYS cc_start: 0.8881 (ttmt) cc_final: 0.8604 (ttpt) REVERT: B 528 ILE cc_start: 0.9306 (mt) cc_final: 0.9014 (mm) REVERT: B 594 TYR cc_start: 0.8444 (t80) cc_final: 0.8209 (t80) REVERT: C 318 LYS cc_start: 0.8906 (ttmt) cc_final: 0.8647 (ttpt) REVERT: C 555 MET cc_start: 0.8619 (tmm) cc_final: 0.8344 (tmm) REVERT: C 559 TRP cc_start: 0.8674 (m100) cc_final: 0.8209 (m100) REVERT: C 594 TYR cc_start: 0.8429 (t80) cc_final: 0.8044 (t80) REVERT: A 227 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8246 (mm110) REVERT: A 318 LYS cc_start: 0.8920 (ttmt) cc_final: 0.8654 (ttpt) REVERT: A 528 ILE cc_start: 0.9294 (mt) cc_final: 0.8974 (mm) REVERT: A 555 MET cc_start: 0.8403 (tmm) cc_final: 0.8185 (tmm) REVERT: A 573 SER cc_start: 0.8411 (t) cc_final: 0.7806 (m) REVERT: A 591 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8436 (mm) REVERT: A 611 LYS cc_start: 0.6083 (OUTLIER) cc_final: 0.4726 (mptt) REVERT: A 690 ARG cc_start: 0.7918 (ptm-80) cc_final: 0.7481 (mtp-110) REVERT: A 712 ARG cc_start: 0.9060 (mtp180) cc_final: 0.8774 (mtm-85) REVERT: D 318 LYS cc_start: 0.8901 (ttmt) cc_final: 0.8638 (ttpt) REVERT: D 569 PHE cc_start: 0.5991 (m-80) cc_final: 0.5735 (t80) REVERT: D 573 SER cc_start: 0.8327 (t) cc_final: 0.7697 (m) REVERT: D 594 TYR cc_start: 0.8489 (t80) cc_final: 0.8104 (t80) REVERT: D 611 LYS cc_start: 0.6502 (OUTLIER) cc_final: 0.5826 (mptt) REVERT: D 745 HIS cc_start: 0.7496 (m-70) cc_final: 0.7290 (m170) outliers start: 65 outliers final: 35 residues processed: 528 average time/residue: 0.1470 time to fit residues: 116.9244 Evaluate side-chains 409 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 371 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 737 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 0.0040 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN B 279 GLN B 284 HIS ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 346 GLN B 452 ASN B 647 ASN C 178 ASN C 284 HIS ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 GLN C 452 ASN C 570 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 HIS ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN A 346 GLN A 452 ASN A 570 GLN A 745 HIS D 205 ASN D 284 HIS ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN D 346 GLN ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 GLN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.136226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.107251 restraints weight = 35325.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.110575 restraints weight = 20562.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.112743 restraints weight = 14693.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114139 restraints weight = 11851.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114914 restraints weight = 10300.886| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18839 Z= 0.135 Angle : 0.605 8.482 25660 Z= 0.311 Chirality : 0.038 0.157 3064 Planarity : 0.004 0.044 3145 Dihedral : 11.625 100.380 2764 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.52 % Rotamer: Outliers : 4.15 % Allowed : 23.29 % Favored : 72.56 % 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: -1.32 (0.17), residues: 2392 helix: 0.21 (0.13), residues: 1572 sheet: -3.83 (0.47), residues: 64 loop : -2.91 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 698 TYR 0.013 0.001 TYR C 451 PHE 0.020 0.001 PHE C 193 TRP 0.025 0.002 TRP C 380 HIS 0.004 0.001 HIS A 745 Details of bonding type rmsd covalent geometry : bond 0.00297 (18839) covalent geometry : angle 0.60458 (25660) hydrogen bonds : bond 0.03923 ( 1173) hydrogen bonds : angle 4.65774 ( 3462) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 429 time to evaluate : 0.673 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: B 318 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8645 (ttpt) REVERT: B 541 LEU cc_start: 0.8398 (mm) cc_final: 0.8130 (tt) REVERT: B 559 TRP cc_start: 0.8864 (m100) cc_final: 0.8664 (m100) REVERT: B 635 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8731 (tt) REVERT: C 318 LYS cc_start: 0.8873 (ttmt) cc_final: 