Starting phenix.real_space_refine on Fri Sep 11 19:19:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ykw_73060/09_2026/9ykw_73060.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ykw_73060/09_2026/9ykw_73060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ykw_73060/09_2026/9ykw_73060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ykw_73060/09_2026/9ykw_73060.map" model { file = "/net/cci-nas-00/data/ceres_data/9ykw_73060/09_2026/9ykw_73060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ykw_73060/09_2026/9ykw_73060.cif" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 6 5.49 5 S 55 5.16 5 C 6881 2.51 5 N 1816 2.21 5 O 2036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 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: 10794 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7751 Classifications: {'peptide': 978} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 925} Chain breaks: 2 Chain: "B" 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: "C" Number of atoms: 1866 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 232, 1862 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 Conformer: "B" Number of residues, atoms: 232, 1862 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 bond proxies already assigned to first conformer: 1911 Chain: "D" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 540 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.68, per 1000 atoms: 0.25 Number of scatterers: 10794 At special positions: 0 Unit cell: (83.52, 96.57, 128.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 P 6 15.00 O 2036 8.00 N 1816 7.00 C 6881 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: 0.96 Conformation dependent library (CDL) restraints added in 565.8 milliseconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2558 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 9 sheets defined 42.2% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 71 through 84 Processing helix chain 'A' and resid 97 through 102 removed outlier: 4.099A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 117 through 123 Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 148 through 154 removed outlier: 3.767A pdb=" N LYS A 153 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 177 Processing helix chain 'A' and resid 301 through 307 removed outlier: 4.011A pdb=" N LYS A 307 " --> pdb=" O GLU A 303 " (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 383 Processing helix chain 'A' and resid 387 through 408 Processing helix chain 'A' and resid 421 through 426 removed outlier: 3.867A pdb=" N VAL A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 437 removed outlier: 3.721A pdb=" N PHE A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 451 through 460 Processing helix chain 'A' and resid 472 through 483 Processing helix chain 'A' and resid 520 through 533 Processing helix chain 'A' and resid 546 through 552 Processing helix chain 'A' and resid 554 through 561 Processing helix chain 'A' and resid 571 through 585 Processing helix chain 'A' and resid 610 through 614 Processing helix chain 'A' and resid 623 through 630 Processing helix chain 'A' and resid 633 through 649 removed outlier: 3.876A 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 669 through 675 Processing helix chain 'A' and resid 683 through 691 Processing helix chain 'A' and resid 695 through 711 Processing helix chain 'A' and resid 711 through 722 Processing helix chain 'A' and resid 751 through 769 removed outlier: 3.697A pdb=" N LYS A 763 " --> pdb=" O GLN A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 787 Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 879 through 889 Processing helix chain 'A' and resid 894 through 914 removed outlier: 3.608A pdb=" N GLY A 914 " --> pdb=" O ILE A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 979 removed outlier: 3.738A pdb=" N TYR A 979 " --> pdb=" O VAL A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1006 Processing helix chain 'A' and resid 1008 through 1014 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.509A pdb=" N ILE C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 174 removed outlier: 3.622A pdb=" N ASN C 173 " --> pdb=" O THR C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 217 removed outlier: 4.063A pdb=" N MET C 217 " --> pdb=" O ILE C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 removed outlier: 4.039A pdb=" N GLU C 225 " --> pdb=" O TYR C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 251 removed outlier: 3.546A pdb=" N ASN C 239 " --> pdb=" O GLY C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 259 removed outlier: 3.834A pdb=" N MET C 257 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 267 through 279 Processing helix chain 'C' and resid 279 through 288 removed outlier: 4.004A pdb=" N ALA C 285 " --> pdb=" O PHE C 281 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS C 286 " --> pdb=" O TYR C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 314 No H-bonds generated for 'chain 'C' and resid 312 through 314' Processing helix chain 'C' and resid 315 through 323 removed outlier: 3.946A pdb=" N LEU C 319 " --> pdb=" O MET C 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 34 removed outlier: 3.815A pdb=" N VAL D 26 " --> pdb=" O THR D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 41 Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 136 removed outlier: 6.792A pdb=" N VAL A 64 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N HIS A 91 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU A 66 " --> pdb=" O HIS A 91 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N HIS A 63 " --> pdb=" O CYS A 156 