Starting phenix.real_space_refine on Tue Dec 31 03:52:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wb8_21586/12_2024/6wb8_21586.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wb8_21586/12_2024/6wb8_21586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wb8_21586/12_2024/6wb8_21586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wb8_21586/12_2024/6wb8_21586.map" model { file = "/net/cci-nas-00/data/ceres_data/6wb8_21586/12_2024/6wb8_21586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wb8_21586/12_2024/6wb8_21586.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 9864 2.51 5 N 2360 2.21 5 O 2596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14888 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3680 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'CIS': 5, 'PTRANS': 10, 'TRANS': 447} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: C, B, D Time building chain proxies: 7.75, per 1000 atoms: 0.52 Number of scatterers: 14888 At special positions: 0 Unit cell: (112.35, 112.35, 101.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2596 8.00 N 2360 7.00 C 9864 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 Links applied NAG-ASN " NAG A 801 " - " ASN A 328 " " NAG A 802 " - " ASN A 362 " " NAG A 803 " - " ASN A 375 " " NAG B 801 " - " ASN B 328 " " NAG B 802 " - " ASN B 362 " " NAG B 803 " - " ASN B 375 " " NAG C 801 " - " ASN C 328 " " NAG C 802 " - " ASN C 362 " " NAG C 803 " - " ASN C 375 " " NAG D 801 " - " ASN D 328 " " NAG D 802 " - " ASN D 362 " " NAG D 803 " - " ASN D 375 " Time building additional restraints: 4.08 Conformation dependent library (CDL) restraints added in 2.0 seconds 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 12 sheets defined 62.7% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 216 through 242 Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.721A pdb=" N TYR A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 285 through 292 removed outlier: 3.550A pdb=" N ASP A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 363 through 367 Processing helix chain 'A' and resid 398 through 412 Processing helix chain 'A' and resid 467 through 491 removed outlier: 3.584A pdb=" N PHE A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 484 " --> pdb=" O PHE A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 528 removed outlier: 3.508A pdb=" N VAL A 513 " --> pdb=" O CYS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 532 through 541 Processing helix chain 'A' and resid 548 through 573 removed outlier: 3.669A pdb=" N LEU A 573 " --> pdb=" O VAL A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 removed outlier: 4.661A pdb=" N ASN A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE A 579 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 619 removed outlier: 4.362A pdb=" N LYS A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 628 through 642 Processing helix chain 'A' and resid 645 through 653 removed outlier: 4.102A pdb=" N ILE A 649 " --> pdb=" O ASN A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 668 Processing helix chain 'A' and resid 670 through 693 removed outlier: 4.008A pdb=" N ASN A 674 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 242 Processing helix chain 'B' and resid 245 through 258 removed outlier: 3.722A pdb=" N TYR B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 275 through 285 Processing helix chain 'B' and resid 285 through 292 removed outlier: 3.549A pdb=" N ASP B 289 " --> pdb=" O GLY B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 363 through 367 Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 467 through 491 removed outlier: 3.584A pdb=" N PHE B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 484 " --> pdb=" O PHE B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 528 removed outlier: 3.508A pdb=" N VAL B 513 " --> pdb=" O CYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'B' and resid 532 through 541 Processing helix chain 'B' and resid 548 through 573 removed outlier: 3.669A pdb=" N LEU B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 579 removed outlier: 4.661A pdb=" N ASN B 578 " --> pdb=" O LYS B 575 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE B 579 " --> pdb=" O PHE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 619 removed