Starting phenix.real_space_refine on Thu Jul 2 04:25:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7li8_23363/07_2026/7li8_23363.cif Found real_map, /net/cci-nas-00/data/ceres_data/7li8_23363/07_2026/7li8_23363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7li8_23363/07_2026/7li8_23363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7li8_23363/07_2026/7li8_23363.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7li8_23363/07_2026/7li8_23363.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7li8_23363/07_2026/7li8_23363.cif" model { file = "/net/cci-nas-00/data/ceres_data/7li8_23363/07_2026/7li8_23363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7li8_23363/07_2026/7li8_23363.cif" } resolution = 3.9 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 4104 2.51 5 N 962 2.21 5 O 1081 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6181 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4303 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 515} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 109 Unusual residues: {'D10': 1, 'D12': 3, 'HP6': 6, 'LNK': 1, 'R16': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Time building chain proxies: 0.92, per 1000 atoms: 0.15 Number of scatterers: 6181 At special positions: 0 Unit cell: (68.688, 77.112, 122.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1081 8.00 N 962 7.00 C 4104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 112 " 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 208 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 357.1 milliseconds 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 8 sheets defined 51.0% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.679A pdb=" N TYR A 107 " --> pdb=" O TRP A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 129 through 143 Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 159 through 176 removed outlier: 4.107A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 removed outlier: 4.028A pdb=" N MET A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 252 through 268 removed outlier: 3.628A pdb=" N CYS A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 removed outlier: 3.769A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 301 removed outlier: 4.317A pdb=" N SER A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.660A pdb=" N GLY A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 349 Processing helix chain 'A' and resid 359 through 389 removed outlier: 3.988A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.802A pdb=" N VAL A 397 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 415 removed outlier: 4.411A pdb=" N PHE A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 448 removed outlier: 4.117A pdb=" N ALA A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 478 through 482 removed outlier: 3.842A pdb=" N THR A 482 " --> pdb=" O VAL A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 496 removed outlier: 4.382A pdb=" N LEU A 491 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 515 removed outlier: 3.769A pdb=" N LEU A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 530 Processing helix chain 'A' and resid 534 through 558 removed outlier: 3.641A pdb=" N ARG A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TRP A 541 " --> pdb=" O TRP A 537 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 543 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N SER A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Proline residue: A 546 - end of helix Processing helix chain 'A' and resid 571 through 585 removed outlier: 4.187A pdb=" N ILE A 575 " --> pdb=" O PRO A 571 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 576 " --> pdb=" O TYR A 572 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 598 removed outlier: 3.813A pdb=" N ILE A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 613 removed outlier: 3.743A pdb=" N THR A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 removed outlier: 4.165A pdb=" N TYR B 50 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER B 51 " --> pdb=" O PHE B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 47 through 51' Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.519A pdb=" N THR C 107 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 565 Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 25 removed outlier: 3.633A pdb=" N GLN B 24 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 42 