0.8662 (ttpt) REVERT: C 452 ASN cc_start: 0.7837 (OUTLIER) cc_final: 0.7433 (t0) REVERT: C 460 TYR cc_start: 0.8101 (t80) cc_final: 0.7804 (t80) REVERT: C 521 TRP cc_start: 0.8701 (m-10) cc_final: 0.7850 (m100) REVERT: C 545 LYS cc_start: 0.6780 (mmtt) cc_final: 0.6381 (mmpt) REVERT: C 591 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8530 (mm) REVERT: C 599 LEU cc_start: 0.8743 (mm) cc_final: 0.7925 (tt) REVERT: C 690 ARG cc_start: 0.7938 (ptp-110) cc_final: 0.7721 (ptm160) REVERT: C 705 LYS cc_start: 0.8929 (mmmt) cc_final: 0.8625 (mmmt) REVERT: C 712 ARG cc_start: 0.8479 (mtp180) cc_final: 0.7878 (mtt180) REVERT: A 318 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8651 (ttpt) REVERT: A 569 PHE cc_start: 0.5806 (m-80) cc_final: 0.5399 (m-80) REVERT: A 591 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8587 (mm) REVERT: A 690 ARG cc_start: 0.7955 (ptm-80) cc_final: 0.7636 (mtp-110) REVERT: D 268 LEU cc_start: 0.9289 (tp) cc_final: 0.8998 (tp) REVERT: D 318 LYS cc_start: 0.8871 (ttmt) cc_final: 0.8666 (ttpt) REVERT: D 521 TRP cc_start: 0.8634 (m-10) cc_final: 0.7772 (m100) REVERT: D 591 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8379 (mm) outliers start: 72 outliers final: 41 residues processed: 465 average time/residue: 0.1193 time to fit residues: 88.8101 Evaluate side-chains 425 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 379 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 26 optimal weight: 3.9990 chunk 169 optimal weight: 0.0170 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 452 ASN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 GLN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.135982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106758 restraints weight = 35614.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.109995 restraints weight = 20708.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.112139 restraints weight = 14905.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113543 restraints weight = 12066.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.114358 restraints weight = 10512.292| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18839 Z= 0.138 Angle : 0.583 8.665 25660 Z= 0.299 Chirality : 0.038 0.143 3064 Planarity : 0.004 0.047 3145 Dihedral : 11.107 89.916 2714 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.14 % Favored : 94.82 % Rotamer: Outliers : 5.01 % Allowed : 24.09 % Favored : 70.89 % 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: -0.65 (0.17), residues: 2392 helix: 0.77 (0.13), residues: 1572 sheet: -3.71 (0.47), residues: 64 loop : -2.76 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 698 TYR 0.017 0.001 TYR C 544 PHE 0.009 0.001 PHE B 527 TRP 0.019 0.001 TRP B 380 HIS 0.005 0.001 HIS B 745 Details of bonding type rmsd covalent geometry : bond 0.00306 (18839) covalent geometry : angle 0.58348 (25660) hydrogen bonds : bond 0.03797 ( 1173) hydrogen bonds : angle 4.46904 ( 3462) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 406 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 LYS cc_start: 0.8848 (ttmt) cc_final: 0.8629 (ttpt) REVERT: B 419 MET cc_start: 0.8196 (ttm) cc_final: 0.7916 (ttm) REVERT: B 431 MET cc_start: 0.7907 (ttt) cc_final: 0.7501 (ttt) REVERT: B 541 LEU cc_start: 0.8400 (mm) cc_final: 0.8125 (tt) REVERT: B 559 TRP cc_start: 0.8854 (m100) cc_final: 0.8596 (m100) REVERT: C 156 ASP cc_start: 0.8478 (t0) cc_final: 0.8261 (t0) REVERT: C 318 LYS cc_start: 0.8867 (ttmt) cc_final: 0.8666 (ttpt) REVERT: C 419 MET cc_start: 0.8234 (ttm) cc_final: 0.7938 (ttm) REVERT: C 521 TRP cc_start: 0.8683 (m-10) cc_final: 0.7839 (m100) REVERT: C 545 LYS cc_start: 0.6657 (mmtt) cc_final: 0.6147 (mmpt) REVERT: C 591 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8523 (mm) REVERT: C 599 LEU cc_start: 0.8680 (mm) cc_final: 0.7901 (tt) REVERT: C 712 ARG cc_start: 0.8476 (mtp180) cc_final: 0.8257 (mtp85) REVERT: A 193 PHE cc_start: 0.7678 (t80) cc_final: 0.7321 (t80) REVERT: A 268 LEU cc_start: 0.9293 (tp) cc_final: 0.8985 (tp) REVERT: A 318 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8647 (ttpt) REVERT: A 419 MET cc_start: 0.8229 (ttm) cc_final: 0.7973 (ttm) REVERT: A 569 PHE cc_start: 0.5698 (m-80) cc_final: 0.5439 (m-80) REVERT: A 591 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8591 (mm) REVERT: A 690 ARG cc_start: 0.7919 (ptm-80) cc_final: 0.7676 (mtp-110) REVERT: D 193 PHE cc_start: 0.7747 (t80) cc_final: 0.7462 (t80) REVERT: D 268 LEU cc_start: 0.9281 (tp) cc_final: 0.8998 (tp) REVERT: D 318 LYS cc_start: 0.8894 (ttmt) cc_final: 0.8672 (ttpt) REVERT: D 419 MET cc_start: 0.8163 (ttm) cc_final: 0.7937 (ttm) REVERT: D 521 TRP cc_start: 0.8640 (m-10) cc_final: 0.7788 (m100) REVERT: D 562 MET cc_start: 0.8591 (tpp) cc_final: 0.8243 (tpp) REVERT: D 591 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8386 (mm) REVERT: D 594 TYR cc_start: 0.8480 (t80) cc_final: 0.8259 (t80) outliers start: 87 outliers final: 59 residues processed: 453 average time/residue: 0.1264 time to fit residues: 90.9700 Evaluate side-chains 446 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 384 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 569 PHE Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 694 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 233 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 184 optimal weight: 0.0870 chunk 69 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 221 optimal weight: 0.9990 overall best weight: 0.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN D 244 HIS ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 ASN D 452 ASN D 671 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.137717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.108561 restraints weight = 35317.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111872 restraints weight = 20468.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.114045 restraints weight = 14683.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.115371 restraints weight = 11883.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.116382 restraints weight = 10389.464| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18839 Z= 0.113 Angle : 0.553 7.015 25660 Z= 0.284 Chirality : 0.037 0.140 3064 Planarity : 0.004 0.044 3145 Dihedral : 11.039 89.873 2713 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.77 % Favored : 95.19 % Rotamer: Outliers : 4.90 % Allowed : 24.15 % Favored : 70.95 % 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: -0.19 (0.17), residues: 2392 helix: 1.16 (0.13), residues: 1572 sheet: -3.47 (0.46), residues: 64 loop : -2.65 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 698 TYR 0.025 0.001 TYR B 594 PHE 0.017 0.001 PHE C 193 TRP 0.019 0.001 TRP B 380 HIS 0.010 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00245 (18839) covalent geometry : angle 0.55251 (25660) hydrogen bonds : bond 0.03573 ( 1173) hydrogen bonds : angle 4.29893 ( 3462) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 415 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 LYS cc_start: 0.8819 (ttmt) cc_final: 0.8606 (ttpt) REVERT: B 419 MET cc_start: 0.8113 (ttm) cc_final: 0.7894 (ttm) REVERT: B 563 LEU cc_start: 0.8949 (tp) cc_final: 0.8741 (tp) REVERT: C 241 VAL cc_start: 0.9228 (p) cc_final: 0.8877 (t) REVERT: C 318 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8653 (ttpt) REVERT: C 419 MET cc_start: 0.8229 (ttm) cc_final: 0.7872 (ttm) REVERT: C 431 MET cc_start: 0.7836 (ttt) cc_final: 0.7454 (ttt) REVERT: C 521 TRP cc_start: 0.8741 (m-10) cc_final: 0.7893 (m100) REVERT: C 545 LYS cc_start: 0.6841 (mmtt) cc_final: 0.6516 (mmpt) REVERT: C 599 LEU cc_start: 0.8668 (mm) cc_final: 0.7927 (tt) REVERT: A 193 PHE cc_start: 0.7624 (t80) cc_final: 0.7298 (t80) REVERT: A 268 LEU cc_start: 0.9225 (tp) cc_final: 0.8897 (tp) REVERT: A 318 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8652 (ttpt) REVERT: A 419 MET cc_start: 0.8176 (ttm) cc_final: 0.7944 (ttm) REVERT: A 562 MET cc_start: 0.8691 (tpp) cc_final: 0.8449 (tpp) REVERT: A 689 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: D 193 PHE cc_start: 0.7644 (t80) cc_final: 0.7359 (t80) REVERT: D 268 LEU cc_start: 0.9254 (tp) cc_final: 