Starting phenix.real_space_refine on Wed Mar 4 10:05:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a9a_15274/03_2026/8a9a_15274.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a9a_15274/03_2026/8a9a_15274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8a9a_15274/03_2026/8a9a_15274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a9a_15274/03_2026/8a9a_15274.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8a9a_15274/03_2026/8a9a_15274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a9a_15274/03_2026/8a9a_15274.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.033 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 16 5.16 5 C 8240 2.51 5 N 2054 2.21 5 O 2462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12772 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 6386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6386 Classifications: {'peptide': 809} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 786} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Restraints were copied for chains: A Time building chain proxies: 6.27, per 1000 atoms: 0.49 Number of scatterers: 12772 At special positions: 0 Unit cell: (86.1, 115.5, 257.25, 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 16 16.00 O 2462 8.00 N 2054 7.00 C 8240 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: 1.00 Conformation dependent library (CDL) restraints added in 710.2 milliseconds 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 6 sheets defined 46.2% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'B' and resid 95 through 106 removed outlier: 4.063A pdb=" N GLY B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 125 removed outlier: 3.766A pdb=" N ALA B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.171A pdb=" N ASN B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 267 Processing helix chain 'B' and resid 268 through 294 removed outlier: 3.554A pdb=" N ILE B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.649A pdb=" N GLU B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 319 removed outlier: 4.023A pdb=" N LYS B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 331 removed outlier: 3.708A pdb=" N ARG B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 342 removed outlier: 3.663A pdb=" N LYS B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.598A pdb=" N ASP B 360 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 371 Processing helix chain 'B' and resid 376 through 382 removed outlier: 3.866A pdb=" N SER B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 393 through 415 removed outlier: 4.583A pdb=" N ASP B 406 " --> pdb=" O GLN B 402 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Proline residue: B 410 - end of helix Processing helix chain 'B' and resid 421 through 429 removed outlier: 3.690A pdb=" N ILE B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 443 Processing helix chain 'B' and resid 443 through 462 Processing helix chain 'B' and resid 465 through 477 Processing helix chain 'B' and resid 478 through 486 removed outlier: 3.882A pdb=" N LEU B 484 " --> pdb=" O ALA B 481 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 486 " --> pdb=" O ASP B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 499 removed outlier: 4.189A pdb=" N ALA B 495 " --> pdb=" O VAL B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 514 removed outlier: 3.976A pdb=" N ASP B 514 " --> pdb=" O GLU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 525 Processing helix chain 'B' and resid 532 through 540 Processing helix chain 'B' and resid 552 through 557 removed outlier: 4.108A pdb=" N GLU B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 552 through 557' Processing helix chain 'B' and resid 565 through 584 removed outlier: 4.136A pdb=" N GLU B 569 " --> pdb=" O ASP B 565 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 593 removed outlier: 4.018A pdb=" N LYS B 593 " --> pdb=" O THR B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 644 removed outlier: 3.584A pdb=" N LEU B 644 " --> pdb=" O MET B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 659 Processing helix chain 'B' and resid 663 through 674 Processing helix chain 'B' and resid 685 through 690 Processing helix chain 'B' and resid 691 through 701 removed outlier: 3.819A pdb=" N PHE B 697 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B 701 " --> pdb=" O PHE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 716 Processing helix chain 'B' and resid 719 through 723 Processing helix chain 'B' and resid 797 through 816 Processing helix chain 'A' and resid 95 through 106 removed outlier: 4.062A pdb=" N GLY A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 125 removed outlier: 3.767A pdb=" N ALA A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 4.171A pdb=" N ASN A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 267 Processing helix chain 'A' and resid 268 through 294 removed outlier: 3.554A pdb=" N ILE A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 304 removed outlier: 3.649A pdb=" N GLU A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 319 removed outlier: 4.023A pdb=" N LYS A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 331 removed outlier: 3.708A pdb=" N ARG A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 342 removed outlier: 3.663A pdb=" N LYS