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL A 158 " --> pdb=" O HIS A 63 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N PHE A 65 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N THR A 160 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N SER A 67 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL A 157 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ALA A 186 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU A 159 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL A 188 " --> pdb=" O LEU A 159 " (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 259 through 262 removed outlier: 3.848A pdb=" N SER A 259 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 289 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE A 250 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY A 285 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N HIS A 284 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASN A 220 " --> pdb=" O HIS A 284 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLY A 286 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SER A 272 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL A 265 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 541 removed outlier: 6.099A pdb=" N ILE A 493 " --> pdb=" O ASP A 539 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N HIS A 541 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL A 495 " --> pdb=" O HIS A 541 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE A 463 " --> pdb=" O THR A 494 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N THR A 496 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU A 465 " --> pdb=" O THR A 496 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN A 462 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE A 565 " --> pdb=" O ASN A 462 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE A 464 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 591 " --> pdb=" O THR A 566 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL A 602 " --> pdb=" O LYS A 922 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LYS A 922 " --> pdb=" O VAL A 602 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 958 through 961 removed outlier: 6.630A pdb=" N TRP A 958 " --> pdb=" O ARG A1044 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N TYR A1046 " --> pdb=" O TRP A 958 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL A 960 " --> pdb=" O TYR A1046 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET A 985 " --> pdb=" O SER A1027 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 16 removed outlier: 4.788A pdb=" N LEU B 43 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 45 " --> pdb=" O LYS B 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 121 through 123 Processing sheet with id=AA8, first strand: chain 'D' and resid 12 through 15 Processing sheet with id=AA9, first strand: chain 'D' and resid 44 through 45 445 hydrogen bonds defined for protein. 1227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.24 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: 3311 1.34 - 1.46: 1661 1.46 - 1.58: 5978 1.58 - 1.70: 6 1.70 - 1.82: 83 Bond restraints: 11039 Sorted by residual: bond pdb=" N GLU B 18 " pdb=" CA GLU B 18 " ideal model delta sigma weight residual 1.453 1.487 -0.034 9.20e-03 1.18e+04 1.33e+01 bond pdb=" N ILE A 932 " pdb=" CA ILE A 932 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.61e+00 bond pdb=" N ILE A 832 " pdb=" CA ILE A 832 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.67e+00 bond pdb=" N VAL A 604 " pdb=" CA VAL A 604 " ideal model delta sigma weight residual 1.461 1.495 -0.033 1.23e-02 6.61e+03 7.34e+00 bond pdb=" N GLN A 843 " pdb=" CA GLN A 843 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.33e-02 5.65e+03 6.84e+00 ... (remaining 11034 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 14224 1.92 - 3.85: 630 3.85 - 5.77: 77 5.77 - 7.69: 26 7.69 - 9.62: 11 Bond angle restraints: 14968 Sorted by residual: angle pdb=" N PRO A 605 " pdb=" CA PRO A 605 " pdb=" C PRO A 605 " ideal model delta sigma weight residual 111.15 118.06 -6.91 1.58e+00 4.01e-01 1.91e+01 angle pdb=" C GLY A 472 " pdb=" N CYS A 473 " pdb=" CA CYS A 473 " ideal model delta sigma weight residual 120.82 127.15 -6.33 1.50e+00 4.44e-01 1.78e+01 angle pdb=" N GLY A 469 " pdb=" CA GLY A 469 " pdb=" C GLY A 469 " ideal model delta sigma weight residual 115.63 109.61 6.02 1.49e+00 4.50e-01 1.63e+01 angle pdb=" N VAL A 50 " pdb=" CA VAL A 50 " pdb=" C VAL A 50 " ideal model delta sigma weight residual 112.12 108.77 3.35 8.40e-01 1.42e+00 1.59e+01 angle pdb=" CA GLU B 18 " pdb=" C GLU B 18 " pdb=" N PRO B 19 " ideal model delta sigma weight residual 117.71 121.35 -3.64 9.20e-01 1.18e+00 1.57e+01 ... (remaining 14963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.25: 6278 28.25 - 56.50: 401 56.50 - 84.74: 42 84.74 - 112.99: 9 112.99 - 141.24: 5 Dihedral angle restraints: 6735 sinusoidal: 2792 harmonic: 3943 Sorted by residual: dihedral pdb=" CA THR A 593 " pdb=" C THR A 593 " pdb=" N MET A 594 " pdb=" CA MET A 594 " ideal model delta harmonic sigma weight residual 180.00 155.63 24.37 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ILE A 471 " pdb=" C ILE A 471 " pdb=" N GLY A 472 " pdb=" CA GLY A 472 " ideal model delta harmonic sigma weight residual 180.00 155.72 24.28 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA PHE C 181 " pdb=" C PHE C 181 " pdb=" N LYS C 182 " pdb=" CA LYS C 182 " ideal model delta harmonic sigma weight residual -180.00 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 6732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.001: 1679 1.001 - 2.002: 0 2.002 - 3.003: 0 3.003 - 4.004: 0 