0.8985 (tp) REVERT: D 318 LYS cc_start: 0.8871 (ttmt) cc_final: 0.8666 (ttpt) REVERT: D 521 TRP cc_start: 0.8713 (m-10) cc_final: 0.7893 (m100) REVERT: D 591 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8387 (mm) REVERT: D 634 LYS cc_start: 0.8901 (mmmt) cc_final: 0.8602 (mmmm) REVERT: D 690 ARG cc_start: 0.7615 (mtp-110) cc_final: 0.7337 (ptm-80) REVERT: D 695 GLN cc_start: 0.8452 (tp40) cc_final: 0.8036 (tp40) outliers start: 85 outliers final: 59 residues processed: 460 average time/residue: 0.1232 time to fit residues: 89.8518 Evaluate side-chains 443 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 382 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 705 LYS Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 569 PHE Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 671 ASN Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 129 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 221 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 127 optimal weight: 20.0000 chunk 222 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN C 410 ASN A 244 HIS ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.135626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.106165 restraints weight = 35206.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.109335 restraints weight = 20984.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.111330 restraints weight = 15262.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112739 restraints weight = 12486.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.113551 restraints weight = 10937.310| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18839 Z= 0.176 Angle : 0.597 8.461 25660 Z= 0.306 Chirality : 0.039 0.145 3064 Planarity : 0.004 0.043 3145 Dihedral : 10.941 89.402 2710 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.85 % Favored : 94.11 % Rotamer: Outliers : 5.76 % Allowed : 25.01 % Favored : 69.22 % 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: -0.02 (0.17), residues: 2392 helix: 1.26 (0.13), residues: 1576 sheet: -3.47 (0.46), residues: 64 loop : -2.54 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 567 TYR 0.025 0.001 TYR A 594 PHE 0.008 0.001 PHE B 157 TRP 0.024 0.002 TRP A 380 HIS 0.009 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00404 (18839) covalent geometry : angle 0.59744 (25660) hydrogen bonds : bond 0.03688 ( 1173) hydrogen bonds : angle 4.34683 ( 3462) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 396 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8655 (ttpt) REVERT: B 541 LEU cc_start: 0.8361 (mm) cc_final: 0.8115 (tt) REVERT: C 419 MET cc_start: 0.8283 (ttm) cc_final: 0.7967 (ttm) REVERT: C 521 TRP cc_start: 0.8762 (m-10) cc_final: 0.7880 (m100) REVERT: C 545 LYS cc_start: 0.6715 (mmtt) cc_final: 0.6339 (mmpt) REVERT: C 599 LEU cc_start: 0.8686 (mm) cc_final: 0.7902 (tt) REVERT: A 193 PHE cc_start: 0.7711 (t80) cc_final: 0.7387 (t80) REVERT: A 419 MET cc_start: 0.8253 (ttm) cc_final: 0.8028 (ttm) REVERT: A 562 MET cc_start: 0.8680 (tpp) cc_final: 0.8460 (tpp) REVERT: A 689 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: D 193 PHE cc_start: 0.7751 (t80) cc_final: 0.7498 (t80) REVERT: D 521 TRP cc_start: 0.8728 (m-10) cc_final: 0.7882 (m100) REVERT: D 591 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8420 (mm) REVERT: D 634 LYS cc_start: 0.8996 (mmmt) cc_final: 0.8637 (mmmt) REVERT: D 671 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8365 (t0) outliers start: 100 outliers final: 72 residues processed: 456 average time/residue: 0.1178 time to fit residues: 85.5793 Evaluate side-chains 447 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 372 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 690 ARG Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 671 ASN Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 737 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 165 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 158 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 236 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 HIS ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.137022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.107534 restraints weight = 35121.