Starting phenix.real_space_refine on Fri Sep 11 16:57:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ylf_73081/09_2026/9ylf_73081.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ylf_73081/09_2026/9ylf_73081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ylf_73081/09_2026/9ylf_73081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ylf_73081/09_2026/9ylf_73081.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ylf_73081/09_2026/9ylf_73081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ylf_73081/09_2026/9ylf_73081.map" } resolution = 3.14 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= 0.002 sd= 0.093 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 54 5.16 5 C 6566 2.51 5 N 1733 2.21 5 O 1942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10302 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7786 Classifications: {'peptide': 983} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 930} Chain breaks: 1 Chain: "C" Number of atoms: 1856 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 232, 1856 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 209} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 2.16, per 1000 atoms: 0.21 Number of scatterers: 10302 At special positions: 0 Unit cell: (83.3, 98.294, 128.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 7 15.00 O 1942 8.00 N 1733 7.00 C 6566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 625 " - pdb=" SG CYS C 188 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 299.9 milliseconds 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2436 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 44.0% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 71 through 84 Processing helix chain 'A' and resid 97 through 104 removed outlier: 3.501A pdb=" N LEU A 101 " --> pdb=" O GLN A 97 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR A 103 " --> pdb=" O TRP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 117 through 130 removed outlier: 4.632A pdb=" N LYS A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N HIS A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 removed outlier: 3.517A pdb=" N ASP A 152 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS A 153 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 177 removed outlier: 3.574A pdb=" N GLN A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 removed outlier: 4.307A pdb=" N LYS A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N HIS A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 340 Processing helix chain 'A' and resid 347 through 365 Processing helix chain 'A' and resid 372 through 382 Processing helix chain 'A' and resid 387 through 408 Processing helix chain 'A' and resid 421 through 427 removed outlier: 4.084A pdb=" N VAL A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 443 through 451 Processing helix chain 'A' and resid 451 through 460 Processing helix chain 'A' and resid 469 through 483 removed outlier: 4.184A pdb=" N GLU A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 removed outlier: 3.531A pdb=" N LEU A 506 " --> pdb=" O LYS A 503 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN A 507 " --> pdb=" O SER A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 533 Processing helix chain 'A' and resid 546 through 550 removed outlier: 3.729A pdb=" N GLU A 550 " --> pdb=" O PRO A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 561 Processing helix chain 'A' and resid 570 through 585 removed outlier: 3.530A pdb=" N ARG A 574 " --> pdb=" O ASN A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 614 Processing helix chain 'A' and resid 623 through 630 removed outlier: 3.571A pdb=" N SER A 629 " --> pdb=" O CYS A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 650 removed outlier: 3.571A pdb=" N THR A 637 " --> pdb=" O ALA A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 663 Processing helix chain 'A' and resid 668 through 675 Processing helix chain 'A' and resid 681 through 691 Processing helix chain 'A' and resid 695 through 712 Processing helix chain 'A' and resid 712 through 722 Processing helix chain 'A' and resid 751 through 769 Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 879 through 888 Processing helix chain 'A' and resid 894 through 914 removed outlier: 3.615A pdb=" N GLY A 914 " --> pdb=" O ILE A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 979 Processing helix chain 'A' and resid 1002 through 1006 Processing helix chain 'A' and resid 1008 through 1014 Processing helix chain 'C' and resid 100 through 114 removed outlier: 4.023A pdb=" N ILE C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 216 Processing helix chain 'C' and resid 220 through 229 removed outlier: 3.802A pdb=" N GLU C 225 " --> pdb=" O TYR C 222 " (cutoff:3.500A) Proline residue: C 226 - end of helix removed outlier: 4.060A pdb=" N GLU C 229 " --> pdb=" O PRO