4.004 - 5.005: 3 Chirality restraints: 1682 Sorted by residual: 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 2.49 -5.01 2.00e-01 2.50e+01 6.26e+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 -2.46 4.94 2.00e-01 2.50e+01 6.09e+02 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 -2.55 4.87 2.00e-01 2.50e+01 5.92e+02 ... (remaining 1679 not shown) Planarity restraints: 1922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 640 " -0.031 2.00e-02 2.50e+03 3.06e-02 2.34e+01 pdb=" CG TRP A 640 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 TRP A 640 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 640 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 640 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 640 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 640 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 640 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 640 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 640 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 418 " 0.015 2.00e-02 2.50e+03 1.64e-02 5.41e+00 pdb=" CG TYR A 418 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 418 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 418 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 418 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 418 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 418 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 418 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 139 " -0.018 2.00e-02 2.50e+03 1.70e-02 5.08e+00 pdb=" CG PHE C 139 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE C 139 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 139 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 139 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 139 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 139 " -0.002 2.00e-02 2.50e+03 ... (remaining 1919 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 215 2.63 - 3.20: 10689 3.20 - 3.77: 18277 3.77 - 4.33: 24713 4.33 - 4.90: 38340 Nonbonded interactions: 92234 Sorted by model distance: nonbonded pdb=" O VAL A 466 " pdb=" OG1 THR A 496 " model vdw 2.063 3.040 nonbonded pdb=" O ILE A 424 " pdb=" OH TYR A 916 " model vdw 2.129 3.040 nonbonded pdb=" O PRO A 623 " pdb=" OG1 THR A 626 " model vdw 2.143 3.040 nonbonded pdb=" O GLN D 62 " pdb=" OG SER D 65 " model vdw 2.180 3.040 nonbonded pdb=" N GLU A 144 " pdb=" OE1 GLU A 144 " model vdw 2.218 3.120 ... (remaining 92229 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 1 through 68) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.010 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 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 0.087 11041 Z= 0.253 Angle : 0.916 9.615 14970 Z= 0.515 Chirality : 0.214 5.005 1682 Planarity : 0.006 0.052 1922 Dihedral : 18.129 141.241 4174 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 25.77 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.35 % Favored : 91.13 % Rotamer: Outliers : 1.58 % Allowed : 30.01 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.38 (0.24), residues: 1342 helix: 0.06 (0.23), residues: 475 sheet: -0.68 (0.39), residues: 213 loop : -1.74 (0.26), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 869 TYR 0.038 0.002 TYR A 418 PHE 0.040 0.002 PHE C 139 TRP 0.081 0.003 TRP A 640 HIS 0.005 0.001 HIS B 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.24 (11039) covalent geometry : angle 0.91548 / 0.52 (14968) SS BOND : bond 0.00126 / 0.07 ( 1) SS BOND : angle 2.00143 / 1.00 ( 2) hydrogen bonds : bond 0.14711 / 9.99 ( 445) hydrogen bonds : angle 7.17247 / 4.98 ( 1227) Misc. bond : bond 0.08659 / 4.56 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 232 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLU cc_start: 0.9187 (pm20) cc_final: 0.8887 (pm20) REVERT: A 420 GLU cc_start: 0.7478 (pp20) cc_final: 0.7203 (pp20) REVERT: A 931 PRO cc_start: 0.7653 (Cg_exo) cc_final: 0.7361 (Cg_endo) outliers start: 17 outliers final: 9 residues processed: 243 average time/residue: 0.1004 time to fit residues: 35.2810 Evaluate side-chains 207 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 198 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 839 LYS Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain D residue 17 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 HIS A 377 HIS ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 HIS ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 HIS ** A 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 ASN ** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.123023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.100310 restraints weight = 33818.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.103317 restraints weight = 20349.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.105352 restraints weight = 14614.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.106545 restraints weight = 11680.