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 39 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET B 100 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.526A pdb=" N ILE B 67 " --> pdb=" O TRP B 55 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.526A pdb=" N ILE B 67 " --> pdb=" O TRP B 55 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.774A pdb=" N TYR C 73 " --> pdb=" O ASN C 77 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TRP C 59 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TYR C 73 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU C 57 " --> pdb=" O TYR C 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.774A pdb=" N TYR C 73 " --> pdb=" O ASN C 77 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TRP C 59 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TYR C 73 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU C 57 " --> pdb=" O TYR C 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 87 through 90 removed outlier: 3.561A pdb=" N SER C 89 " --> pdb=" O SER C 96 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 756 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: 0.92 Time building geometry restraints manager: 0.55 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: 1811 1.34 - 1.46: 1452 1.46 - 1.58: 3037 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6349 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C2 NAG D 1 " pdb=" N2 NAG D 1 " ideal model delta sigma weight residual 1.439 1.464 -0.025 2.00e-02 2.50e+03 1.56e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.50e+00 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.33e+00 bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.24e+00 ... (remaining 6344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 8193 1.08 - 2.16: 247 2.16 - 3.24: 65 3.24 - 4.32: 79 4.32 - 5.40: 12 Bond angle restraints: 8596 Sorted by residual: angle pdb=" N VAL A 102 " pdb=" CA VAL A 102 " pdb=" C VAL A 102 " ideal model delta sigma weight residual 113.53 109.27 4.26 9.80e-01 1.04e+00 1.89e+01 angle pdb=" N VAL A 92 " pdb=" CA VAL A 92 " pdb=" C VAL A 92 " ideal model delta sigma weight residual 113.71 110.54 3.17 9.50e-01 1.11e+00 1.11e+01 angle pdb=" N VAL A 446 " pdb=" CA VAL A 446 " pdb=" C VAL A 446 " ideal model delta sigma weight residual 112.96 109.70 3.26 1.00e+00 1.00e+00 1.07e+01 angle pdb=" C GLY B 121 " pdb=" N SER B 122 " pdb=" CA SER B 122 " ideal model delta sigma weight residual 120.38 124.54 -4.16 1.37e+00 5.33e-01 9.22e+00 angle pdb=" C MET B 127 " pdb=" N ASP B 128 " pdb=" CA ASP B 128 " ideal model delta sigma weight residual 121.54 126.14 -4.60 1.91e+00 2.74e-01 5.79e+00 ... (remaining 8591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.73: 3292 14.73 - 29.46: 270 29.46 - 44.19: 55 44.19 - 58.91: 7 58.91 - 73.64: 2 Dihedral angle restraints: 3626 sinusoidal: 1420 harmonic: 2206 Sorted by residual: dihedral pdb=" CB CYS B 41 " pdb=" SG CYS B 41 " pdb=" SG CYS B 115 " pdb=" CB CYS B 115 " ideal model delta sinusoidal sigma weight residual 93.00 166.64 -73.64 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CA TRP A 204 " pdb=" C TRP A 204 " pdb=" N ASN A 205 " pdb=" CA ASN A 205 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ASP A 87 " pdb=" CB ASP A 87 " pdb=" CG ASP A 87 " pdb=" OD1 ASP A 87 " ideal model delta sinusoidal sigma weight residual -30.00 -82.66 52.66 1 2.00e+01 2.50e-03 9.44e+00 ... (remaining 3623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 929 0.103 - 0.206: 12 0.206 - 0.309: 0 0.309 - 0.413: 0 0.413 - 0.516: 1 Chirality restraints: 942 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-02 2.50e+03 6.65e+02 chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CB THR C 107 " pdb=" CA THR C 107 " pdb=" OG1 THR C 107 " pdb=" CG2 THR C 107 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 939 not shown) Planarity restraints: 1048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 338 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO A 339 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 130 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO A 131 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 128 " -0.005 2.00e-02 2.50e+03 1.07e-02 1.15e+00 pdb=" C ASP B 128 " 0.019 2.00e-02 2.50e+03 pdb=" O ASP B 128 " -0.007 2.00e-02 2.50e+03 pdb=" N TYR B 129 " -0.006 2.00e-02 2.50e+03 ... (remaining 1045 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1068 2.76 - 3.30: 5736 3.30 - 3.83: 9932 3.83 - 4.37: 