outlier: 4.362A pdb=" N LYS B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 627 Processing helix chain 'B' and resid 628 through 642 Processing helix chain 'B' and resid 645 through 653 removed outlier: 4.101A pdb=" N ILE B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 668 Processing helix chain 'B' and resid 670 through 693 removed outlier: 4.007A pdb=" N ASN B 674 " --> pdb=" O PHE B 670 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 242 Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.722A pdb=" N TYR C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 275 through 285 Processing helix chain 'C' and resid 285 through 292 removed outlier: 3.550A pdb=" N ASP C 289 " --> pdb=" O GLY C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 363 through 367 Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 467 through 491 removed outlier: 3.584A pdb=" N PHE C 483 " --> pdb=" O ILE C 479 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE C 484 " --> pdb=" O PHE C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 528 removed outlier: 3.508A pdb=" N VAL C 513 " --> pdb=" O CYS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 531 No H-bonds generated for 'chain 'C' and resid 529 through 531' Processing helix chain 'C' and resid 532 through 541 Processing helix chain 'C' and resid 548 through 573 removed outlier: 3.669A pdb=" N LEU C 573 " --> pdb=" O VAL C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 579 removed outlier: 4.661A pdb=" N ASN C 578 " --> pdb=" O LYS C 575 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE C 579 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 619 removed outlier: 4.361A pdb=" N LYS C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASP C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 627 Processing helix chain 'C' and resid 628 through 642 Processing helix chain 'C' and resid 645 through 653 removed outlier: 4.101A pdb=" N ILE C 649 " --> pdb=" O ASN C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 668 Processing helix chain 'C' and resid 670 through 693 removed outlier: 4.008A pdb=" N ASN C 674 " --> pdb=" O PHE C 670 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 242 Processing helix chain 'D' and resid 245 through 258 removed outlier: 3.722A pdb=" N TYR D 249 " --> pdb=" O ASN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 285 through 292 removed outlier: 3.550A pdb=" N ASP D 289 " --> pdb=" O GLY D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 341 Processing helix chain 'D' and resid 363 through 367 Processing helix chain 'D' and resid 398 through 412 Processing helix chain 'D' and resid 467 through 491 removed outlier: 3.584A pdb=" N PHE D 483 " --> pdb=" O ILE D 479 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 484 " --> pdb=" O PHE D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 528 removed outlier: 3.508A pdb=" N VAL D 513 " --> pdb=" O CYS D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 531 No H-bonds generated for 'chain 'D' and resid 529 through 531' Processing helix chain 'D' and resid 532 through 541 Processing helix chain 'D' and resid 548 through 573 removed outlier: 3.669A pdb=" N LEU D 573 " --> pdb=" O VAL D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 579 removed outlier: 4.661A pdb=" N ASN D 578 " --> pdb=" O LYS D 575 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE D 579 " --> pdb=" O PHE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 619 removed outlier: 4.360A pdb=" N LYS D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 627 Processing helix chain 'D' and resid 628 through 642 Processing helix chain 'D' and resid 645 through 653 removed outlier: 4.101A pdb=" N ILE D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 668 Processing helix chain 'D' and resid 670 through 693 removed outlier: 4.007A pdb=" N ASN D 674 " --> pdb=" O PHE D 670 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AA2, first strand: chain 'A' and resid 308 through 309 removed outlier: 6.355A pdb=" N LEU A 316 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR A 429 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL A 318 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER A 427 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 421 