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.107595 restraints weight = 10149.991| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11041 Z= 0.210 Angle : 0.784 11.108 14970 Z= 0.389 Chirality : 0.048 0.249 1682 Planarity : 0.006 0.057 1922 Dihedral : 7.304 55.969 1498 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.83 % Favored : 91.80 % Rotamer: Outliers : 4.90 % Allowed : 26.43 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.29 (0.23), residues: 1342 helix: 0.20 (0.23), residues: 488 sheet: -0.74 (0.39), residues: 206 loop : -1.72 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 316 TYR 0.022 0.002 TYR A 418 PHE 0.041 0.002 PHE C 139 TRP 0.037 0.002 TRP A 640 HIS 0.006 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (11039) covalent geometry : angle 0.78349 / 0.39 (14968) SS BOND : bond 0.00320 / 0.17 ( 1) SS BOND : angle 2.13544 / 1.10 ( 2) hydrogen bonds : bond 0.04442 / 2.92 ( 445) hydrogen bonds : angle 5.84900 / 4.07 ( 1227) Misc. bond : bond 0.00454 / 0.24 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 205 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6749 (tmm) REVERT: A 183 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7479 (t80) REVERT: A 330 LEU cc_start: 0.8792 (tt) cc_final: 0.8455 (tt) REVERT: A 793 GLN cc_start: 0.7527 (mp10) cc_final: 0.6945 (pp30) REVERT: A 839 LYS cc_start: 0.5590 (OUTLIER) cc_final: 0.5272 (pttm) REVERT: C 224 ASN cc_start: 0.7093 (p0) cc_final: 0.6884 (p0) REVERT: C 278 TYR cc_start: 0.8302 (m-80) cc_final: 0.7846 (m-80) REVERT: C 299 ASP cc_start: 0.6628 (OUTLIER) cc_final: 0.6297 (p0) outliers start: 57 outliers final: 26 residues processed: 243 average time/residue: 0.0856 time to fit residues: 31.7355 Evaluate side-chains 213 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 839 LYS Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 299 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 123 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 59 optimal weight: 0.0470 chunk 119 optimal weight: 0.8980 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 377 HIS A 614 HIS ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.124391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.101484 restraints weight = 33982.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.104542 restraints weight = 20580.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.106585 restraints weight = 14765.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.108008 restraints weight = 11854.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.108495 restraints weight = 10175.840| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11041 Z= 0.151 Angle : 0.712 11.043 14970 Z= 0.354 Chirality : 0.046 0.265 1682 Planarity : 0.005 0.060 1922 Dihedral : 6.319 46.274 1492 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.83 % Favored : 91.80 % Rotamer: Outliers : 4.90 % Allowed : 26.77 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.14 (0.23), residues: 1342 helix: 0.35 (0.23), residues: 489 sheet: -0.75 (0.38), residues: 206 loop : -1.62 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 316 TYR 0.017 0.001 TYR C 282 PHE 0.036 0.002 PHE C 139 TRP 0.022 0.001 TRP A 640 HIS 0.003 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (11039) covalent geometry : angle 0.71208 / 0.35 (14968) SS BOND : bond 0.00044 / 0.02 ( 1) SS BOND : angle 1.43827 / 0.73 ( 2) hydrogen bonds : bond 0.03855 / 2.54 ( 445) hydrogen bonds : angle 5.51432 / 3.83 ( 1227) Misc. bond : bond 0.00135 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 208 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6511 (tmm) REVERT: A 230 THR cc_start: 0.7532 (p) cc_final: 0.7306 (t) REVERT: A 621 GLU cc_start: 0.7289 (tp30) cc_final: 0.6830 (pm20) REVERT: A 628 LYS cc_start: 0.8784 (tttt) cc_final: 0.8528 (tttp) REVERT: A 793 GLN cc_start: 0.7585 (mp10) cc_final: 0.6975 (pp30) REVERT: A 839 LYS cc_start: 0.5678 (OUTLIER) cc_final: 0.5308 (pttm) REVERT: A 850 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7523 (tm-30) REVERT: B 62 GLN cc_start: 0.7058 (pp30) cc_final: 0.6799 (pp30) REVERT: C 224 ASN cc_start: 0.7089 (p0) cc_final: 0.6662 (p0) REVERT: C 278 TYR cc_start: 0.8154 (m-80) cc_final: 0.7757 (m-80) REVERT: C 299 ASP cc_start: 0.6428 (p0) cc_final: 0.6064 (p0) outliers start: 57 outliers final: 32 residues processed: 247 average time/residue: 0.0832 time to fit residues: 31.3817 Evaluate side-chains 226 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 839 LYS Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 17 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 32 optimal weight: 0.0270 overall best weight: 2.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 377 HIS ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 HIS ** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.122274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.099280 restraints weight = 34652.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.102287 restraints weight = 20691.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.104321 restraints weight = 14799.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.105568 restraints weight = 11814.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.106651 restraints weight = 10271.935| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11041 Z= 0.183 Angle : 0.716 10.166 14970 Z= 0.357 Chirality : 0.046 0.258 1682 Planarity : 0.005 0.073 1922 Dihedral : 6.503 45.684 1491 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.35 % Favored : 91.28 % Rotamer: Outliers : 6.07 % Allowed : 26.93 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.19 (0.23), residues: 1342 helix: 0.38 (0.23), residues: 493 sheet: -0.92 (0.37), residues: 208 loop : -1.68 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 316 TYR 0.015 0.002 TYR C 222 PHE 0.036 0.002 PHE C 139 TRP 0.016 0.002 TRP A 640 HIS 0.004 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (11039) covalent geometry : angle 0.71551 / 0.36 (14968) SS BOND : bond 0.00115 / 0.06 ( 1) SS BOND : angle 2.01508 / 1.03 ( 2) hydrogen bonds : bond 0.03704 / 2.43 ( 445) hydrogen bonds : angle 5.45741 / 3.80 ( 1227) Misc. bond : bond 0.00151 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 201 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7150 (ppp) cc_final: 0.5897 (tmm) REVERT: A 155 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8245 (pm20) REVERT: A 183 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7280 (t80) REVERT: A 287 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8080 (mm) REVERT: A 628 LYS cc_start: 0.8792 (tttt) cc_final: 0.8508 (tttp) REVERT: A 789 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7306 (pm20) REVERT: A 793 GLN cc_start: 0.7466 (mp10) cc_final: 0.7030 (pp30) REVERT: A 850 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7553 (tm-30) REVERT: A 916 TYR cc_start: 0.8379 (m-80) cc_final: 0.8157 (m-80) REVERT: B 62 GLN cc_start: 0.7293 (pp30) cc_final: 0.7001 (pp30) REVERT: C 224 ASN cc_start: 0.7136 (p0) cc_final: 0.6833 (p0) REVERT: C 278 TYR cc_start: 0.8204 (m-80) cc_final: 0.7790 (m-80) outliers start: 71 outliers final: 47 residues processed: 247 average time/residue: 0.0835 time to fit residues: 31.0981 Evaluate side-chains 232 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 839 LYS Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 17 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 80 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 30 optimal weight: 0.4980 chunk 109 optimal weight: 0.6980 chunk 123 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 377 HIS A 570 ASN A 614 HIS ** A 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.123615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.100849 restraints weight = 33997.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.103794 restraints weight = 20428.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.105803 restraints weight = 14678.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.107182 restraints weight = 11789.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.107962 restraints weight = 10143.727| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11041 Z= 0.147 Angle : 0.704 9.731 14970 Z= 0.350 Chirality : 0.046 0.268 1682 Planarity : 0.005 0.063 1922 Dihedral : 6.557 51.410 1491 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.83 % Favored : 91.80 % Rotamer: Outliers : 5.74 % Allowed : 27.93 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.11 (0.23), residues: 1342 helix: 0.38 (0.23), residues: 496 sheet: -0.81 (0.38), residues: 202 loop : -1.61 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 316 TYR 0.015 0.001 TYR C 222 PHE 0.034 0.002 PHE C 139 TRP 0.014 0.001 TRP A 640 HIS 0.011 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (11039) covalent geometry : angle 0.70346 / 0.35 (14968) SS BOND : bond 0.00216 / 0.11 ( 1) SS BOND : angle 1.80187 / 0.91 ( 2) hydrogen bonds : bond 0.03487 / 2.29 ( 445) hydrogen bonds : angle 5.32536 / 3.71 ( 1227) Misc. bond : bond 0.00118 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 200 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7193 (ppp) cc_final: 0.6170 (tmm) REVERT: A 115 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7404 (mtpp) REVERT: A 155 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8258 (pm20) REVERT: A 183 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7304 (t80) REVERT: A 230 THR cc_start: 0.7500 (OUTLIER) cc_final: 0.7267 (t) REVERT: A 401 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8548 (mt-10) REVERT: A 621 GLU cc_start: 0.7266 (tp30) cc_final: 0.6675 (pm20) REVERT: A 628 LYS cc_start: 0.8750 (tttt) cc_final: 0.8440 (tttp) REVERT: A 793 GLN cc_start: 0.7499 (mp10) cc_final: 0.7100 (pp30) REVERT: A 850 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7498 (tm-30) REVERT: A 916 TYR cc_start: 0.8255 (m-80) cc_final: 0.8036 (m-80) REVERT: B 62 GLN cc_start: 0.7271 (pp30) cc_final: 0.6907 (pp30) REVERT: C 161 HIS cc_start: 0.8686 (m170) cc_final: 0.8465 (m170) REVERT: C 224 ASN cc_start: 0.7191 (p0) cc_final: 0.6888 (p0) REVERT: C 278 TYR cc_start: 0.8063 (m-80) cc_final: 0.7675 (m-80) REVERT: C 299 ASP cc_start: 0.6437 (p0) cc_final: 0.6185 (p0) outliers start: 67 outliers final: 45 residues processed: 246 average time/residue: 0.0831 time to fit residues: 31.0704 Evaluate side-chains 237 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 839 LYS Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 17 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 126 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 51 optimal weight: 0.0770 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 overall best weight: 1.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 377 HIS ** A 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.123069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.100179 restraints weight = 34195.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.103174 restraints weight = 20707.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.105163 restraints weight = 14867.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.106587 restraints weight = 11945.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.107354 restraints weight = 10279.473| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11041 Z= 0.156 Angle : 0.717 9.574 14970 Z= 0.358 Chirality : 0.047 0.267 1682 Planarity : 0.005 0.064 1922 Dihedral : 6.628 59.150 1491 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.13 % Favored : 91.50 % Rotamer: Outliers : 6.40 % Allowed : 27.27 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.10 (0.23), residues: 1342 helix: 0.39 (0.23), residues: 496 sheet: -0.82 (0.38), residues: 202 loop : -1.60 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 175 TYR 0.016 0.001 TYR C 222 PHE 0.033 0.002 PHE C 139 TRP 0.012 0.001 TRP A 640 HIS 0.003 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (11039) covalent geometry : angle 0.71666 / 0.36 (14968) SS BOND : bond 0.00501 / 0.26 ( 1) SS BOND : angle 1.91135 / 0.96 ( 2) hydrogen bonds : bond 0.03447 / 2.28 ( 445) hydrogen bonds : angle 5.31489 / 3.72 ( 1227) Misc. bond : bond 0.00119 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 200 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.6898 (OUTLIER) cc_final: 0.6518 (tmm) REVERT: A 69 MET cc_start: 0.7231 (ppp) cc_final: 0.6127 (tmm) REVERT: A 115 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7417 (mtpp) REVERT: A 155 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8314 (pm20) REVERT: A 183 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7359 (t80) REVERT: A 230 THR cc_start: 0.7499 (OUTLIER) cc_final: 0.7290 (t) REVERT: A 287 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8124 (mm) REVERT: A 401 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8561 (mt-10) REVERT: A 628 LYS cc_start: 0.8789 (tttt) cc_final: 0.8460 (tttp) REVERT: A 639 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7589 (pp30) REVERT: A 789 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7423 (pm20) REVERT: A 793 GLN cc_start: 0.7492 (mp10) cc_final: 0.7129 (pp30) REVERT: A 850 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7499 (tm-30) REVERT: A 916 TYR cc_start: 0.8228 (m-10) cc_final: 0.7939 (m-80) REVERT: B 62 GLN cc_start: 0.7224 (pp30) cc_final: 0.6830 (pp30) REVERT: C 161 HIS cc_start: 0.8681 (m170) cc_final: 0.8463 (m170) REVERT: C 173 ASN cc_start: 0.8834 (m-40) cc_final: 0.8243 (t0) REVERT: C 278 TYR cc_start: 0.7995 (m-80) cc_final: 0.7604 (m-80) REVERT: C 299 ASP cc_start: 0.6435 (p0) cc_final: 0.5991 (p0) outliers start: 75 outliers final: 53 residues processed: 251 average time/residue: 0.0827 time to fit residues: 31.2208 Evaluate side-chains 245 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 183 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 839 LYS Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 936 THR Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 65 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 86 optimal weight: 0.0870 chunk 35 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 110 optimal weight: 0.0270 chunk 50 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 377 HIS ** A 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.123044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.100577 restraints weight = 34118.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.103618 restraints weight = 20484.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.105593 restraints weight = 14600.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.106987 restraints weight = 11666.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.107797 restraints weight = 10010.850| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11041 Z= 0.145 Angle : 0.718 9.597 14970 Z= 0.356 Chirality : 0.047 0.287 1682 Planarity : 0.005 0.063 1922 Dihedral : 6.613 59.668 1490 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.68 % Favored : 92.02 % Rotamer: Outliers : 6.65 % Allowed : 27.18 % Favored : 66.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.08 (0.23), residues: 1342 helix: 0.38 (0.23), residues: 496 sheet: -0.82 (0.37), residues: 202 loop : -1.55 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 186 TYR 0.015 0.001 TYR C 222 PHE 0.035 0.002 PHE C 139 TRP 0.012 0.001 TRP A 640 HIS 0.003 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (11039) covalent geometry : angle 0.71770 / 0.36 (14968) SS BOND : bond 0.00350 / 0.18 ( 1) SS BOND : angle 2.30857 / 1.15 ( 2) hydrogen bonds : bond 0.03426 / 2.29 ( 445) hydrogen bonds : angle 5.27902 / 3.70 ( 1227) Misc. bond : bond 0.00112 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 195 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6508 (tmm) REVERT: A 69 MET cc_start: 0.7172 (ppp) cc_final: 0.6163 (tmm) REVERT: A 115 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7406 (mtpp) REVERT: A 125 HIS cc_start: 0.8387 (OUTLIER) cc_final: 0.7789 (m-70) REVERT: A 155 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8276 (pm20) REVERT: A 183 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7416 (t80) REVERT: A 287 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8153 (mm) REVERT: A 401 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8579 (mt-10) REVERT: A 628 LYS cc_start: 0.8763 (tttt) cc_final: 0.8442 (tttp) REVERT: A 639 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7608 (pp30) REVERT: A 789 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7431 (pm20) REVERT: A 793 GLN cc_start: 0.7455 (mp10) cc_final: 0.7150 (pp30) REVERT: A 850 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7494 (tm-30) REVERT: A 916 TYR cc_start: 0.8198 (m-10) cc_final: 0.7901 (m-80) REVERT: B 62 GLN cc_start: 0.7297 (pp30) cc_final: 0.6878 (pp30) REVERT: C 161 HIS cc_start: 0.8670 (m170) cc_final: 0.8456 (m170) REVERT: C 173 ASN cc_start: 0.8831 (m-40) cc_final: 0.8208 (t0) REVERT: C 278 TYR cc_start: 0.7986 (m-80) cc_final: 0.7610 (m-80) REVERT: C 299 ASP cc_start: 0.6369 (p0) cc_final: 0.5928 (p0) REVERT: D 34 GLU cc_start: 0.5481 (mm-30) cc_final: 0.4862 (pm20) outliers start: 78 outliers final: 56 residues processed: 245 average time/residue: 0.0773 time to fit residues: 29.3159 Evaluate side-chains 254 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 189 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 839 LYS Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 17 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 71 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 98 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 110 optimal weight: 0.0570 chunk 38 optimal weight: 2.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 377 HIS ** A 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.124181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.101749 restraints weight = 34419.