10836 4.37 - 4.90: 19149 Nonbonded interactions: 46721 Sorted by model distance: nonbonded pdb=" OH TYR A 110 " pdb=" O VAL A 394 " model vdw 2.230 3.040 nonbonded pdb=" OG SER B 49 " pdb=" O PRO B 72 " model vdw 2.256 3.040 nonbonded pdb=" O LYS A 201 " pdb=" NE1 TRP B 52 " model vdw 2.296 3.120 nonbonded pdb=" O SER A 477 " pdb=" OG SER A 477 " model vdw 2.303 3.040 nonbonded pdb=" OG SER B 36 " pdb=" O LEU B 102 " model vdw 2.330 3.040 ... (remaining 46716 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.920 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 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 : 0.002 0.065 6355 Z= 0.117 Angle : 0.636 14.044 8608 Z= 0.308 Chirality : 0.041 0.516 942 Planarity : 0.003 0.033 1047 Dihedral : 10.783 69.682 2217 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.27), residues: 761 helix: -1.23 (0.23), residues: 353 sheet: -2.94 (0.51), residues: 82 loop : -2.92 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 298 TYR 0.011 0.001 TYR A 175 PHE 0.013 0.000 PHE B 125 TRP 0.012 0.000 TRP A 204 HIS 0.001 0.000 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.11 ( 6349) covalent geometry : angle 0.60121 / 0.30 ( 8596) SS BOND : bond 0.00070 / 0.04 ( 3) SS BOND : angle 0.24147 / 0.12 ( 6) hydrogen bonds : bond 0.18544 / 11.55 ( 265) hydrogen bonds : angle 5.83901 / 4.17 ( 756) Misc. bond : bond 0.00023 / 0.01 ( 1) link_BETA1-4 : bond 0.06516 / 3.43 ( 1) link_BETA1-4 : angle 11.10597 / 5.75 ( 3) link_NAG-ASN : bond 0.00293 / 0.15 ( 1) link_NAG-ASN : angle 1.61201 / 0.87 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6008 (mmpt) cc_final: 0.5241 (ptmt) REVERT: A 152 ARG cc_start: 0.8690 (mmm-85) cc_final: 0.8428 (mmt90) REVERT: A 222 LEU cc_start: 0.7905 (tp) cc_final: 0.7315 (tp) REVERT: B 58 GLN cc_start: 0.8476 (tt0) cc_final: 0.8096 (tt0) REVERT: C 62 GLN cc_start: 0.8044 (tt0) cc_final: 0.7838 (tt0) REVERT: C 110 TYR cc_start: 0.7845 (m-80) cc_final: 0.7568 (m-80) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.0718 time to fit residues: 13.9672 Evaluate side-chains 117 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.0570 chunk 74 optimal weight: 1.9990 overall best weight: 0.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN A 194 GLN A 354 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 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 = 0.4130 r_free = 0.4130 target = 0.158777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.125238 restraints weight = 9787.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.129684 restraints weight = 5895.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.132490 restraints weight = 4241.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.134563 restraints weight = 3417.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.135721 restraints weight = 2948.449| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6355 Z= 0.143 Angle : 0.597 9.489 8608 Z= 0.295 Chirality : 0.041 0.240 942 Planarity : 0.004 0.030 1047 Dihedral : 3.653 22.853 904 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.11 % Allowed : 12.91 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.31), residues: 761 helix: -0.17 (0.27), residues: 350 sheet: -2.36 (0.53), residues: 86 loop : -2.04 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 523 TYR 0.026 0.002 TYR A 358 PHE 0.023 0.001 PHE A 287 TRP 0.010 0.001 TRP A 535 HIS 0.003 0.001 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 6349) covalent geometry : angle 0.59168 / 0.29 ( 8596) SS BOND : bond 0.00435 / 0.22 ( 3) SS BOND : angle 2.74659 / 1.33 ( 6) hydrogen bonds : bond 0.03170 / 2.10 ( 265) hydrogen bonds : angle 4.24830 / 2.94 ( 756) Misc. bond : bond 0.00056 / 0.03 ( 1) link_BETA1-4 : bond 0.00419 / 0.22 ( 1) link_BETA1-4 : angle 1.41078 / 0.73 ( 3) link_NAG-ASN : bond 0.00202 / 0.11 ( 1) link_NAG-ASN : angle 1.52251 / 0.83 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.5895 (mmpt) cc_final: 0.5157 (ptmt) REVERT: A 222 LEU cc_start: 0.7857 (tp) cc_final: 0.7610 (tp) REVERT: A 260 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7212 (tmm) REVERT: A 592 TYR cc_start: 0.8652 (t80) cc_final: 0.8388 (t80) REVERT: B 53 MET cc_start: 0.7390 (ttm) cc_final: 0.7150 (ttm) REVERT: B 58 GLN cc_start: 0.8516 (tt0) cc_final: 0.8115 (tt0) REVERT: C 110 TYR cc_start: 0.7753 (m-80) cc_final: 0.7477 (m-80) REVERT: C 116 LYS cc_start: 0.5484 (mttp) cc_final: 0.3611 (ttmt) outliers start: 20 outliers final: 16 residues processed: 138 average time/residue: 0.0620 time to fit residues: 11.3356 Evaluate side-chains 123 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 12 optimal weight: 0.0770 chunk 41 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.158083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.123672 restraints weight = 10246.