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA4, first strand: chain 'B' and resid 308 through 309 Processing sheet with id=AA5, first strand: chain 'B' and resid 308 through 309 removed outlier: 6.356A pdb=" N LEU B 316 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR B 429 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 318 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N SER B 427 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 421 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 379 through 380 Processing sheet with id=AA7, first strand: chain 'C' and resid 308 through 309 Processing sheet with id=AA8, first strand: chain 'C' and resid 308 through 309 removed outlier: 6.356A pdb=" N LEU C 316 " --> pdb=" O TYR C 429 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR C 429 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL C 318 " --> pdb=" O SER C 427 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER C 427 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA C 421 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 379 through 380 Processing sheet with id=AB1, first strand: chain 'D' and resid 308 through 309 Processing sheet with id=AB2, first strand: chain 'D' and resid 308 through 309 removed outlier: 6.356A pdb=" N LEU D 316 " --> pdb=" O TYR D 429 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR D 429 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL D 318 " --> pdb=" O SER D 427 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER D 427 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA D 421 " --> pdb=" O LEU D 324 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 379 through 380 945 hydrogen bonds defined for protein. 2655 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: 4.71 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 2020 1.24 - 1.38: 4381 1.38 - 1.52: 7660 1.52 - 1.66: 1111 1.66 - 1.81: 104 Bond restraints: 15276 Sorted by residual: bond pdb=" C ALA D 356 " pdb=" N PRO D 357 " ideal model delta sigma weight residual 1.334 1.099 0.235 2.34e-02 1.83e+03 1.01e+02 bond pdb=" C ALA A 356 " pdb=" N PRO A 357 " ideal model delta sigma weight residual 1.334 1.099 0.235 2.34e-02 1.83e+03 1.01e+02 bond pdb=" C ALA C 356 " pdb=" N PRO C 357 " ideal model delta sigma weight residual 1.334 1.099 0.235 2.34e-02 1.83e+03 1.00e+02 bond pdb=" C ALA B 356 " pdb=" N PRO B 357 " ideal model delta sigma weight residual 1.334 1.099 0.235 2.34e-02 1.83e+03 1.00e+02 bond pdb=" CA ILE B 341 " pdb=" C ILE B 341 " ideal model delta sigma weight residual 1.523 1.558 -0.035 1.27e-02 6.20e+03 7.55e+00 ... (remaining 15271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 20316 2.53 - 5.06: 407 5.06 - 7.60: 61 7.60 - 10.13: 12 10.13 - 12.66: 4 Bond angle restraints: 20800 Sorted by residual: angle pdb=" N ALA B 303 " pdb=" CA ALA B 303 " pdb=" C ALA B 303 " ideal model delta sigma weight residual 111.36 118.20 -6.84 1.09e+00 8.42e-01 3.93e+01 angle pdb=" N ALA C 303 " pdb=" CA ALA C 303 " pdb=" C ALA C 303 " ideal model delta sigma weight residual 111.36 118.19 -6.83 1.09e+00 8.42e-01 3.93e+01 angle pdb=" N ALA A 303 " pdb=" CA ALA A 303 " pdb=" C ALA A 303 " ideal model delta sigma weight residual 111.36 118.19 -6.83 1.09e+00 8.42e-01 3.93e+01 angle pdb=" N ALA D 303 " pdb=" CA ALA D 303 " pdb=" C ALA D 303 " ideal model delta sigma weight residual 111.36 118.16 -6.80 1.09e+00 8.42e-01 3.89e+01 angle pdb=" CA ILE C 341 " pdb=" C ILE C 341 " pdb=" N LYS C 342 " ideal model delta sigma weight residual 116.60 124.56 -7.96 1.45e+00 4.76e-01 3.01e+01 ... (remaining 20795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 8640 16.09 - 32.19: 184 32.19 - 48.28: 56 48.28 - 64.37: 0 64.37 - 80.47: 12 Dihedral angle restraints: 8892 sinusoidal: 3408 harmonic: 5484 Sorted by residual: dihedral pdb=" CA ASN A 432 " pdb=" C ASN A 432 " pdb=" N ILE A 433 " pdb=" CA ILE A 433 " ideal model delta harmonic sigma weight residual 180.00 150.00 30.00 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ASN C 432 " pdb=" C ASN C 432 " pdb=" N ILE C 433 " pdb=" CA ILE C 433 " ideal model delta harmonic sigma weight residual 180.00 150.04 29.96 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ASN B 432 " pdb=" C ASN B 432 " pdb=" N ILE B 433 " pdb=" CA ILE B 433 " ideal model delta