A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.598A pdb=" N ASP A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 371 Processing helix chain 'A' and resid 376 through 382 removed outlier: 3.867A pdb=" N SER A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 393 through 415 removed outlier: 4.584A pdb=" N ASP A 406 " --> pdb=" O GLN A 402 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Proline residue: A 410 - end of helix Processing helix chain 'A' and resid 421 through 429 removed outlier: 3.690A pdb=" N ILE A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 443 through 462 Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 478 through 486 removed outlier: 3.882A pdb=" N LEU A 484 " --> pdb=" O ALA A 481 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A 486 " --> pdb=" O ASP A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 499 removed outlier: 4.189A pdb=" N ALA A 495 " --> pdb=" O VAL A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.977A pdb=" N ASP A 514 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 525 Processing helix chain 'A' and resid 532 through 540 Processing helix chain 'A' and resid 552 through 557 removed outlier: 4.110A pdb=" N GLU A 556 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 552 through 557' Processing helix chain 'A' and resid 565 through 584 removed outlier: 4.137A pdb=" N GLU A 569 " --> pdb=" O ASP A 565 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 4.017A pdb=" N LYS A 593 " --> pdb=" O THR A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 644 removed outlier: 3.583A pdb=" N LEU A 644 " --> pdb=" O MET A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 Processing helix chain 'A' and resid 663 through 674 Processing helix chain 'A' and resid 685 through 690 Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.818A pdb=" N PHE A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 701 " --> pdb=" O PHE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 716 Processing helix chain 'A' and resid 719 through 723 Processing helix chain 'A' and resid 797 through 816 Processing sheet with id=AA1, first strand: chain 'B' and resid 135 through 143 removed outlier: 5.485A pdb=" N LEU B 136 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR B 160 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ALA B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ARG B 158 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG B 140 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA B 151 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ALA B 193 " --> pdb=" O ALA B 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 184 through 194 current: chain 'B' and resid 211 through 219 removed outlier: 7.590A pdb=" N MET B 213 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N SER B 228 " --> pdb=" O MET B 213 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASP B 215 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE B 217 " --> pdb=" O VAL B 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 167 through 168 removed outlier: 3.551A pdb=" N VAL B 179 " --> pdb=" O GLN B 167 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 595 through 598 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 595 through 598 current: chain 'B' and resid 615 through 620 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 615 through 620 current: chain 'B' and resid 728 through 750 removed outlier: 9.593A pdb=" N TYR B 740 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N ILE B 770 " --> pdb=" O TYR B 740 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N GLY B 742 " --> pdb=" O THR B 768 " (cutoff:3.500A) removed outlier: 9.987A pdb=" N THR B 768 " --> pdb=" O GLY B 742 " (cutoff:3.500A) removed outlier: 11.562A pdb=" N ASN B 744 " --> pdb=" O VAL B 766 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N VAL B 766 " --> pdb=" O ASN B 744 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN B 746 " --> pdb=" O ILE B 764 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 135 through 143 removed outlier: 5.485A pdb=" N LEU A 136 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR A 160 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ALA A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ARG A 158 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG A 140 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA A 151 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA A 193 " --> pdb=" O ALA A 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 184 through 194 current: chain 'A' and resid 211 through 219 removed outlier: 7.589A pdb=" N MET A 213 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N SER A 228 " --> pdb=" O MET A 213 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASP A 215 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE A 217 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 167 through 168 removed outlier: 3.552A pdb=" N VAL A 179 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 595 through 598 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 595 through 598 current: chain 'A' and resid 615 through 620 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 615 through 620 current: chain 'A' and resid 728 through 750 removed outlier: 9.594A pdb=" N TYR A 740 