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.127771 restraints weight = 6469.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.130692 restraints weight = 4816.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.132567 restraints weight = 3948.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.133512 restraints weight = 3469.884| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6355 Z= 0.124 Angle : 0.563 9.299 8608 Z= 0.278 Chirality : 0.040 0.243 942 Planarity : 0.004 0.030 1047 Dihedral : 3.726 22.134 904 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.04 % Allowed : 15.09 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.31), residues: 761 helix: 0.30 (0.28), residues: 351 sheet: -1.87 (0.55), residues: 86 loop : -2.04 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 38 TYR 0.016 0.001 TYR B 120 PHE 0.019 0.001 PHE A 377 TRP 0.008 0.001 TRP A 535 HIS 0.002 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 6349) covalent geometry : angle 0.56059 / 0.28 ( 8596) SS BOND : bond 0.00275 / 0.14 ( 3) SS BOND : angle 1.78991 / 0.87 ( 6) hydrogen bonds : bond 0.02839 / 1.89 ( 265) hydrogen bonds : angle 4.02953 / 2.77 ( 756) Misc. bond : bond 0.00032 / 0.02 ( 1) link_BETA1-4 : bond 0.00219 / 0.12 ( 1) link_BETA1-4 : angle 0.93802 / 0.49 ( 3) link_NAG-ASN : bond 0.00210 / 0.11 ( 1) link_NAG-ASN : angle 1.32278 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6056 (mmpt) cc_final: 0.5205 (ptmt) REVERT: A 548 PHE cc_start: 0.7197 (OUTLIER) cc_final: 0.6013 (t80) REVERT: A 592 TYR cc_start: 0.8633 (t80) cc_final: 0.8423 (t80) REVERT: B 58 GLN cc_start: 0.8357 (tt0) cc_final: 0.8122 (tt0) REVERT: C 102 MET cc_start: 0.7653 (tmm) cc_final: 0.7357 (tmm) REVERT: C 110 TYR cc_start: 0.7793 (m-80) cc_final: 0.7547 (m-80) outliers start: 26 outliers final: 19 residues processed: 131 average time/residue: 0.0585 time to fit residues: 10.3738 Evaluate side-chains 122 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.151433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.116677 restraints weight = 10601.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.120566 restraints weight = 6786.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.123209 restraints weight = 5127.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.125003 restraints weight = 4276.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.125734 restraints weight = 3777.442| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 6355 Z= 0.187 Angle : 0.619 9.293 8608 Z= 0.310 Chirality : 0.042 0.239 942 Planarity : 0.004 0.033 1047 Dihedral : 4.296 22.283 904 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 5.13 % Allowed : 16.49 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.31), residues: 761 helix: 0.35 (0.28), residues: 350 sheet: -1.64 (0.56), residues: 86 loop : -1.99 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 44 TYR 0.042 0.002 TYR A 358 PHE 0.021 0.001 PHE A 377 TRP 0.018 0.001 TRP A 204 HIS 0.002 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 ( 6349) covalent geometry : angle 0.61565 / 0.31 ( 8596) SS BOND : bond 0.00545 / 0.27 ( 3) SS BOND : angle 2.22843 / 1.09 ( 6) hydrogen bonds : bond 0.03148 / 2.13 ( 265) hydrogen bonds : angle 4.21531 / 2.89 ( 756) Misc. bond : bond 0.00012 / 0.01 ( 1) link_BETA1-4 : bond 0.00245 / 0.13 ( 1) link_BETA1-4 : angle 1.09337 / 0.57 ( 3) link_NAG-ASN : bond 0.00202 / 0.11 ( 1) link_NAG-ASN : angle 1.31917 / 0.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.5964 (mmpt) cc_final: 0.5088 (ptmt) REVERT: A 260 MET cc_start: 0.7786 (tmm) cc_final: 0.7414 (tmt) REVERT: A 548 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6308 (t80) REVERT: B 53 MET cc_start: 0.7356 (ttm) cc_final: 0.7009 (ttm) REVERT: C 102 MET cc_start: 0.7585 (tmm) cc_final: 0.7231 (tmm) REVERT: C 110 TYR cc_start: 0.7989 (m-80) cc_final: 0.7491 (m-10) outliers start: 33 outliers final: 24 residues processed: 131 average time/residue: 0.0549 time to fit residues: 9.7803 Evaluate side-chains 128 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 204 TRP Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN ** C 113 GLN ** 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 = 0.3872 r_free = 0.3872 target = 0.146341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.114251 restraints weight = 10562.