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110769 restraints weight = 20916.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112864 restraints weight = 15213.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114206 restraints weight = 12424.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.115118 restraints weight = 10893.826| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18839 Z= 0.135 Angle : 0.584 7.629 25660 Z= 0.296 Chirality : 0.038 0.140 3064 Planarity : 0.004 0.042 3145 Dihedral : 10.844 89.400 2710 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.14 % Favored : 94.82 % Rotamer: Outliers : 5.59 % Allowed : 25.94 % Favored : 68.47 % 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: 0.18 (0.17), residues: 2392 helix: 1.42 (0.13), residues: 1576 sheet: -3.31 (0.47), residues: 64 loop : -2.47 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 567 TYR 0.030 0.001 TYR B 594 PHE 0.016 0.001 PHE C 193 TRP 0.020 0.001 TRP A 380 HIS 0.003 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00305 (18839) covalent geometry : angle 0.58361 (25660) hydrogen bonds : bond 0.03604 ( 1173) hydrogen bonds : angle 4.25836 ( 3462) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 395 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 541 LEU cc_start: 0.8348 (mm) cc_final: 0.8107 (tt) REVERT: C 241 VAL cc_start: 0.9247 (p) cc_final: 0.8874 (t) REVERT: C 419 MET cc_start: 0.8268 (ttm) cc_final: 0.7929 (ttm) REVERT: C 521 TRP cc_start: 0.8748 (m-10) cc_final: 0.7972 (m100) REVERT: C 545 LYS cc_start: 0.6799 (mmtt) cc_final: 0.6480 (mmpt) REVERT: C 599 LEU cc_start: 0.8626 (mm) cc_final: 0.7896 (tt) REVERT: A 562 MET cc_start: 0.8639 (tpp) cc_final: 0.8420 (tpp) REVERT: A 689 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: D 193 PHE cc_start: 0.7740 (t80) cc_final: 0.7496 (t80) REVERT: D 521 TRP cc_start: 0.8727 (m-10) cc_final: 0.7909 (m100) REVERT: D 591 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8422 (mm) REVERT: D 634 LYS cc_start: 0.8939 (mmmt) cc_final: 0.8739 (mmmt) outliers start: 97 outliers final: 70 residues processed: 451 average time/residue: 0.1181 time to fit residues: 85.2647 Evaluate side-chains 447 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 375 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 705 LYS Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 671 ASN Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 127 optimal weight: 0.3980 chunk 230 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 chunk 120 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 189 optimal weight: 0.6980 chunk 43 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.138130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.108577 restraints weight = 35239.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111931 restraints weight = 20619.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.114115 restraints weight = 14786.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115550 restraints weight = 11967.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.116393 restraints weight = 10412.460| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 18839 Z= 0.117 Angle : 0.585 11.665 25660 Z= 0.297 Chirality : 0.038 0.185 3064 Planarity : 0.003 0.042 3145 Dihedral : 10.768 88.548 2710 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.85 % Favored : 95.11 % Rotamer: Outliers : 5.07 % Allowed : 25.48 % Favored : 69.45 % 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: 0.32 (0.18), residues: 2392 helix: 1.50 (0.13), residues: 1576 sheet: -3.10 (0.49), residues: 64 loop : -2.37 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 567 TYR 0.034 0.001 TYR A 594 PHE 0.022 0.001 PHE A 193 TRP 0.023 0.001 TRP B 380 HIS 0.008 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00257 (18839) covalent geometry : angle 0.58516 (25660) hydrogen bonds : bond 0.03561 ( 1173) hydrogen bonds : angle 4.21283 ( 3462) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 