harmonic sigma weight residual 180.00 150.04 29.96 0 5.00e+00 4.00e-02 3.59e+01 ... (remaining 8889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2345 0.102 - 0.204: 79 0.204 - 0.306: 0 0.306 - 0.409: 0 0.409 - 0.511: 4 Chirality restraints: 2428 Sorted by residual: chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.52e+00 chirality pdb=" C1 NAG C 801 " pdb=" ND2 ASN C 328 " pdb=" C2 NAG C 801 " pdb=" O5 NAG C 801 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.49e+00 chirality pdb=" C1 NAG D 801 " pdb=" ND2 ASN D 328 " pdb=" C2 NAG D 801 " pdb=" O5 NAG D 801 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.48e+00 ... (remaining 2425 not shown) Planarity restraints: 2568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 458 " -0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO D 459 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 459 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 459 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 458 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.59e+00 pdb=" N PRO B 459 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 459 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 459 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 458 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO C 459 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 459 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 459 " -0.029 5.00e-02 4.00e+02 ... (remaining 2565 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 413 2.68 - 3.23: 16979 3.23 - 3.79: 25543 3.79 - 4.34: 32429 4.34 - 4.90: 52321 Nonbonded interactions: 127685 Sorted by model distance: nonbonded pdb=" OH TYR B 227 " pdb=" O VAL B 569 " model vdw 2.124 3.040 nonbonded pdb=" OH TYR D 227 " pdb=" O VAL D 569 " model vdw 2.124 3.040 nonbonded pdb=" OH TYR C 227 " pdb=" O VAL C 569 " model vdw 2.125 3.040 nonbonded pdb=" OH TYR A 227 " pdb=" O VAL A 569 " model vdw 2.125 3.040 nonbonded pdb=" O PRO A 334 " pdb=" NH1 ARG A 338 " model vdw 2.203 3.120 ... (remaining 127680 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.040 Find NCS groups from input model: 0.540 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.011 0.235 15276 Z= 0.689 Angle : 0.905 12.660 20800 Z= 0.504 Chirality : 0.051 0.511 2428 Planarity : 0.005 0.054 2556 Dihedral : 8.890 80.467 5340 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.91 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.16), residues: 1828 helix: -3.19 (0.11), residues: 996 sheet: 0.97 (0.33), residues: 184 loop : -1.92 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP C 380 HIS 0.004 0.002 HIS D 550 PHE 0.018 0.002 PHE A 310 TYR 0.014 0.002 TYR C 386 ARG 0.009 0.001 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 675 MET cc_start: 0.8569 (tpt) cc_final: 0.7933 (tpt) REVERT: D 675 MET cc_start: 0.8600 (tpt) cc_final: 0.7693 (tpt) outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.2755 time to fit residues: 153.2430 Evaluate side-chains 221 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 144 optimal weight: 0.1980 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN A 379 HIS A 458 GLN A 543 ASN A 550 HIS A 636 GLN B 323 GLN B 379 HIS B 458 GLN B 543 ASN B 550 HIS B 636 GLN C 323 GLN C 379 HIS C 458 GLN C 543 ASN C 550 HIS C 636 GLN D 323 GLN D 379 HIS D 458 GLN D 543 ASN D 550 HIS D 636 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15276 Z= 0.248 Angle : 0.656 7.425 20800 Z= 0.364 Chirality : 0.047 0.449 2428 Planarity : 0.005 0.048 2556 Dihedral : 5.274 32.930 2268 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.50 % Favored : 96.28 % Rotamer: Outliers : 1.71 % Allowed : 8.68 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.18), residues: 1828 helix: 0.83 (0.15), residues: 1040 sheet: 1.05 (0.34), residues: 184 loop : -1.50 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 293 HIS 0.002 0.001 HIS B 379 PHE 0.018 0.002 PHE A 676 TYR 0.020 0.002 TYR A 527 ARG 0.004 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 270 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 675 MET cc_start: 0.8026 (tpt) cc_final: 0.7534 (tpt) REVERT: B 675 MET cc_start: 0.8020 (tpt) cc_final: 0.7475 (tpt) outliers start: 26 outliers final: 12 residues processed: 278 average time/residue: 0.2947 time to