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N ILE A 770 " --> pdb=" O TYR A 740 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N GLY A 742 " --> pdb=" O THR A 768 " (cutoff:3.500A) removed outlier: 9.987A pdb=" N THR A 768 " --> pdb=" O GLY A 742 " (cutoff:3.500A) removed outlier: 11.562A pdb=" N ASN A 744 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N VAL A 766 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN A 746 " --> pdb=" O ILE A 764 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1332 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: 2.25 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4078 1.34 - 1.46: 2682 1.46 - 1.58: 6202 1.58 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 12994 Sorted by residual: bond pdb=" CB LYS A 363 " pdb=" CG LYS A 363 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.40e+00 bond pdb=" CB LYS B 363 " pdb=" CG LYS B 363 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.37e+00 bond pdb=" N PRO B 61 " pdb=" CA PRO B 61 " ideal model delta sigma weight residual 1.469 1.454 0.014 1.28e-02 6.10e+03 1.26e+00 bond pdb=" N PRO A 61 " pdb=" CA PRO A 61 " ideal model delta sigma weight residual 1.469 1.455 0.014 1.28e-02 6.10e+03 1.23e+00 bond pdb=" CB ASN B 328 " pdb=" CG ASN B 328 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.11e-01 ... (remaining 12989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 17081 1.80 - 3.60: 340 3.60 - 5.40: 53 5.40 - 7.20: 22 7.20 - 9.00: 16 Bond angle restraints: 17512 Sorted by residual: angle pdb=" N PRO A 61 " pdb=" CA PRO A 61 " pdb=" CB PRO A 61 " ideal model delta sigma weight residual 103.25 110.58 -7.33 1.05e+00 9.07e-01 4.88e+01 angle pdb=" N PRO B 61 " pdb=" CA PRO B 61 " pdb=" CB PRO B 61 " ideal model delta sigma weight residual 103.25 110.55 -7.30 1.05e+00 9.07e-01 4.83e+01 angle pdb=" N LEU B 546 " pdb=" CA LEU B 546 " pdb=" C LEU B 546 " ideal model delta sigma weight residual 114.31 109.99 4.32 1.29e+00 6.01e-01 1.12e+01 angle pdb=" N LEU A 546 " pdb=" CA LEU A 546 " pdb=" C LEU A 546 " ideal model delta sigma weight residual 114.31 110.03 4.28 1.29e+00 6.01e-01 1.10e+01 angle pdb=" CA LYS B 363 " pdb=" CB LYS B 363 " pdb=" CG LYS B 363 " ideal model delta sigma weight residual 114.10 120.36 -6.26 2.00e+00 2.50e-01 9.80e+00 ... (remaining 17507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 6597 17.65 - 35.29: 991 35.29 - 52.94: 244 52.94 - 70.59: 46 70.59 - 88.24: 20 Dihedral angle restraints: 7898 sinusoidal: 3178 harmonic: 4720 Sorted by residual: dihedral pdb=" CA PHE B 817 " pdb=" C PHE B 817 " pdb=" N GLN B 818 " pdb=" CA GLN B 818 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA PHE A 817 " pdb=" C PHE A 817 " pdb=" N GLN A 818 " pdb=" CA GLN A 818 " ideal model delta harmonic sigma weight residual -180.00 -156.79 -23.21 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA LEU B 524 " pdb=" C LEU B 524 " pdb=" N LEU B 525 " pdb=" CA LEU B 525 " ideal model delta harmonic sigma weight residual 180.00 162.57 17.43 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 7895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1509 0.044 - 0.088: 378 0.088 - 0.132: 94 0.132 - 0.176: 11 0.176 - 0.219: 6 Chirality restraints: 1998 Sorted by residual: chirality pdb=" CA PRO B 61 " pdb=" N PRO B 61 " pdb=" C PRO B 61 " pdb=" CB PRO B 61 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA PRO A 61 " pdb=" N PRO A 61 " pdb=" C PRO A 61 " pdb=" CB PRO A 61 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA PHE B 111 " pdb=" N PHE B 111 " pdb=" C PHE B 111 " pdb=" CB PHE B 111 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1995 not shown) Planarity restraints: 2242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 331 " 0.059 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO B 332 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO B 332 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 332 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 331 " 0.059 5.00e-02 4.00e+02 8.95e-02 1.28e+01 pdb=" N PRO A 332 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 374 " -0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO A 375 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " -0.045 5.00e-02 4.00e+02 ... (remaining 2239 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 265 2.67 - 3.23: 12490 3.23 - 3.79: 19940 3.79 - 4.34: 27205 4.34 - 4.90: 44018 Nonbonded interactions: 103918 Sorted by model distance: nonbonded pdb=" OG1 THR B 144 " pdb=" OG SER B 152 " model vdw 2.116 3.040 nonbonded pdb=" OG1 THR A 144 " pdb=" OG SER A 152 " model vdw 2.117 3.040 nonbonded pdb=" O THR A 610 " pdb=" OG1 THR A 613 " model vdw 2.201 3.040 nonbonded pdb=" O THR B 610 " pdb=" OG1 THR B 613 " model vdw 2.202 3.040 nonbonded pdb=" O ILE B 816 " pdb=" OH TYR B 821 " model vdw 2.233 3.040 ... (remaining 103913 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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: 14.