389 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 521 TRP cc_start: 0.8585 (m-10) cc_final: 0.7981 (m100) REVERT: B 541 LEU cc_start: 0.8353 (mm) cc_final: 0.8096 (tt) REVERT: C 241 VAL cc_start: 0.9252 (p) cc_final: 0.8894 (t) REVERT: C 521 TRP cc_start: 0.8750 (m-10) cc_final: 0.7988 (m100) REVERT: C 545 LYS cc_start: 0.6818 (mmtt) cc_final: 0.6588 (mmpt) REVERT: C 599 LEU cc_start: 0.8586 (mm) cc_final: 0.7901 (tt) REVERT: C 627 ASP cc_start: 0.8267 (m-30) cc_final: 0.8012 (m-30) REVERT: A 241 VAL cc_start: 0.9349 (p) cc_final: 0.8991 (t) REVERT: A 487 ARG cc_start: 0.5438 (mtt180) cc_final: 0.4944 (ttt180) REVERT: A 562 MET cc_start: 0.8612 (tpp) cc_final: 0.8382 (tpp) REVERT: A 689 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: D 193 PHE cc_start: 0.7753 (t80) cc_final: 0.7520 (t80) REVERT: D 521 TRP cc_start: 0.8778 (m-10) cc_final: 0.7981 (m100) REVERT: D 578 MET cc_start: 0.7885 (ptp) cc_final: 0.7626 (ptp) REVERT: D 591 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8378 (mm) REVERT: D 671 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.7902 (t0) outliers start: 88 outliers final: 67 residues processed: 437 average time/residue: 0.1245 time to fit residues: 87.0403 Evaluate side-chains 442 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 372 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 705 LYS Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 671 ASN Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 142 optimal weight: 0.8980 chunk 18 optimal weight: 0.0050 chunk 216 optimal weight: 5.9990 chunk 196 optimal weight: 0.0970 chunk 215 optimal weight: 6.9990 chunk 181 optimal weight: 0.5980 chunk 51 optimal weight: 0.0770 chunk 206 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 overall best weight: 0.3350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** 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 = 0.3810 r_free = 0.3810 target = 0.138193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.108733 restraints weight = 35133.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.112024 restraints weight = 20955.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114175 restraints weight = 15162.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115361 restraints weight = 12327.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.116402 restraints weight = 10878.817| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 18839 Z= 0.117 Angle : 0.585 11.665 25660 Z= 0.297 Chirality : 0.038 0.185 3064 Planarity : 0.003 0.042 3145 Dihedral : 10.759 88.548 2707 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.85 % Favored : 95.11 % Rotamer: Outliers : 4.03 % Allowed : 27.38 % Favored : 68.59 % 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: 0.32 (0.18), residues: 2392 helix: 1.50 (0.13), residues: 1576 sheet: -3.10 (0.49), residues: 64 loop : -2.37 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 567 TYR 0.034 0.001 TYR A 594 PHE 0.022 0.001 PHE A 193 TRP 0.023 0.001 TRP B 380 HIS 0.008 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00257 (18839) covalent geometry : angle 0.58516 (25660) hydrogen bonds : bond 0.03561 ( 1173) hydrogen bonds : angle 4.21283 ( 3462) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 372 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 521 TRP cc_start: 0.8583 (m-10) cc_final: 0.7990 (m100) REVERT: B 541 LEU cc_start: 0.8323 (mm) cc_final: 0.8078 (tt) REVERT: C 241 VAL cc_start: 0.9243 (p) cc_final: 0.8886 (t) REVERT: C 521 TRP cc_start: 0.8743 (m-10) cc_final: 0.7997 (m100) REVERT: C 545 LYS cc_start: 0.6796 (mmtt) cc_final: 0.6578 (mmpt) REVERT: C 599 LEU cc_start: 0.8588 (mm) cc_final: 0.7904 (tt) REVERT: C 627 ASP cc_start: 0.8249 (m-30) cc_final: 0.7991 (m-30) REVERT: A 241 VAL cc_start: 0.9329 (p) cc_final: 0.8980 (t) REVERT: A 487 ARG cc_start: 0.5451 (mtt180) cc_final: 0.4955 (ttt180) REVERT: A 562 MET cc_start: 0.8615 (tpp) cc_final: 0.8401 (tpp) REVERT: A 689 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: D 193 PHE cc_start: 0.7715 (t80) cc_final: 0.7480 (t80) REVERT: D 521 