fit residues: 117.0453 Evaluate side-chains 211 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 199 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 236 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 46 optimal weight: 20.0000 chunk 167 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 GLN B 542 GLN C 542 GLN D 542 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.052 15276 Z= 0.553 Angle : 0.738 7.555 20800 Z= 0.401 Chirality : 0.050 0.412 2428 Planarity : 0.005 0.050 2556 Dihedral : 5.395 30.336 2268 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.54 % Favored : 95.08 % Rotamer: Outliers : 3.49 % Allowed : 11.71 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.19), residues: 1828 helix: 1.31 (0.15), residues: 1028 sheet: 0.43 (0.33), residues: 192 loop : -1.68 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 293 HIS 0.002 0.001 HIS C 379 PHE 0.018 0.002 PHE D 576 TYR 0.026 0.002 TYR B 249 ARG 0.006 0.001 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 226 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 675 MET cc_start: 0.8148 (tpt) cc_final: 0.7770 (tpt) REVERT: B 675 MET cc_start: 0.8145 (tpt) cc_final: 0.7719 (tpt) outliers start: 53 outliers final: 31 residues processed: 247 average time/residue: 0.2683 time to fit residues: 98.6222 Evaluate side-chains 208 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 526 ILE Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 662 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 519 VAL Chi-restraints excluded: chain D residue 526 ILE Chi-restraints excluded: chain D residue 662 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN A 434 ASN A 542 GLN B 313 ASN B 434 ASN B 542 GLN C 313 ASN C 434 ASN C 542 GLN D 434 ASN D 542 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15276 Z= 0.195 Angle : 0.573 7.385 20800 Z= 0.316 Chirality : 0.043 0.389 2428 Planarity : 0.004 0.046 2556 Dihedral : 4.729 30.112 2268 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.32 % Favored : 95.46 % Rotamer: Outliers : 1.71 % Allowed : 13.95 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1828 helix: 1.80 (0.16), residues: 1040 sheet: 0.59 (0.34), residues: 192 loop : -1.64 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 293 HIS 0.002 0.000 HIS B 379 PHE 0.018 0.001 PHE B 676 TYR 0.017 0.001 TYR B 239 ARG 0.003 0.000 ARG D 581 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 1.628 Fit side-chains outliers start: 26 outliers final: 8 residues processed: 237 average time/residue: 0.2871 time to fit residues: 97.9646 Evaluate side-chains 211 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 203 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 484 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 2 optimal weight: 30.0000 chunk 132 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15276 Z= 0.224 Angle : 0.573 7.285 20800 Z= 0.315 Chirality : 0.043 0.372 2428 Planarity : 0.004 0.047 2556 Dihedral : 4.563 26.772 2268 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.77 % Favored : 96.01 % Rotamer: Outliers : 2.24 % Allowed : 15.07 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.20), residues: 1828 helix: 1.87 (0.16), residues: 1028 sheet: 0.47 (0.34), residues: 192 loop : -1.57 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 293 HIS 0.002 0.000 HIS B 379 PHE 0.017 0.001 PHE A 600 TYR 0.017 0.001 TYR A 486 ARG 0.004 0.000 ARG D 581 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 232 time to evaluate : 1.740 Fit side-chains outliers start: 34 outliers final: 21 residues processed: 255 average time/residue: 0.2941 time to fit residues: 110.0131 Evaluate side-chains 235 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 572 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 5.9990 chunk 160 optimal weight: 0.0170 chunk 35 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 313 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15276 Z= 0.206 Angle : 0.552 7.219 20800 Z= 0.305 Chirality : 0.042 0.360 2428 Planarity : 0.004 0.047 2556 Dihedral : 4.392 22.682 2268 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.77 % Favored : 96.01 % Rotamer: Outliers : 1.78 % Allowed : 15.66 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.20), residues: 1828 helix: 1.85 (0.16), residues: 