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 16.260 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5657 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 : 0.003 0.036 12994 Z= 0.138 Angle : 0.666 8.999 17512 Z= 0.345 Chirality : 0.043 0.219 1998 Planarity : 0.005 0.090 2242 Dihedral : 18.003 88.236 4838 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.53 % Favored : 89.10 % Rotamer: Outliers : 0.14 % Allowed : 29.36 % Favored : 70.50 % 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: -1.45 (0.21), residues: 1614 helix: 0.19 (0.21), residues: 640 sheet: -0.07 (0.46), residues: 136 loop : -2.12 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 331 TYR 0.010 0.001 TYR A 761 PHE 0.016 0.001 PHE B 485 TRP 0.004 0.001 TRP A 681 HIS 0.005 0.001 HIS B 580 Details of bonding type rmsd covalent geometry : bond 0.00295 (12994) covalent geometry : angle 0.66562 (17512) hydrogen bonds : bond 0.15909 ( 464) hydrogen bonds : angle 7.16635 ( 1332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 284 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 LEU cc_start: 0.8492 (mt) cc_final: 0.8268 (mt) REVERT: B 465 MET cc_start: 0.5288 (mmp) cc_final: 0.5043 (mmm) REVERT: B 711 PHE cc_start: 0.7701 (m-80) cc_final: 0.7487 (m-80) REVERT: A 534 ASP cc_start: 0.4215 (t70) cc_final: 0.3934 (t0) outliers start: 2 outliers final: 1 residues processed: 286 average time/residue: 0.1262 time to fit residues: 51.0661 Evaluate side-chains 148 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 781 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN B 245 ASN B 279 ASN B 361 ASN A 584 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 GLN A 803 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.221434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.190954 restraints weight = 19704.959| |-----------------------------------------------------------------------------| r_work (start): 0.4365 rms_B_bonded: 2.31 r_work: 0.4002 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 12994 Z= 0.296 Angle : 0.839 9.070 17512 Z= 0.435 Chirality : 0.050 0.256 1998 Planarity : 0.005 0.072 2242 Dihedral : 5.775 35.566 1682 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.71 % Favored : 87.98 % Rotamer: Outliers : 6.00 % Allowed : 23.93 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.20), residues: 1614 helix: -0.76 (0.19), residues: 646 sheet: -0.81 (0.44), residues: 156 loop : -2.04 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 832 TYR 0.026 0.003 TYR A 752 PHE 0.030 0.002 PHE B 458 TRP 0.015 0.002 TRP B 681 HIS 0.008 0.002 HIS B 580 Details of bonding type rmsd covalent geometry : bond 0.00679 (12994) covalent geometry : angle 0.83929 (17512) hydrogen bonds : bond 0.05098 ( 464) hydrogen bonds : angle 5.92630 ( 1332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 155 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7749 (tt) REVERT: B 567 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6890 (mttm) REVERT: B 667 MET cc_start: 0.7553 (tmm) cc_final: 0.7265 (tmm) REVERT: B 695 ASN cc_start: 0.7734 (t0) cc_final: 0.7199 (t0) REVERT: A 341 LEU cc_start: 0.8044 (tt) cc_final: 0.7830 (tp) REVERT: A 361 ASN cc_start: 0.4577 (OUTLIER) cc_final: 0.4250 (p0) REVERT: A 393 ASP cc_start: 0.4434 (OUTLIER) cc_final: 0.3679 (t70) REVERT: A 427 GLU cc_start: 0.4006 (OUTLIER) cc_final: 0.1535 (mp0) REVERT: A 668 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6729 (tttt) REVERT: A 669 ASP cc_start: 0.8478 (m-30) cc_final: 0.8249 (m-30) REVERT: A 695 ASN cc_start: 0.6705 (t0) cc_final: 0.6152 (t0) REVERT: A 714 MET cc_start: 0.8354 (ttt) cc_final: 0.8113 (ttt) REVERT: A 739 LYS cc_start: 0.6470 (mmtt) cc_final: 0.6195 (tptp) REVERT: A 785 LYS cc_start: 0.6985 (mttp) cc_final: 0.6760 (tttt) outliers start: 84 outliers final: 32 residues processed: 230 average time/residue: 0.1075 time to fit residues: 37.0024 Evaluate side-chains 152 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 773 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 11 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 128 optimal weight: 0.5980 chunk 57 optimal weight: 0.4980 chunk 118 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 111 optimal weight: 0.7980 chunk 141 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 ASN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 ASN A 235 ASN A 431 GLN A 449 ASN ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.220517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.187456 restraints weight = 19850.516| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 2.28 r_work: 0.3987 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12994 Z= 0.174 Angle : 0.669 8.373 17512 Z= 0.345 Chirality : 0.044 0.159 1998 Planarity : 0.004 0.061 2242 Dihedral : 5.357 31.908 1682 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.91 % Favored : 89.78 % Rotamer: Outliers : 5.07 % Allowed : 25.43 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.20), residues: 1614 helix: -0.67 (0.19), residues: 662 sheet: -1.30 (0.40), residues: 178 loop : -2.09 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 400 TYR 0.018 0.002 TYR B 79 PHE 0.017 0.002 PHE A 327 TRP 0.005 0.001 TRP B 681 HIS 0.006 0.001 HIS B 580 Details of bonding type rmsd covalent geometry : bond 0.00396 (12994) covalent geometry : angle 0.66870 (17512) hydrogen bonds : bond 0.04142 ( 464) hydrogen bonds : angle 5.60308 ( 1332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 131 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 567 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6948 (mttp) REVERT: B 637 ILE cc_start: 0.6995 (OUTLIER) cc_final: 0.6773 (tt) REVERT: B 667 MET cc_start: 0.7524 (tmm) cc_final: 