TRP cc_start: 0.8769 (m-10) cc_final: 0.7986 (m100) REVERT: D 578 MET cc_start: 0.7868 (ptp) cc_final: 0.7607 (ptp) REVERT: D 591 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8384 (mm) REVERT: D 671 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.7910 (t0) outliers start: 70 outliers final: 67 residues processed: 407 average time/residue: 0.1219 time to fit residues: 79.4777 Evaluate side-chains 441 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 371 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 705 LYS Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 671 ASN Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 105 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 ASN ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.137914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.108377 restraints weight = 35283.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111696 restraints weight = 20721.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.113834 restraints weight = 14914.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.115258 restraints weight = 12100.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116036 restraints weight = 10546.849| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18839 Z= 0.131 Angle : 0.620 13.622 25660 Z= 0.307 Chirality : 0.039 0.208 3064 Planarity : 0.003 0.041 3145 Dihedral : 10.741 88.119 2707 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.38 % Allowed : 27.20 % Favored : 68.41 % 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: 0.35 (0.18), residues: 2392 helix: 1.52 (0.13), residues: 1576 sheet: -2.99 (0.50), residues: 64 loop : -2.36 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 690 TYR 0.015 0.001 TYR C 594 PHE 0.022 0.001 PHE B 193 TRP 0.027 0.001 TRP C 380 HIS 0.005 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00297 (18839) covalent geometry : angle 0.62049 (25660) hydrogen bonds : bond 0.03597 ( 1173) hydrogen bonds : angle 4.21147 ( 3462) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 380 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: B 521 TRP cc_start: 0.8586 (m-10) cc_final: 0.7979 (m100) REVERT: B 541 LEU cc_start: 0.8356 (mm) cc_final: 0.8101 (tt) REVERT: C 241 VAL cc_start: 0.9246 (p) cc_final: 0.8888 (t) REVERT: C 521 TRP cc_start: 0.8751 (m-10) cc_final: 0.7989 (m100) REVERT: C 545 LYS cc_start: 0.6815 (mmtt) cc_final: 0.6586 (mmpt) REVERT: C 599 LEU cc_start: 0.8560 (mm) cc_final: 0.7827 (tt) REVERT: C 627 ASP cc_start: 0.8278 (m-30) cc_final: 0.8021 (m-30) REVERT: C 694 LEU cc_start: 0.9101 (mp) cc_final: 0.8880 (mp) REVERT: A 241 VAL cc_start: 0.9346 (p) cc_final: 0.8997 (t) REVERT: A 487 ARG cc_start: 0.5444 (mtt180) cc_final: 0.4933 (ttt180) REVERT: A 562 MET cc_start: 0.8613 (tpp) cc_final: 0.8389 (tpp) REVERT: A 689 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: D 193 PHE cc_start: 0.7774 (t80) cc_final: 0.7542 (t80) REVERT: D 521 TRP cc_start: 0.8774 (m-10) cc_final: 0.7983 (m100) REVERT: D 591 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8400 (mm) REVERT: D 671 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.7991 (t0) outliers start: 76 outliers final: 69 residues processed: 420 average time/residue: 0.1236 time to fit residues: 83.5952 Evaluate side-chains 444 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 372 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 705 LYS Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 671 ASN Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 188 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 213 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 239 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 113 optimal weight: 0.6980 chunk 237 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 HIS ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.137578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.108051 restraints weight = 35188.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.111295 restraints weight = 20995.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.113405 restraints weight = 15245.