C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 251 Processing helix chain 'C' and resid 253 through 258 removed outlier: 3.537A pdb=" N MET C 257 " --> pdb=" O VAL C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 290 removed outlier: 5.046A pdb=" N ASP C 280 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N PHE C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 314 removed outlier: 3.666A pdb=" N LEU C 314 " --> pdb=" O GLN C 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 311 through 314' Processing helix chain 'C' and resid 315 through 323 removed outlier: 3.847A pdb=" N LEU C 319 " --> pdb=" O MET C 315 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 34 removed outlier: 3.525A pdb=" N VAL D 26 " --> pdb=" O THR D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.759A pdb=" N TYR D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 138 removed outlier: 6.276A pdb=" N VAL A 88 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N SER A 138 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 90 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL A 64 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N HIS A 91 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU A 66 " --> pdb=" O HIS A 91 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N HIS A 63 " --> pdb=" O CYS A 156 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N VAL A 158 " --> pdb=" O HIS A 63 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N PHE A 65 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 222 removed outlier: 3.545A pdb=" N ILE A 228 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 266 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE A 250 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLY A 285 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N HIS A 284 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ASN A 220 " --> pdb=" O HIS A 284 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLY A 286 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 541 removed outlier: 6.445A pdb=" N ILE A 493 " --> pdb=" O ASP A 539 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N HIS A 541 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A 495 " --> pdb=" O HIS A 541 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 463 " --> pdb=" O THR A 494 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N THR A 496 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU A 465 " --> pdb=" O THR A 496 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE A 564 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N SER A 591 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR A 566 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N THR A 593 " --> pdb=" O THR A 566 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL A 602 " --> pdb=" O LYS A 922 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LYS A 922 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 934 " --> pdb=" O PHE A 925 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 944 through 946 removed outlier: 3.566A pdb=" N ILE A 950 " --> pdb=" O ILE A 946 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.754A pdb=" N TRP A 958 " --> pdb=" O ARG A1044 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N TYR A1046 " --> pdb=" O TRP A 958 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL A 960 " --> pdb=" O TYR A1046 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL A 986 " --> pdb=" O LEU A 993 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.754A pdb=" N TRP A 958 " --> pdb=" O ARG A1044 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N TYR A1046 " --> pdb=" O TRP A 958 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL A 960 " --> pdb=" O TYR A1046 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 119 through 123 Processing sheet with id=AA9, first strand: chain 'D' and resid 12 through 15 removed outlier: 3.584A pdb=" N ILE D 3 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE D 4 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU D 69 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS D 6 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG D 42 " --> pdb=" O VAL D 70 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1236 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: 1.77 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3291 1.34 - 1.46: 1479 1.46 - 1.58: 5685 1.58 - 1.69: 7 1.69 - 1.81: 81 Bond restraints: 10543 Sorted by residual: bond pdb=" C4 AMP D1101 " pdb=" C5 AMP D1101 " ideal model delta sigma weight residual 1.490 1.391 0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C5 AMP D1101 " pdb=" C6 AMP D1101 " ideal model delta sigma weight residual 1.490 1.393 0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" N VAL D 70 " pdb=" CA VAL D 70 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.11e+00 