0.7300 (tmm) REVERT: B 695 ASN cc_start: 0.7621 (t0) cc_final: 0.7156 (t0) REVERT: B 864 LEU cc_start: 0.4753 (tp) cc_final: 0.4530 (tp) REVERT: A 294 MET cc_start: 0.7254 (ptp) cc_final: 0.6934 (ptm) REVERT: A 347 GLN cc_start: 0.6841 (tp-100) cc_final: 0.5325 (mp10) REVERT: A 496 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8178 (tt0) REVERT: A 695 ASN cc_start: 0.6752 (t0) cc_final: 0.6234 (t0) REVERT: A 739 LYS cc_start: 0.6609 (mmtt) cc_final: 0.6257 (tptt) REVERT: A 748 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.7018 (pp) outliers start: 71 outliers final: 33 residues processed: 193 average time/residue: 0.0881 time to fit residues: 26.7671 Evaluate side-chains 145 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 746 ASN Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 835 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 105 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 chunk 123 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 66 optimal weight: 0.0470 chunk 148 optimal weight: 6.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 367 ASN ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 803 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.223152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.191861 restraints weight = 19526.227| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 2.42 r_work: 0.4014 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12994 Z= 0.152 Angle : 0.653 12.493 17512 Z= 0.333 Chirality : 0.043 0.148 1998 Planarity : 0.004 0.050 2242 Dihedral : 5.145 22.911 1680 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.22 % Favored : 89.47 % Rotamer: Outliers : 5.64 % Allowed : 25.29 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.20), residues: 1614 helix: -0.55 (0.19), residues: 658 sheet: -1.05 (0.44), residues: 154 loop : -2.13 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 400 TYR 0.016 0.001 TYR B 79 PHE 0.018 0.001 PHE B 232 TRP 0.007 0.001 TRP A 121 HIS 0.007 0.001 HIS A 580 Details of bonding type rmsd covalent geometry : bond 0.00341 (12994) covalent geometry : angle 0.65265 (17512) hydrogen bonds : bond 0.03822 ( 464) hydrogen bonds : angle 5.47711 ( 1332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 128 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 MET cc_start: 0.6669 (ppp) cc_final: 0.6421 (ppp) REVERT: B 341 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7728 (tt) REVERT: B 404 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.6809 (t80) REVERT: B 427 GLU cc_start: 0.5602 (pm20) cc_final: 0.4909 (pt0) REVERT: B 567 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6896 (mttp) REVERT: B 637 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6783 (tt) REVERT: B 667 MET cc_start: 0.7512 (tmm) cc_final: 0.7303 (tmm) REVERT: B 695 ASN cc_start: 0.7512 (t0) cc_final: 0.7088 (t0) REVERT: B 864 LEU cc_start: 0.4704 (tp) cc_final: 0.4447 (tp) REVERT: A 213 MET cc_start: 0.6857 (pmm) cc_final: 0.5477 (mmt) REVERT: A 294 MET cc_start: 0.7296 (ptp) cc_final: 0.6987 (ptm) REVERT: A 347 GLN cc_start: 0.6673 (tp-100) cc_final: 0.5230 (mp10) REVERT: A 496 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8169 (tt0) REVERT: A 668 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6694 (tttt) REVERT: A 695 ASN cc_start: 0.6827 (t0) cc_final: 0.6312 (t0) REVERT: A 739 LYS cc_start: 0.6408 (mmtt) cc_final: 0.6099 (tptt) REVERT: A 748 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7070 (pp) REVERT: A 762 GLN cc_start: 0.5590 (OUTLIER) cc_final: 0.5375 (tm-30) outliers start: 79 outliers final: 40 residues processed: 200 average time/residue: 0.0975 time to fit residues: 30.1769 Evaluate side-chains 156 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 109 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 835 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 54 optimal weight: 0.0970 chunk 26 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 459 GLN B 718 ASN B 746 ASN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 803 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.221796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.190841 restraints weight = 19509.846| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 2.32 r_work: 0.3970 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12994 Z= 0.178 Angle : 0.677 10.152 17512 Z= 0.345 Chirality : 0.045 0.184 1998 Planarity : 0.004 0.043 2242 Dihedral : 5.238 23.910 1680 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.97 % Favored : 88.79 % Rotamer: Outliers : 5.36 % Allowed : 25.79 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.20), residues: 1614 helix: -0.53 (0.20), residues: 642 sheet: -1.06 (0.43), residues: 158 loop : -2.16 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 400 TYR 0.013 0.001 TYR A 761 PHE 0.016 0.001 PHE B 127 TRP 0.006 0.001 TRP A 121 HIS 0.008 0.002 HIS A 580 Details of bonding type rmsd covalent geometry : bond 0.00409 (12994) covalent geometry : angle 0.67709 (17512) hydrogen bonds : bond 0.04021 ( 464) hydrogen bonds : angle 5.54920 ( 1332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 122 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 MET cc_start: 0.6684 (ppp) cc_final: 0.6398 (ppp) REVERT: B 341 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7759 (tt) REVERT: B 404 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.6893 (t80) REVERT: B 427 GLU cc_start: 0.5797 (OUTLIER) cc_final: 0.5211 (pt0) REVERT: B 567 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6978 (mttm) REVERT: B 667 MET cc_start: 0.7548 (tmm) cc_final: 0.7344 (tmm) REVERT: B 695 ASN cc_start: 0.7483 (t0) cc_final: 0.7081 (t0) REVERT: B 864 LEU cc_start: 0.4804 (tp) cc_final: 0.4558 (tp) REVERT: A 213 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6208 (mmt) REVERT: A 294 MET cc_start: 0.7375 (ptp) cc_final: 0.7070 (ptm) REVERT: A 347 GLN cc_start: 0.6812 (tp-100) cc_final: 0.5291 (mp10) REVERT: A 496 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8231 (tt0) REVERT: A 695 ASN cc_start: 0.7161 (t0) cc_final: 0.6608 (t0) REVERT: A 748 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6912 (pp) REVERT: A 799 GLN cc_start: 0.7289 (tm130) cc_final: 0.6818 (tm-30) outliers start: 75 outliers final: 41 residues processed: 189 average time/residue: 0.0978 time to fit residues: 28.6013 Evaluate side-chains 152 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 105 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 805 TRP Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 835 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 106 optimal weight: 0.3980 chunk 109 optimal weight: 0.1980 chunk 112 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 0.0170 chunk 140 optimal weight: 0.6980 chunk 76 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 overall best weight: 0.2418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN A 347 GLN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 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 = 0.4679 r_free = 0.4679 target = 0.224160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.194318 restraints weight = 19423.883| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 2.20 r_work: 0.4032 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12994 Z= 0.126 Angle : 0.635 9.091 17512 Z= 0.323 Chirality : 0.043 0.145 1998 Planarity : 0.004 0.042 2242 Dihedral : 4.971 23.648 1680 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.67 % Favored : 90.09 % Rotamer: Outliers : 4.07 % Allowed : 26.79 % Favored : 69.14 % 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: -1.95 (0.20), residues: 1614 helix: -0.42 (0.20), residues: 666 sheet: -0.96 (0.43), residues: 158 loop : -2.16 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 400 TYR 0.017 0.001 TYR B 79 PHE 0.029 0.001 PHE B 454 TRP 0.007 0.001 TRP A 121 HIS 0.006 0.001 HIS A 580 Details of bonding type rmsd covalent geometry : bond 0.00276 (12994) covalent geometry : angle 0.63549 (17512) hydrogen bonds : bond 0.03579 ( 464) hydrogen bonds : angle 5.40584 ( 1332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 116 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7579 (tt) REVERT: B 404 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.6877 (t80) REVERT: B 427 GLU cc_start: 0.5509 (OUTLIER) cc_final: 0.4902 (pt0) REVERT: B 695 ASN cc_start: 0.7256 (t0) cc_final: 0.6892 (t0) REVERT: A 213 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.5877 (mmt) REVERT: A 294 MET cc_start: 0.7253 (ptp) cc_final: 0.6927 (ptm) REVERT: A 487 GLU cc_start: 0.6869 (pp20) cc_final: 0.6505 (pp20) REVERT: A 496 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8176 (tt0) REVERT: A 668 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6617 (tttt) REVERT: A 695 ASN cc_start: 0.6948 (t0) cc_final: 0.6440 (t0) REVERT: A 748 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.7044 (pp) outliers start: 57 outliers final: 39 residues processed: 163 average time/residue: 0.0924 time to fit residues: 23.5073 Evaluate side-chains 149 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 104 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 835 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 59 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 141 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 0.0670 chunk 146 optimal weight: 1.9990 chunk 133 optimal weight: 0.0770 chunk 137 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 100 optimal weight: 0.0040 chunk 58 optimal weight: 0.4980 overall best weight: 0.2888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.222223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.194579 restraints weight = 19693.915| |-----------------------------------------------------------------------------| r_work (start): 0.4421 rms_B_bonded: 2.29 r_work: 0.4058 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12994 Z= 0.131 Angle : 0.641 8.457 17512 Z= 0.324 Chirality : 0.043 0.157 1998 Planarity : 0.004 0.042 2242 Dihedral : 4.907 22.703 1680 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.16 % Favored : 89.59 % Rotamer: Outliers : 4.36 % Allowed : 26.57 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.20), residues: 1614 helix: -0.38 (0.20), residues: 654 sheet: -0.85 (0.44), residues: 154 loop : -2.18 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 400 TYR 0.015 0.001 TYR B 79 PHE 0.020 0.001 PHE B 232 TRP 0.007 0.001 TRP A 121 HIS 0.005 0.001 HIS A 580 Details of bonding type rmsd covalent geometry : bond 0.00292 (12994) covalent geometry : angle 0.64056 (17512) hydrogen bonds : bond 0.03627 ( 464) hydrogen bonds : angle 5.37242 ( 