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.114742 restraints weight = 12441.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115509 restraints weight = 10916.460| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18839 Z= 0.144 Angle : 0.638 14.820 25660 Z= 0.315 Chirality : 0.040 0.337 3064 Planarity : 0.003 0.041 3145 Dihedral : 10.719 87.948 2707 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.32 % Allowed : 27.38 % Favored : 68.30 % 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: 0.36 (0.18), residues: 2392 helix: 1.54 (0.13), residues: 1572 sheet: -3.01 (0.49), residues: 64 loop : -2.36 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 567 TYR 0.014 0.001 TYR D 575 PHE 0.015 0.001 PHE D 157 TRP 0.026 0.002 TRP A 380 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00326 (18839) covalent geometry : angle 0.63777 (25660) hydrogen bonds : bond 0.03646 ( 1173) hydrogen bonds : angle 4.24144 ( 3462) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 377 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: B 521 TRP cc_start: 0.8588 (m-10) cc_final: 0.7993 (m100) REVERT: B 541 LEU cc_start: 0.8351 (mm) cc_final: 0.8095 (tt) REVERT: C 241 VAL cc_start: 0.9241 (p) cc_final: 0.8874 (t) REVERT: C 521 TRP cc_start: 0.8750 (m-10) cc_final: 0.7995 (m100) REVERT: C 545 LYS cc_start: 0.6858 (mmtt) cc_final: 0.6649 (mmpt) REVERT: C 599 LEU cc_start: 0.8576 (mm) cc_final: 0.7844 (tt) REVERT: C 694 LEU cc_start: 0.9094 (mp) cc_final: 0.8862 (mp) REVERT: A 241 VAL cc_start: 0.9352 (p) cc_final: 0.8989 (t) REVERT: A 487 ARG cc_start: 0.5441 (mtt180) cc_final: 0.4951 (ttt180) REVERT: A 562 MET cc_start: 0.8628 (tpp) cc_final: 0.8402 (tpp) REVERT: A 689 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: D 193 PHE cc_start: 0.7728 (t80) cc_final: 0.7491 (t80) REVERT: D 453 ILE cc_start: 0.8709 (tp) cc_final: 0.8455 (tt) REVERT: D 521 TRP cc_start: 0.8771 (m-10) cc_final: 0.7989 (m100) REVERT: D 591 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8410 (mm) REVERT: D 671 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8027 (t0) outliers start: 75 outliers final: 67 residues processed: 415 average time/residue: 0.1213 time to fit residues: 80.5998 Evaluate side-chains 441 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 371 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 705 LYS Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 545 LYS Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 671 ASN Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 104 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 182 optimal weight: 6.9990 chunk 238 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 ASN ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.137262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.107618 restraints weight = 35346.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.110854 restraints weight = 21122.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112908 restraints weight = 15358.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114332 restraints weight = 12524.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.115118 restraints weight = 10973.734| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18839 Z= 0.154 Angle : 0.642 14.540 25660 Z= 0.320 Chirality : 0.040 0.318 3064 Planarity : 0.004 0.041 3145 Dihedral : 10.730 88.836 2707 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.21 % Allowed : 27.44 % Favored : 68.36 % 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: 0.36 (0.18), residues: 2392 helix: 1.54 (0.13), residues: 1572 sheet: -3.03 (0.49), residues: 64 loop : -2.36 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 567 TYR 0.024 0.001 TYR D 594 PHE 0.016 0.001 PHE C 193 TRP 0.030 0.002 TRP B 380 HIS 0.027 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00352 (18839) covalent geometry : angle 0.64243 (25660) hydrogen bonds : bond 0.03662 ( 1173) hydrogen bonds : angle 4.27001 ( 3462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3256.07 seconds wall clock time: 57 minutes 2.78 seconds (3422.78 seconds total)