bond pdb=" N ARG D 72 " pdb=" CA ARG D 72 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.21e-02 6.83e+03 8.10e+00 bond pdb=" N LEU D 73 " pdb=" CA LEU D 73 " ideal model delta sigma weight residual 1.452 1.488 -0.037 1.30e-02 5.92e+03 7.97e+00 ... (remaining 10538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 14105 2.33 - 4.67: 169 4.67 - 7.00: 18 7.00 - 9.34: 7 9.34 - 11.67: 5 Bond angle restraints: 14304 Sorted by residual: angle pdb=" O1P AMP D1101 " pdb=" P AMP D1101 " pdb=" O2P AMP D1101 " ideal model delta sigma weight residual 119.90 108.23 11.67 3.00e+00 1.11e-01 1.51e+01 angle pdb=" O1P AMP D1101 " pdb=" P AMP D1101 " pdb=" O3P AMP D1101 " ideal model delta sigma weight residual 119.90 108.60 11.30 3.00e+00 1.11e-01 1.42e+01 angle pdb=" C4' AMP D1101 " pdb=" C5' AMP D1101 " pdb=" O5' AMP D1101 " ideal model delta sigma weight residual 111.70 106.21 5.49 1.50e+00 4.44e-01 1.34e+01 angle pdb=" CA PRO A 268 " pdb=" N PRO A 268 " pdb=" CD PRO A 268 " ideal model delta sigma weight residual 112.00 107.05 4.95 1.40e+00 5.10e-01 1.25e+01 angle pdb=" O14 IHP A1101 " pdb=" P4 IHP A1101 " pdb=" O34 IHP A1101 " ideal model delta sigma weight residual 101.64 111.77 -10.13 3.00e+00 1.11e-01 1.14e+01 ... (remaining 14299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.60: 5808 25.60 - 51.21: 510 51.21 - 76.81: 79 76.81 - 102.41: 11 102.41 - 128.02: 6 Dihedral angle restraints: 6414 sinusoidal: 2657 harmonic: 3757 Sorted by residual: dihedral pdb=" CD ARG D 74 " pdb=" NE ARG D 74 " pdb=" CZ ARG D 74 " pdb=" NH1 ARG D 74 " ideal model delta sinusoidal sigma weight residual 0.00 -68.41 68.41 1 1.00e+01 1.00e-02 6.07e+01 dihedral pdb=" CA TYR A 994 " pdb=" C TYR A 994 " pdb=" N VAL A 995 " pdb=" CA VAL A 995 " ideal model delta harmonic sigma weight residual 180.00 153.24 26.76 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA CYS A 178 " pdb=" C CYS A 178 " pdb=" N PRO A 179 " pdb=" CA PRO A 179 " ideal model delta harmonic sigma weight residual 180.00 158.02 21.98 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 6411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.981: 1599 0.981 - 1.962: 0 1.962 - 2.943: 0 2.943 - 3.923: 0 3.923 - 4.904: 3 Chirality restraints: 1602 Sorted by residual: chirality pdb=" C1 IHP A1101 " pdb=" C2 IHP A1101 " pdb=" C6 IHP A1101 " pdb=" O11 IHP A1101 " both_signs ideal model delta sigma weight residual False 2.32 -2.59 4.90 2.00e-01 2.50e+01 6.01e+02 chirality pdb=" C2 IHP A1101 " pdb=" C1 IHP A1101 " pdb=" C3 IHP A1101 " pdb=" O12 IHP A1101 " both_signs ideal model delta sigma weight residual False -2.52 2.35 -4.87 2.00e-01 2.50e+01 5.93e+02 chirality pdb=" C4 IHP A1101 " pdb=" C3 IHP A1101 " pdb=" C5 IHP A1101 " pdb=" O14 IHP A1101 " both_signs ideal model delta sigma weight residual False 2.48 -2.11 4.59 2.00e-01 2.50e+01 5.27e+02 ... (remaining 1599 not shown) Planarity restraints: 1833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 74 " 1.019 9.50e-02 1.11e+02 4.56e-01 1.26e+02 pdb=" NE ARG D 74 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG D 74 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 74 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 74 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 72 " -0.337 9.50e-02 1.11e+02 1.51e-01 1.40e+01 pdb=" NE ARG D 72 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG D 72 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D 72 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 72 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 267 " 0.052 5.00e-02 4.00e+02 7.66e-02 9.40e+00 pdb=" N PRO A 268 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 268 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 268 " 0.043 5.00e-02 4.00e+02 ... (remaining 1830 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 22 2.39 - 3.02: 5888 3.02 - 3.65: 15577 3.65 - 4.27: 23026 4.27 - 4.90: 39546 Nonbonded interactions: 84059 Sorted by model distance: nonbonded pdb=" OD2 ASP A 499 " pdb=" O2' AMP D1101 " model vdw 1.768 3.040 nonbonded pdb=" O GLY C 145 " pdb=" OH TYR C 282 " model vdw 2.130 3.040 nonbonded pdb=" O CYS C 188 " pdb=" OG1 THR C 194 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR D 55 " pdb=" OD1 ASP D 58 " model vdw 2.212 3.040 nonbonded pdb=" O SER A 629 " pdb=" OH TYR A 873 " model vdw 2.242 3.040 ... (remaining 84054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.080 Find NCS groups from input model: 0.170 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 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 : 0.004 0.141 10545 Z= 0.224 Angle : 0.615 11.671 14306 Z= 0.303 Chirality : 0.211 4.904 1602 Planarity : 0.012 0.456 1833 Dihedral : 18.953 128.017 3975 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.05 % Allowed : 27.82 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: 1.06 (0.24), residues: 1282 helix: 2.14 (0.23), residues: 