1332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 116 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7633 (tt) REVERT: B 404 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.6966 (t80) REVERT: B 620 ASP cc_start: 0.6917 (OUTLIER) cc_final: 0.6223 (p0) REVERT: B 667 MET cc_start: 0.7576 (tmm) cc_final: 0.7276 (tmm) REVERT: B 695 ASN cc_start: 0.7282 (t0) cc_final: 0.6919 (t0) REVERT: A 213 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.5749 (mmm) REVERT: A 450 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6304 (pp) REVERT: A 487 GLU cc_start: 0.6841 (pp20) cc_final: 0.6345 (pp20) REVERT: A 499 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7991 (mt) REVERT: A 668 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6734 (tttt) REVERT: A 748 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.7027 (pp) REVERT: A 799 GLN cc_start: 0.7362 (tm130) cc_final: 0.6924 (tm-30) outliers start: 61 outliers final: 40 residues processed: 166 average time/residue: 0.0926 time to fit residues: 24.0243 Evaluate side-chains 152 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 104 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 805 TRP Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 835 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 112 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 105 optimal weight: 0.4980 chunk 133 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 44 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 chunk 159 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN B 245 ASN B 361 ASN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.217986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.192248 restraints weight = 19334.570| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 1.99 r_work: 0.4016 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.6232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12994 Z= 0.198 Angle : 0.718 8.782 17512 Z= 0.365 Chirality : 0.045 0.160 1998 Planarity : 0.004 0.044 2242 Dihedral : 5.191 22.214 1680 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.15 % Favored : 88.60 % Rotamer: Outliers : 4.71 % Allowed : 27.64 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.20), residues: 1614 helix: -0.68 (0.19), residues: 660 sheet: -0.95 (0.44), residues: 158 loop : -2.18 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 400 TYR 0.013 0.001 TYR B 79 PHE 0.023 0.002 PHE B 232 TRP 0.008 0.001 TRP A 121 HIS 0.006 0.002 HIS B 580 Details of bonding type rmsd covalent geometry : bond 0.00459 (12994) covalent geometry : angle 0.71752 (17512) hydrogen bonds : bond 0.04065 ( 464) hydrogen bonds : angle 5.57334 ( 1332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 104 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7695 (tt) REVERT: B 404 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.7051 (m-80) REVERT: B 484 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6621 (mt) REVERT: B 667 MET cc_start: 0.7477 (tmm) cc_final: 0.7206 (tmm) REVERT: B 695 ASN cc_start: 0.7434 (t0) cc_final: 0.6873 (t0) REVERT: A 213 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.5553 (mmm) REVERT: A 450 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6243 (pp) REVERT: A 491 VAL cc_start: 0.8169 (p) cc_final: 0.7941 (t) REVERT: A 668 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6818 (tttt) REVERT: A 714 MET cc_start: 0.8243 (ttt) cc_final: 0.8027 (ttt) REVERT: A 748 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6958 (pp) REVERT: A 799 GLN cc_start: 0.7356 (tm130) cc_final: 0.6909 (tm-30) outliers start: 66 outliers final: 43 residues processed: 162 average time/residue: 0.1026 time to fit residues: 25.1406 Evaluate side-chains 145 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 95 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 805 TRP Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 835 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 62 optimal weight: 0.0570 chunk 135 optimal weight: 0.7980 chunk 115 optimal weight: 0.0970 chunk 157 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 129 optimal weight: 0.0270 chunk 37 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN A 303 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.219867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.195568 restraints weight = 19478.651| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 1.83 r_work: 0.4068 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.6344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12994 Z= 0.149 Angle : 0.674 9.058 17512 Z= 0.343 Chirality : 0.043 0.162 1998 Planarity : 0.004 0.043 2242 Dihedral : 5.102 23.933 1680 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.41 % Favored : 89.34 % Rotamer: Outliers : 4.14 % Allowed : 28.14 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.20), residues: 1614 helix: -0.63 (0.19), residues: 670 sheet: -0.93 (0.44), residues: 158 loop : -2.22 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 400 TYR 0.014 0.001 TYR B 79 PHE 0.023 0.001 PHE B 232 TRP 0.007 0.001 TRP A 121 HIS 0.004 0.001 HIS A 580 Details of bonding type rmsd covalent geometry : bond 0.00339 (12994) covalent geometry : angle 0.67383 (17512) hydrogen bonds : bond 0.03733 ( 464) hydrogen bonds : angle 5.53692 ( 1332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 