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.117793 restraints weight = 7166.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.120161 restraints weight = 5555.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.121767 restraints weight = 4701.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.122488 restraints weight = 4194.232| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6355 Z= 0.132 Angle : 0.585 9.322 8608 Z= 0.290 Chirality : 0.041 0.237 942 Planarity : 0.004 0.032 1047 Dihedral : 4.140 22.097 904 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.20 % Allowed : 19.28 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.31), residues: 761 helix: 0.52 (0.28), residues: 352 sheet: -1.62 (0.56), residues: 85 loop : -1.93 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 38 TYR 0.024 0.002 TYR B 120 PHE 0.026 0.001 PHE A 586 TRP 0.014 0.001 TRP A 204 HIS 0.002 0.000 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 6349) covalent geometry : angle 0.58206 / 0.29 ( 8596) SS BOND : bond 0.00505 / 0.25 ( 3) SS BOND : angle 1.96491 / 0.96 ( 6) hydrogen bonds : bond 0.02725 / 1.83 ( 265) hydrogen bonds : angle 4.02761 / 2.75 ( 756) Misc. bond : bond 0.00008 / 0.00 ( 1) link_BETA1-4 : bond 0.00451 / 0.24 ( 1) link_BETA1-4 : angle 1.10270 / 0.58 ( 3) link_NAG-ASN : bond 0.00262 / 0.14 ( 1) link_NAG-ASN : angle 1.17570 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.5925 (mmpt) cc_final: 0.5063 (ptmt) REVERT: A 260 MET cc_start: 0.7807 (tmm) cc_final: 0.7444 (tmt) REVERT: A 271 TRP cc_start: 0.7347 (OUTLIER) cc_final: 0.6982 (t60) REVERT: A 548 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.6406 (t80) REVERT: B 101 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6848 (mt0) REVERT: C 102 MET cc_start: 0.7497 (tmm) cc_final: 0.7129 (tmm) REVERT: C 110 TYR cc_start: 0.7812 (m-80) cc_final: 0.7347 (m-10) outliers start: 27 outliers final: 19 residues processed: 128 average time/residue: 0.0507 time to fit residues: 8.9954 Evaluate side-chains 125 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 204 TRP Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 3 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** 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 = 0.3828 r_free = 0.3828 target = 0.142082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109725 restraints weight = 10334.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.112999 restraints weight = 7039.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.115282 restraints weight = 5525.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.116829 restraints weight = 4695.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.117814 restraints weight = 4207.915| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 6355 Z= 0.185 Angle : 0.651 9.787 8608 Z= 0.322 Chirality : 0.042 0.231 942 Planarity : 0.004 0.040 1047 Dihedral : 4.592 23.935 904 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 5.29 % Allowed : 19.75 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.31), residues: 761 helix: 0.50 (0.28), residues: 347 sheet: -1.53 (0.55), residues: 86 loop : -1.85 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 38 TYR 0.026 0.002 TYR A 385 PHE 0.023 0.001 PHE A 377 TRP 0.023 0.001 TRP A 204 HIS 0.007 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 ( 6349) covalent geometry : angle 0.64831 / 0.32 ( 8596) SS BOND : bond 0.00527 / 0.26 ( 3) SS BOND : angle 2.35212 / 1.13 ( 6) hydrogen bonds : bond 0.03120 / 2.10 ( 265) hydrogen bonds : angle 4.22040 / 2.86 ( 756) Misc. bond : bond 0.00019 / 0.01 ( 1) link_BETA1-4 : bond 0.00317 / 0.17 ( 1) link_BETA1-4 : angle 1.04672 / 0.56 ( 3) link_NAG-ASN : bond 0.00296 / 0.16 ( 1) link_NAG-ASN : angle 1.14976 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 85 LYS cc_start: 0.5890 (mmpt) cc_final: 0.5035 (ptmt) REVERT: A 260 MET cc_start: 0.7893 (tmm) cc_final: 0.7553 (tmt) REVERT: A 271 TRP cc_start: 0.7444 (OUTLIER) cc_final: 0.7044 (t60) REVERT: A 301 THR cc_start: 0.7194 (p) cc_final: 0.6990 (p) REVERT: A 548 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6873 (t80) REVERT: B 109 ASP cc_start: 0.8372 (m-30) cc_final: 0.8166 (m-30) outliers start: 34 outliers final: 27 residues processed: 136 average time/residue: 0.0516 time to fit residues: 9.7027 Evaluate side-chains 129 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 48 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 68 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** 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 = 0.4104 r_free = 0.4104 target = 0.168890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.141831 restraints weight = 8851.