487 sheet: 0.71 (0.40), residues: 174 loop : -0.46 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 106 TYR 0.007 0.001 TYR C 279 PHE 0.024 0.001 PHE A 510 TRP 0.004 0.001 TRP A 378 HIS 0.003 0.000 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.18 (10543) covalent geometry : angle 0.61550 / 0.30 (14304) SS BOND : bond 0.00150 / 0.08 ( 1) SS BOND : angle 0.58708 / 0.32 ( 2) hydrogen bonds : bond 0.16614 / 11.13 ( 434) hydrogen bonds : angle 6.55805 / 4.52 ( 1236) Misc. bond : bond 0.14115 / 7.43 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.441 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 143 average time/residue: 0.1138 time to fit residues: 22.8147 Evaluate side-chains 134 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain C residue 165 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 HIS ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.149595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.109345 restraints weight = 13340.412| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.76 r_work: 0.3102 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10545 Z= 0.173 Angle : 0.571 8.205 14306 Z= 0.282 Chirality : 0.042 0.199 1602 Planarity : 0.004 0.057 1833 Dihedral : 6.388 56.855 1431 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.80 % Allowed : 26.77 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.24), residues: 1282 helix: 1.97 (0.23), residues: 496 sheet: 0.41 (0.40), residues: 182 loop : -0.47 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.008 0.001 TYR C 279 PHE 0.023 0.001 PHE A 510 TRP 0.006 0.001 TRP A 378 HIS 0.009 0.001 HIS A 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (10543) covalent geometry : angle 0.57120 / 0.28 (14304) SS BOND : bond 0.00099 / 0.05 ( 1) SS BOND : angle 0.56046 / 0.31 ( 2) hydrogen bonds : bond 0.04171 / 2.78 ( 434) hydrogen bonds : angle 5.25283 / 3.65 ( 1236) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 384 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.8961 (mp10) REVERT: A 475 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8262 (mmm) REVERT: A 1007 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8798 (pp) outliers start: 32 outliers final: 16 residues processed: 156 average time/residue: 0.1129 time to fit residues: 24.4973 Evaluate side-chains 149 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 384 GLN Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 256 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 HIS ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.149826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.107512 restraints weight = 13555.396| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.91 r_work: 0.3083 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10545 Z= 0.163 Angle : 0.548 6.667 14306 Z= 0.272 Chirality : 0.042 0.253 1602 Planarity : 0.004 0.048 1833 Dihedral : 6.242 57.928 1427 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.94 % Allowed : 26.25 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.24), residues: 1282 helix: 1.94 (0.23), residues: 496 sheet: 0.30 (0.38), residues: 184 loop : -0.53 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.008 0.001 TYR C 279 PHE 0.024 0.001 PHE A 510 TRP 0.006 0.001 TRP A 99 HIS 0.008 0.001 HIS A 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 (10543) covalent geometry : angle 0.54789 / 0.27 (14304) SS BOND : bond 0.00068 / 0.04 ( 1) SS BOND : angle 0.25503 / 0.14 ( 2) hydrogen bonds : bond 0.03672 / 2.45 ( 434) hydrogen bonds : angle 4.93265 / 3.43 ( 1236) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 136 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8456 (mp) REVERT: A 85 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8553 (tt) REVERT: A 384 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.8947 (mp10) REVERT: A 475 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.7491 (mpp) REVERT: C 279 TYR cc_start: 0.7573 (t80) cc_final: 0.7291 (t80) outliers start: 45 outliers final: 23 residues processed: 169 average time/residue: 0.1153 time to fit residues: 27.1209 Evaluate side-chains 163 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 384 GLN Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1010 HIS Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 256 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 34 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 47 optimal weight: 0.0370 chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 ASN A 237 HIS A 507 ASN ** D 25 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 = 0.3808 r_free = 0.3808 target = 0.151753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110151 restraints weight = 13412.061| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.87 r_work: 0.3134 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10545 Z= 0.111 Angle : 0.519 6.805 14306 