105 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7540 (tt) REVERT: B 404 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.6942 (m-80) REVERT: B 453 ASN cc_start: 0.7173 (p0) cc_final: 0.6854 (p0) REVERT: B 667 MET cc_start: 0.7436 (tmm) cc_final: 0.7223 (tmm) REVERT: B 695 ASN cc_start: 0.7301 (t0) cc_final: 0.6749 (t0) REVERT: A 213 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.5587 (mmm) REVERT: A 450 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6250 (pp) REVERT: A 487 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6323 (pp20) REVERT: A 499 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7936 (mt) REVERT: A 668 LYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6770 (tttt) REVERT: A 748 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7045 (pp) outliers start: 58 outliers final: 40 residues processed: 156 average time/residue: 0.0932 time to fit residues: 22.6438 Evaluate side-chains 142 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 94 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 805 TRP Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 835 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 131 optimal weight: 0.7980 chunk 87 optimal weight: 8.9990 chunk 143 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 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 245 ASN B 361 ASN A 343 GLN A 803 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.218524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.188231 restraints weight = 19274.801| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 2.15 r_work: 0.3934 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.6701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12994 Z= 0.228 Angle : 0.752 11.707 17512 Z= 0.383 Chirality : 0.046 0.167 1998 Planarity : 0.004 0.048 2242 Dihedral : 5.408 22.655 1680 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.65 % Favored : 88.04 % Rotamer: Outliers : 4.21 % Allowed : 27.57 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.20), residues: 1614 helix: -0.80 (0.19), residues: 646 sheet: -0.58 (0.50), residues: 128 loop : -2.25 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 502 TYR 0.012 0.002 TYR B 79 PHE 0.036 0.002 PHE B 454 TRP 0.008 0.001 TRP B 121 HIS 0.007 0.002 HIS B 580 Details of bonding type rmsd covalent geometry : bond 0.00532 (12994) covalent geometry : angle 0.75165 (17512) hydrogen bonds : bond 0.04173 ( 464) hydrogen bonds : angle 5.67187 ( 1332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 106 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7649 (tt) REVERT: B 404 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: B 453 ASN cc_start: 0.7351 (p0) cc_final: 0.7107 (p0) REVERT: B 667 MET cc_start: 0.7461 (tmm) cc_final: 0.7233 (tmm) REVERT: B 695 ASN cc_start: 0.7638 (t0) cc_final: 0.7144 (t0) REVERT: A 213 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.5827 (mmm) REVERT: A 450 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6377 (pp) REVERT: A 499 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8092 (mt) REVERT: A 668 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6702 (tttt) REVERT: A 748 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7295 (pp) outliers start: 59 outliers final: 44 residues processed: 156 average time/residue: 0.0970 time to fit residues: 23.5241 Evaluate side-chains 148 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 97 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 216 HIS Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 805 TRP Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 835 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 121 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 67 optimal weight: 0.0970 chunk 159 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 65 optimal weight: 0.0970 chunk 11 optimal weight: 0.6980 chunk 109 optimal weight: 0.0870 chunk 92 optimal weight: 5.9990 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN B 361 ASN ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 ASN A 343 GLN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.218450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.187426 restraints weight = 19480.092| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 2.31 r_work: 0.3977 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.6697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12994 Z= 0.133 Angle : 0.686 14.639 17512 Z= 0.346 Chirality : 0.043 0.172 1998 Planarity : 0.004 0.043 2242 Dihedral : 5.122 25.091 1680 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.48 % Favored : 90.27 % Rotamer: Outliers : 3.29 % Allowed : 28.93 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.20), residues: 1614 helix: -0.63 (0.19), residues: 668 sheet: -0.38 (0.50), residues: 128 loop : -2.31 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 502 TYR 0.026 0.001 TYR A 740 PHE 0.026 0.001 PHE B 232 TRP 0.006 0.001 TRP B 121 HIS 0.005 0.001 HIS A 580 Details of bonding type rmsd covalent geometry : bond 0.00299 (12994) covalent geometry : angle 0.68618 (17512) hydrogen bonds : bond 0.03669 ( 464) hydrogen bonds : angle 5.52799 ( 1332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3252.21 seconds wall clock time: 56 minutes 34.49 seconds (3394.49 seconds total)