1040 sheet: 0.47 (0.34), residues: 192 loop : -1.39 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 293 HIS 0.002 0.000 HIS B 379 PHE 0.028 0.001 PHE A 469 TYR 0.017 0.001 TYR A 486 ARG 0.003 0.000 ARG D 581 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 1.841 Fit side-chains REVERT: B 603 MET cc_start: 0.8437 (ttp) cc_final: 0.8167 (ttp) REVERT: C 590 MET cc_start: 0.7291 (mmm) cc_final: 0.6999 (mmm) REVERT: C 688 LYS cc_start: 0.7889 (ttmm) cc_final: 0.7645 (mttm) outliers start: 27 outliers final: 23 residues processed: 248 average time/residue: 0.2993 time to fit residues: 106.8575 Evaluate side-chains 238 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 215 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 572 LYS Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 572 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 0.0270 chunk 99 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15276 Z= 0.169 Angle : 0.537 7.221 20800 Z= 0.299 Chirality : 0.042 0.351 2428 Planarity : 0.004 0.045 2556 Dihedral : 4.229 20.551 2268 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.67 % Favored : 96.12 % Rotamer: Outliers : 2.04 % Allowed : 16.91 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.20), residues: 1828 helix: 1.83 (0.16), residues: 1048 sheet: 0.62 (0.35), residues: 184 loop : -1.19 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 293 HIS 0.002 0.001 HIS B 379 PHE 0.037 0.001 PHE D 469 TYR 0.019 0.001 TYR C 486 ARG 0.003 0.000 ARG D 397 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 1.636 Fit side-chains REVERT: A 583 MET cc_start: 0.7377 (mmm) cc_final: 0.7113 (mmm) REVERT: A 597 LEU cc_start: 0.7806 (mt) cc_final: 0.7338 (mt) REVERT: B 583 MET cc_start: 0.7328 (mmm) cc_final: 0.7002 (mmm) REVERT: B 597 LEU cc_start: 0.7830 (mt) cc_final: 0.7361 (mt) REVERT: B 603 MET cc_start: 0.8411 (ttp) cc_final: 0.8128 (ttt) REVERT: C 590 MET cc_start: 0.7241 (mmm) cc_final: 0.7010 (mmm) REVERT: C 668 MET cc_start: 0.8581 (tpp) cc_final: 0.8364 (mmp) REVERT: D 464 ARG cc_start: 0.7161 (mtp85) cc_final: 0.6955 (mtp85) REVERT: D 583 MET cc_start: 0.7370 (mmm) cc_final: 0.7116 (mmm) REVERT: D 597 LEU cc_start: 0.7833 (mt) cc_final: 0.7356 (mt) REVERT: D 668 MET cc_start: 0.8593 (tpp) cc_final: 0.8372 (mmp) outliers start: 31 outliers final: 23 residues processed: 260 average time/residue: 0.3005 time to fit residues: 111.7732 Evaluate side-chains 252 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 229 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 484 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 105 optimal weight: 0.0170 chunk 53 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 120 optimal weight: 0.0050 chunk 87 optimal weight: 0.5980 chunk 16 optimal weight: 0.0670 chunk 139 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.2570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15276 Z= 0.140 Angle : 0.511 7.218 20800 Z= 0.284 Chirality : 0.041 0.336 2428 Planarity : 0.004 0.043 2556 Dihedral : 4.014 21.596 2268 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.28 % Favored : 96.50 % Rotamer: Outliers : 1.97 % Allowed : 17.37 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.20), residues: 1828 helix: 1.92 (0.16), residues: 1044 sheet: 0.80 (0.35), residues: 184 loop : -1.06 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 293 HIS 0.002 0.001 HIS D 379 PHE 0.031 0.001 PHE C 469 TYR 0.022 0.001 TYR D 486 ARG 0.003 0.000 ARG C 581 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 268 time to evaluate : 1.762 Fit side-chains REVERT: A 464 ARG cc_start: 0.7179 (mtp85) cc_final: 0.6779 (mtt90) REVERT: A 583 MET cc_start: 0.7286 (mmm) cc_final: 0.7020 (mmm) REVERT: A 668 MET cc_start: 0.8534 (tpp) cc_final: 0.8284 (mmp) REVERT: B 583 MET cc_start: 0.7336 (mmm) cc_final: 0.7043 (mmm) REVERT: B 668 MET cc_start: 0.8534 (tpp) cc_final: 0.8223 (mmp) REVERT: C 464 ARG cc_start: 0.7176 (mtp85) cc_final: 0.6775 (mtt90) REVERT: C 668 MET cc_start: 0.8485 (tpp) cc_final: 0.8251 (mmp) REVERT: D 668 MET cc_start: 0.8511 (tpp) cc_final: 0.8284 (mmp) outliers start: 30 outliers final: 8 residues processed: 286 average time/residue: 0.2793 time to fit residues: 116.7563 Evaluate side-chains 235 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 227 