Z= 0.257 Chirality : 0.041 0.219 1602 Planarity : 0.004 0.050 1833 Dihedral : 6.028 54.942 1425 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.89 % Allowed : 27.03 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.24), residues: 1282 helix: 1.96 (0.23), residues: 502 sheet: 0.39 (0.39), residues: 176 loop : -0.61 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 106 TYR 0.018 0.001 TYR C 222 PHE 0.024 0.001 PHE A 510 TRP 0.006 0.001 TRP A 378 HIS 0.009 0.001 HIS A 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (10543) covalent geometry : angle 0.51887 / 0.26 (14304) SS BOND : bond 0.00018 / 0.01 ( 1) SS BOND : angle 0.24129 / 0.12 ( 2) hydrogen bonds : bond 0.03157 / 2.10 ( 434) hydrogen bonds : angle 4.71948 / 3.28 ( 1236) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8430 (mp) REVERT: A 264 THR cc_start: 0.7393 (m) cc_final: 0.7019 (p) REVERT: A 475 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8351 (mpp) REVERT: A 490 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.6792 (tptm) REVERT: A 1007 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8775 (pp) REVERT: D 74 ARG cc_start: 0.8362 (ttp-110) cc_final: 0.8156 (ttp-110) outliers start: 33 outliers final: 17 residues processed: 163 average time/residue: 0.1179 time to fit residues: 26.4884 Evaluate side-chains 152 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1010 HIS Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain C residue 256 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 92 optimal weight: 0.3980 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 0.0020 chunk 108 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 HIS ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.149234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.107081 restraints weight = 13457.012| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.86 r_work: 0.3116 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10545 Z= 0.147 Angle : 0.542 7.015 14306 Z= 0.267 Chirality : 0.041 0.228 1602 Planarity : 0.004 0.048 1833 Dihedral : 5.967 52.375 1424 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.94 % Allowed : 26.16 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.24), residues: 1282 helix: 1.95 (0.23), residues: 502 sheet: 0.32 (0.39), residues: 176 loop : -0.60 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 72 TYR 0.017 0.001 TYR C 222 PHE 0.026 0.001 PHE A 510 TRP 0.005 0.001 TRP A 378 HIS 0.008 0.001 HIS A 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (10543) covalent geometry : angle 0.54178 / 0.27 (14304) SS BOND : bond 0.00056 / 0.03 ( 1) SS BOND : angle 0.65363 / 0.35 ( 2) hydrogen bonds : bond 0.03323 / 2.21 ( 434) hydrogen bonds : angle 4.69900 / 3.26 ( 1236) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 133 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8454 (mp) REVERT: A 85 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8603 (tt) REVERT: A 225 ASN cc_start: 0.6768 (OUTLIER) cc_final: 0.6438 (t0) REVERT: A 264 THR cc_start: 0.7392 (m) cc_final: 0.7003 (p) REVERT: A 384 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.8932 (mp10) REVERT: A 490 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.6853 (tptm) REVERT: A 789 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7435 (tm-30) outliers start: 45 outliers final: 28 residues processed: 166 average time/residue: 0.1140 time to fit residues: 26.2400 Evaluate side-chains 162 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 384 GLN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1010 HIS Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 256 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 11 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.148229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106438 restraints weight = 13634.317| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.09 r_work: 0.3072 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10545 Z= 0.164 Angle : 0.552 6.686 14306 Z= 0.273 Chirality : 0.042 0.229 1602 Planarity : 0.004 0.052 1833 Dihedral : 5.902 54.021 1424 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.55 % Allowed : 25.46 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.24), residues: 1282 helix: 1.95 (0.23), residues: 496 sheet: 0.28 (0.39), residues: 176 loop : -0.56 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.021 0.001 TYR C 222 PHE 0.027 0.001 PHE A 510 TRP 0.006 0.001 TRP A 99 HIS 0.004 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.16 (10543) covalent geometry : angle 0.55233 / 0.27 (14304) SS BOND : bond 0.00040 / 0.02 ( 1) SS BOND : angle 0.50801 / 0.27 ( 2) hydrogen bonds : bond 0.03402 / 2.26 ( 434) hydrogen bonds : angle 4.71102 / 3.27 ( 1236) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 131 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8430 (mp) REVERT: A 85 