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.104822 restraints weight = 20709.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.106780 restraints weight = 14765.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.108250 restraints weight = 11837.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.108850 restraints weight = 10085.228| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11041 Z= 0.132 Angle : 0.715 9.812 14970 Z= 0.352 Chirality : 0.047 0.328 1682 Planarity : 0.005 0.064 1922 Dihedral : 6.542 57.277 1490 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.61 % Favored : 92.10 % Rotamer: Outliers : 5.74 % Allowed : 28.26 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.01 (0.23), residues: 1342 helix: 0.46 (0.23), residues: 494 sheet: -0.81 (0.37), residues: 202 loop : -1.51 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 74 TYR 0.016 0.001 TYR C 222 PHE 0.033 0.002 PHE C 139 TRP 0.013 0.001 TRP A 640 HIS 0.004 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (11039) covalent geometry : angle 0.71426 / 0.35 (14968) SS BOND : bond 0.00279 / 0.15 ( 1) SS BOND : angle 2.26720 / 1.14 ( 2) hydrogen bonds : bond 0.03277 / 2.21 ( 445) hydrogen bonds : angle 5.20863 / 3.63 ( 1227) Misc. bond : bond 0.00109 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 211 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.6898 (OUTLIER) cc_final: 0.6486 (tmm) REVERT: A 69 MET cc_start: 0.7057 (ppp) cc_final: 0.6177 (tmm) REVERT: A 125 HIS cc_start: 0.8376 (OUTLIER) cc_final: 0.7786 (m-70) REVERT: A 167 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7794 (pm20) REVERT: A 401 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8538 (mt-10) REVERT: A 496 THR cc_start: 0.7776 (OUTLIER) cc_final: 0.7517 (p) REVERT: A 628 LYS cc_start: 0.8705 (tttt) cc_final: 0.8405 (tttp) REVERT: A 636 HIS cc_start: 0.8649 (m90) cc_final: 0.8001 (m90) REVERT: A 639 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7587 (pp30) REVERT: A 781 ASP cc_start: 0.8661 (m-30) cc_final: 0.8410 (m-30) REVERT: A 789 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7415 (pm20) REVERT: A 793 GLN cc_start: 0.7430 (mp10) cc_final: 0.7134 (pp30) REVERT: A 850 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7530 (tm-30) REVERT: A 916 TYR cc_start: 0.8130 (m-10) cc_final: 0.7391 (m-80) REVERT: A 1009 MET cc_start: 0.8007 (mmm) cc_final: 0.7588 (mmm) REVERT: B 62 GLN cc_start: 0.7380 (pp30) cc_final: 0.6928 (pp30) REVERT: C 161 HIS cc_start: 0.8636 (m170) cc_final: 0.8432 (m170) REVERT: C 173 ASN cc_start: 0.8567 (m-40) cc_final: 0.7887 (t0) REVERT: C 192 LEU cc_start: 0.8019 (tp) cc_final: 0.7579 (tt) REVERT: C 278 TYR cc_start: 0.7752 (m-80) cc_final: 0.7527 (m-80) REVERT: C 299 ASP cc_start: 0.6264 (p0) cc_final: 0.5849 (p0) outliers start: 67 outliers final: 52 residues processed: 251 average time/residue: 0.0790 time to fit residues: 30.8022 Evaluate side-chains 254 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 195 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 839 LYS Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 65 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 102 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 130 optimal weight: 0.4980 chunk 118 optimal weight: 9.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 377 HIS ** A 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.121399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.099088 restraints weight = 34269.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.102101 restraints weight = 20450.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.103970 restraints weight = 14555.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.105436 restraints weight = 11703.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.106218 restraints weight = 9991.969| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11041 Z= 0.205 Angle : 0.764 9.442 14970 Z= 0.380 Chirality : 0.048 0.301 1682 Planarity : 0.005 0.069 1922 Dihedral : 6.637 56.209 1490 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.83 % Favored : 91.95 % Rotamer: Outliers : 5.82 % Allowed : 28.84 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.29 (0.23), residues: 1342 helix: 0.18 (0.23), residues: 509 sheet: -0.97 (0.37), residues: 202 loop : -1.68 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1044 TYR 0.014 0.002 TYR C 222 PHE 0.034 0.002 PHE C 139 TRP 0.011 0.002 TRP A 381 HIS 0.007 0.001 HIS A 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 (11039) covalent geometry : angle 0.76343 / 0.38 (14968) SS BOND : bond 0.00928 / 0.49 ( 1) SS BOND : angle 3.17314 / 1.60 ( 2) hydrogen bonds : bond 0.03591 / 2.40 ( 445) hydrogen bonds : angle 5.32669 / 3.72 ( 1227) Misc. bond : bond 0.00133 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 189 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.6917 (ttt) cc_final: 0.6517 (tmm) REVERT: A 69 MET cc_start: 0.7147 (ppp) cc_final: 0.6400 (tmm) REVERT: A 115 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7438 (mtpp) REVERT: A 125 HIS cc_start: 0.8382 (OUTLIER) cc_final: 0.7788 (m-70) REVERT: A 287 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8159 (mm) REVERT: A 401 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8523 (mt-10) REVERT: A 628 LYS cc_start: 0.8676 (tttt) cc_final: 0.8395 (tttp) REVERT: A 636 HIS cc_start: 0.8689 (m90) cc_final: 0.7937 (m90) REVERT: A 639 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7670 (pp30) REVERT: A 781 ASP cc_start: 0.8617 (m-30) cc_final: 0.8347 (m-30) REVERT: A 789 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7281 (pm20) REVERT: A 793 GLN cc_start: 0.7380 (mp10) cc_final: 0.7125 (pp30) REVERT: A 850 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7430 (tm-30) REVERT: A 916 TYR cc_start: 0.8029 (m-10) cc_final: 0.7250 (m-10) REVERT: B 62 GLN cc_start: 0.7421 (pp30) cc_final: 0.6969 (pp30) REVERT: C 173 ASN cc_start: 0.8704 (m-40) cc_final: 0.8095 (t0) REVERT: C 222 TYR cc_start: 0.7206 (t80) cc_final: 0.6794 (t80) REVERT: C 299 ASP cc_start: 0.6363 (p0) cc_final: 0.5948 (p0) outliers start: 68 outliers final: 52 residues processed: 231 average time/residue: 0.0836 time to fit residues: 29.4411 Evaluate side-chains 240 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 182 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 839 LYS Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 89 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 106 optimal weight: 0.0570 chunk 79 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 HIS ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.124195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.101960 restraints weight = 33987.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.105061 restraints weight = 20268.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.107155 restraints weight = 14355.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.108435 restraints weight = 11365.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.109504 restraints weight = 9765.654| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3740 r_free = 0.3740 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3740 r_free = 0.3740 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11041 Z= 0.138 Angle : 0.766 13.087 14970 Z= 0.374 Chirality : 0.049 0.382 1682 Planarity : 0.005 0.057 1922 Dihedral : 6.616 55.483 1490 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.08 % Favored : 92.69 % Rotamer: Outliers : 4.41 % Allowed : 29.84 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.16 (0.23), residues: 1342 helix: 0.22 (0.23), residues: 502 sheet: -0.83 (0.37), residues: 200 loop : -1.55 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1044 TYR 0.019 0.001 TYR C 278 PHE 0.032 0.002 PHE C 139 TRP 0.015 0.001 TRP A 640 HIS 0.005 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (11039) covalent geometry : angle 0.76574 / 0.37 (14968) SS BOND : bond 0.00155 / 0.08 ( 1) SS BOND : angle 2.42025 / 1.22 ( 2) hydrogen bonds : bond 0.03465 / 2.34 ( 445) hydrogen bonds : angle 5.36392 / 3.71 ( 1227) Misc. bond : bond 0.00090 / 0.05 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 197 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.6871 (ttt) cc_final: 0.6511 (tmm) REVERT: A 69 MET cc_start: 0.7148 (ppp) cc_final: 0.6263 (tmm) REVERT: A 115 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7372 (mtpp) REVERT: A 154 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.6867 (m-10) REVERT: A 401 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8490 (mt-10) REVERT: A 614 HIS cc_start: 0.7738 (m-70) cc_final: 0.7421 (m170) REVERT: A 636 HIS cc_start: 0.8577 (m90) cc_final: 0.7914 (m90) REVERT: A 781 ASP cc_start: 0.8552 (m-30) cc_final: 0.8311 (m-30) REVERT: A 793 GLN cc_start: 0.7431 (mp10) cc_final: 0.7139 (pp30) REVERT: A 850 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7428 (tm-30) REVERT: A 916 TYR cc_start: 0.7872 (m-10) cc_final: 0.7151 (m-10) REVERT: B 62 GLN cc_start: 0.7415 (pp30) cc_final: 0.6961 (pp30) REVERT: C 173 ASN cc_start: 0.8596 (m-40) cc_final: 0.7929 (t0) outliers start: 51 outliers final: 41 residues processed: 227 average time/residue: 0.0819 time to fit residues: 28.4433 Evaluate side-chains 233 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 449 CYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 839 LYS Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 909 MET Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 39 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 72 optimal weight: 0.3980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 ASN A 377 HIS A 543 ASN ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 HIS ** 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 = 0.3969 r_free = 0.3969 target = 0.123548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.101573 restraints weight = 34381.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.104658 restraints weight = 20609.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.106793 restraints weight = 14588.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.108012 restraints weight = 11499.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.109181 restraints weight = 9901.209| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11041 Z= 0.138 Angle : 0.753 13.320 14970 Z= 0.368 Chirality : 0.048 0.396 1682 Planarity : 0.005 0.061 1922 Dihedral : 6.480 52.929 1490 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.94 % Favored : 92.84 % Rotamer: Outliers : 4.41 % Allowed : 30.09 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.14 (0.23), residues: 1342 helix: 0.29 (0.23), residues: 502 sheet: -0.82 (0.37), residues: 202 loop : -1.58 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1044 TYR 0.021 0.001 TYR C 278 PHE 0.032 0.002 PHE C 139 TRP 0.014 0.001 TRP A 640 HIS 0.004 0.001 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (11039) covalent geometry : angle 0.75212 / 0.37 (14968) SS BOND : bond 0.00014 / 0.01 ( 1) SS BOND : angle 2.80131 / 1.40 ( 2) hydrogen bonds : bond 0.03381 / 2.27 ( 445) hydrogen bonds : angle 5.33564 / 3.69 ( 1227) Misc. bond : bond 0.00071 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2034.48 seconds wall clock time: 36 minutes 4.97 seconds (2164.97 seconds total)