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 484 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.2980 chunk 155 optimal weight: 6.9990 chunk 165 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 585 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15276 Z= 0.179 Angle : 0.534 7.207 20800 Z= 0.295 Chirality : 0.041 0.332 2428 Planarity : 0.004 0.045 2556 Dihedral : 4.178 21.833 2268 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.34 % Favored : 96.44 % Rotamer: Outliers : 1.64 % Allowed : 18.75 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.20), residues: 1828 helix: 1.97 (0.16), residues: 1044 sheet: 0.68 (0.36), residues: 184 loop : -1.10 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 293 HIS 0.003 0.001 HIS C 379 PHE 0.028 0.001 PHE D 469 TYR 0.021 0.001 TYR D 486 ARG 0.004 0.000 ARG D 464 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 1.705 Fit side-chains REVERT: A 464 ARG cc_start: 0.7206 (mtp85) cc_final: 0.6786 (mtt90) REVERT: A 668 MET cc_start: 0.8595 (tpp) cc_final: 0.8352 (mmp) REVERT: B 668 MET cc_start: 0.8558 (tpp) cc_final: 0.8239 (mmp) REVERT: C 464 ARG cc_start: 0.7148 (mtp85) cc_final: 0.6727 (mtt90) REVERT: C 668 MET cc_start: 0.8573 (tpp) cc_final: 0.8338 (mmp) REVERT: D 464 ARG cc_start: 0.7229 (mtp85) cc_final: 0.6933 (mtt90) REVERT: D 668 MET cc_start: 0.8593 (tpp) cc_final: 0.8354 (mmp) outliers start: 25 outliers final: 12 residues processed: 240 average time/residue: 0.2819 time to fit residues: 99.5955 Evaluate side-chains 232 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 220 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 411 LYS Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 411 LYS Chi-restraints excluded: chain D residue 484 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15276 Z= 0.228 Angle : 0.558 7.188 20800 Z= 0.307 Chirality : 0.042 0.331 2428 Planarity : 0.004 0.048 2556 Dihedral : 4.199 19.584 2268 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.56 % Favored : 96.23 % Rotamer: Outliers : 1.25 % Allowed : 19.14 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.20), residues: 1828 helix: 1.86 (0.16), residues: 1048 sheet: 0.39 (0.35), residues: 184 loop : -1.13 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 293 HIS 0.003 0.001 HIS D 379 PHE 0.024 0.001 PHE A 469 TYR 0.022 0.001 TYR D 486 ARG 0.007 0.000 ARG C 581 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 223 time to evaluate : 1.548 Fit side-chains REVERT: A 597 LEU cc_start: 0.7851 (mt) cc_final: 0.7381 (mt) REVERT: A 668 MET cc_start: 0.8592 (tpp) cc_final: 0.8353 (mmp) REVERT: B 597 LEU cc_start: 0.7878 (mt) cc_final: 0.7397 (mt) REVERT: C 597 LEU cc_start: 0.7833 (mt) cc_final: 0.7368 (mt) REVERT: C 668 MET cc_start: 0.8606 (tpp) cc_final: 0.8352 (mmp) REVERT: D 464 ARG cc_start: 0.7271 (mtp85) cc_final: 0.6978 (mtt90) REVERT: D 668 MET cc_start: 0.8613 (tpp) cc_final: 0.8373 (mmp) outliers start: 19 outliers final: 14 residues processed: 234 average time/residue: 0.2863 time to fit residues: 98.4701 Evaluate side-chains 232 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 483 PHE Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 484 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 134 optimal weight: 0.0970 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 146 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.132413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.097975 restraints weight = 22714.339| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.56 r_work: 0.3067 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15276 Z= 0.172 Angle : 0.540 7.193 20800 Z= 0.297 Chirality : 0.042 0.332 2428 Planarity : 0.004 0.045 2556 Dihedral : 4.110 19.759 2268 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.72 % Favored : 96.06 % Rotamer: Outliers : 1.45 % Allowed : 18.88 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.20), residues: 1828 helix: 1.83 (0.16), residues: 1048 sheet: 0.43 (0.35), residues: 184 loop : -1.10 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 293 HIS 0.002 0.001 HIS A 379 PHE 0.029 0.001 PHE B 469 TYR 0.022 0.001 TYR D 486 ARG 0.007 0.000 ARG C 581 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3005.77 seconds wall clock time: 55 minutes 50.50 seconds (3350.50 seconds total)