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8594 (tt) REVERT: A 264 THR cc_start: 0.7144 (m) cc_final: 0.6771 (p) REVERT: A 304 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8098 (ttp-110) REVERT: A 384 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.8877 (mp10) REVERT: A 490 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.6774 (tptm) REVERT: A 789 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7472 (tm-30) REVERT: A 1007 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8819 (pp) outliers start: 52 outliers final: 33 residues processed: 170 average time/residue: 0.1167 time to fit residues: 27.5903 Evaluate side-chains 168 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 384 GLN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1010 HIS Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 256 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 19 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 HIS ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.144705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.105026 restraints weight = 13540.206| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.86 r_work: 0.3037 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 10545 Z= 0.265 Angle : 0.627 8.208 14306 Z= 0.313 Chirality : 0.045 0.258 1602 Planarity : 0.005 0.053 1833 Dihedral : 6.083 55.811 1424 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.99 % Allowed : 25.02 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.24), residues: 1282 helix: 1.70 (0.23), residues: 496 sheet: 0.20 (0.38), residues: 181 loop : -0.64 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 116 TYR 0.023 0.002 TYR C 222 PHE 0.029 0.002 PHE A 510 TRP 0.009 0.002 TRP A 99 HIS 0.007 0.001 HIS A 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.27 (10543) covalent geometry : angle 0.62702 / 0.31 (14304) SS BOND : bond 0.00021 / 0.01 ( 1) SS BOND : angle 1.02883 / 0.57 ( 2) hydrogen bonds : bond 0.04102 / 2.74 ( 434) hydrogen bonds : angle 4.92922 / 3.42 ( 1236) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 129 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8521 (mp) REVERT: A 264 THR cc_start: 0.7376 (m) cc_final: 0.7011 (p) REVERT: A 304 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8137 (ttp-110) REVERT: A 384 GLN cc_start: 0.9271 (OUTLIER) cc_final: 0.8892 (mp10) REVERT: A 490 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.6990 (tptm) REVERT: A 499 ASP cc_start: 0.7927 (m-30) cc_final: 0.7665 (m-30) REVERT: A 789 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7482 (tm-30) outliers start: 57 outliers final: 37 residues processed: 175 average time/residue: 0.1165 time to fit residues: 28.3639 Evaluate side-chains 167 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 384 GLN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 959 THR Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1010 HIS Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain C residue 141 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.150899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.109192 restraints weight = 13454.665| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.88 r_work: 0.3118 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10545 Z= 0.116 Angle : 0.539 7.145 14306 Z= 0.267 Chirality : 0.041 0.221 1602 Planarity : 0.004 0.053 1833 Dihedral : 5.820 58.080 1424 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.89 % Allowed : 27.12 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.24), residues: 1282 helix: 1.87 (0.23), residues: 500 sheet: 0.38 (0.39), residues: 171 loop : -0.66 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 341 TYR 0.020 0.001 TYR C 222 PHE 0.026 0.001 PHE A 510 TRP 0.006 0.001 TRP A 378 HIS 0.003 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (10543) covalent geometry : angle 0.53929 / 0.27 (14304) SS BOND : bond 0.00009 / 0.00 ( 1) SS BOND : angle 0.56856 / 0.31 ( 2) hydrogen bonds : bond 0.03110 / 2.07 ( 434) hydrogen bonds : angle 4.64131 / 3.21 ( 1236) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8490 (mp) REVERT: A 264 THR cc_start: 0.7368 (m) cc_final: 0.7021 (p) REVERT: A 475 MET cc_start: 0.8540 (mpp) cc_final: 0.8252 (mmm) REVERT: A 490 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.6820 (tptm) REVERT: A 499 ASP cc_start: 0.7855 (m-30) cc_final: 0.7602 (m-30) outliers start: 33 outliers final: 27 residues processed: 159 average time/residue: 0.1073 time to fit residues: 23.9910 Evaluate side-chains 156 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain C residue 141 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 82 optimal weight: 0.0870 chunk 120 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 0.3980 chunk 64 optimal weight: 0.0570 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 HIS A 636 HIS D 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.149503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.108755 restraints weight = 13257.606| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.81 r_work: 0.3150 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10545 Z= 0.102 Angle : 0.526 8.112 14306 Z= 0.260 Chirality : 0.040 0.201 1602 Planarity : 0.004 0.053 1833 Dihedral : 5.575 59.457 1424 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.89 % Allowed : 27.21 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.24), residues: 1282 helix: 1.96 (0.23), residues: 501 sheet: 0.34 (0.39), residues: 173 loop : -0.59 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 106 TYR 0.020 0.001 TYR C 222 PHE 0.041 0.001 PHE C 275 TRP 0.006 0.001 TRP A 378 HIS 0.005 0.001 HIS A 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (10543) covalent geometry : angle 0.52560 / 0.26 (14304) SS BOND : bond 0.00107 / 0.06 ( 1) SS BOND : angle 0.48729 / 0.25 ( 2) hydrogen bonds : bond 0.02814 / 1.88 ( 434) hydrogen bonds : angle 4.46117 / 3.08 ( 1236) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.423 Fit side-chains REVERT: A 264 THR cc_start: 0.7430 (m) cc_final: 0.7124 (p) REVERT: A 1007 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8804 (pp) REVERT: C 106 ARG cc_start: 0.8620 (ttt90) cc_final: 0.8411 (ttm-80) outliers start: 33 outliers final: 24 residues processed: 164 average time/residue: 0.1114 time to fit residues: 25.7481 Evaluate side-chains 158 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 141 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 34 optimal weight: 2.9990 chunk 124 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 HIS D 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.147957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.107078 restraints weight = 13221.761| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.81 r_work: 0.3121 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10545 Z= 0.125 Angle : 0.550 8.334 14306 Z= 0.269 Chirality : 0.041 0.207 1602 Planarity : 0.004 0.053 1833 Dihedral : 5.558 59.639 1424 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.45 % Allowed : 27.82 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.24), residues: 1282 helix: 1.95 (0.23), residues: 501 sheet: 0.36 (0.39), residues: 173 loop : -0.60 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.023 0.001 TYR C 222 PHE 0.044 0.001 PHE C 275 TRP 0.006 0.001 TRP A 378 HIS 0.011 0.001 HIS A 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (10543) covalent geometry : angle 0.55001 / 0.27 (14304) SS BOND : bond 0.00068 / 0.04 ( 1) SS BOND : angle 0.59452 / 0.31 ( 2) hydrogen bonds : bond 0.02983 / 1.99 ( 434) hydrogen bonds : angle 4.48307 / 3.09 ( 1236) Misc. bond : bond 0.00004 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.306 Fit side-chains REVERT: A 264 THR cc_start: 0.7372 (m) cc_final: 0.7071 (p) REVERT: A 503 LYS cc_start: 0.4799 (OUTLIER) cc_final: 0.4222 (tttp) REVERT: A 1007 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8815 (pp) REVERT: C 106 ARG cc_start: 0.8616 (ttt90) cc_final: 0.8397 (ttm-80) outliers start: 28 outliers final: 25 residues processed: 153 average time/residue: 0.1043 time to fit residues: 22.5864 Evaluate side-chains 158 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 237 HIS Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 503 LYS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 966 PHE Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain C residue 141 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 50 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 124 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 HIS D 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.148948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.108168 restraints weight = 13386.580| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.83 r_work: 0.3144 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10545 Z= 0.111 Angle : 0.544 8.107 14306 Z= 0.266 Chirality : 0.041 0.206 1602 Planarity : 0.004 0.052 1833 Dihedral : 5.518 59.882 1424 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.54 % Allowed : 28.00 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.24), residues: 1282 helix: 1.98 (0.23), residues: 501 sheet: 0.59 (0.39), residues: 168 loop : -0.63 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 116 TYR 0.022 0.001 TYR C 222 PHE 0.039 0.001 PHE C 275 TRP 0.006 0.001 TRP A 378 HIS 0.007 0.001 HIS A 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (10543) covalent geometry : angle 0.54440 / 0.27 (14304) SS BOND : bond 0.00070 / 0.04 ( 1) SS BOND : angle 0.54008 / 0.28 ( 2) hydrogen bonds : bond 0.02905 / 1.93 ( 434) hydrogen bonds : angle 4.44952 / 3.07 ( 1236) Misc. bond : bond 0.00000 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2307.17 seconds wall clock time: 40 minutes 32.06 seconds (2432.06 seconds total)