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.144339 restraints weight = 6591.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.146011 restraints weight = 5370.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.147193 restraints weight = 4681.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.147679 restraints weight = 4277.655| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6355 Z= 0.133 Angle : 0.653 10.113 8608 Z= 0.318 Chirality : 0.041 0.231 942 Planarity : 0.004 0.032 1047 Dihedral : 4.399 22.436 904 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.98 % Allowed : 21.15 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.31), residues: 761 helix: 0.56 (0.28), residues: 352 sheet: -1.40 (0.56), residues: 86 loop : -1.90 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 38 TYR 0.027 0.001 TYR B 120 PHE 0.022 0.001 PHE A 377 TRP 0.017 0.001 TRP C 59 HIS 0.014 0.003 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 ( 6349) covalent geometry : angle 0.65041 / 0.32 ( 8596) SS BOND : bond 0.00350 / 0.17 ( 3) SS BOND : angle 2.19864 / 1.03 ( 6) hydrogen bonds : bond 0.02762 / 1.85 ( 265) hydrogen bonds : angle 4.06407 / 2.74 ( 756) Misc. bond : bond 0.00011 / 0.01 ( 1) link_BETA1-4 : bond 0.00566 / 0.30 ( 1) link_BETA1-4 : angle 1.19173 / 0.64 ( 3) link_NAG-ASN : bond 0.00313 / 0.16 ( 1) link_NAG-ASN : angle 1.16336 / 0.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 85 LYS cc_start: 0.5375 (mmpt) cc_final: 0.4849 (ptmt) REVERT: A 260 MET cc_start: 0.7875 (tmm) cc_final: 0.7652 (tmt) REVERT: A 271 TRP cc_start: 0.7062 (OUTLIER) cc_final: 0.6647 (t60) REVERT: A 464 ARG cc_start: 0.7303 (mmp80) cc_final: 0.5300 (tpp80) REVERT: A 548 PHE cc_start: 0.7201 (OUTLIER) cc_final: 0.6627 (t80) REVERT: B 47 ARG cc_start: 0.7076 (mtm180) cc_final: 0.6791 (mtm-85) REVERT: C 26 GLN cc_start: 0.7871 (mp10) cc_final: 0.7590 (mp10) REVERT: C 71 LEU cc_start: 0.8643 (tp) cc_final: 0.8281 (tt) REVERT: C 99 ILE cc_start: 0.7034 (pt) cc_final: 0.6343 (tt) outliers start: 32 outliers final: 28 residues processed: 134 average time/residue: 0.0584 time to fit residues: 10.4552 Evaluate side-chains 138 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 204 TRP Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** C 113 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 = 0.4152 r_free = 0.4152 target = 0.172109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.144560 restraints weight = 8945.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.146944 restraints weight = 6685.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.148349 restraints weight = 5494.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.149656 restraints weight = 4843.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.150270 restraints weight = 4412.930| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6355 Z= 0.150 Angle : 0.662 10.735 8608 Z= 0.323 Chirality : 0.042 0.231 942 Planarity : 0.004 0.032 1047 Dihedral : 4.416 22.384 904 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 4.98 % Allowed : 21.00 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.31), residues: 761 helix: 0.60 (0.28), residues: 352 sheet: -1.34 (0.55), residues: 86 loop : -1.89 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 38 TYR 0.025 0.002 TYR B 120 PHE 0.023 0.001 PHE A 377 TRP 0.014 0.001 TRP C 59 HIS 0.009 0.002 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 6349) covalent geometry : angle 0.66011 / 0.32 ( 8596) SS BOND : bond 0.00522 / 0.26 ( 3) SS BOND : angle 2.07702 / 1.00 ( 6) hydrogen bonds : bond 0.02788 / 1.87 ( 265) hydrogen bonds : angle 4.08462 / 2.75 ( 756) Misc. bond : bond 0.00007 / 0.00 ( 1) link_BETA1-4 : bond 0.00312 / 0.16 ( 1) link_BETA1-4 : angle 1.04768 / 0.56 ( 3) link_NAG-ASN : bond 0.00368 / 0.19 ( 1) link_NAG-ASN : angle 1.04953 / 0.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 85 LYS cc_start: 0.5431 (mmpt) cc_final: 0.4832 (ptmt) REVERT: A 103 TRP cc_start: 0.7514 (t60) cc_final: 0.7305 (t60) REVERT: A 260 MET cc_start: 0.7898 (tmm) cc_final: 0.7686 (tmt) REVERT: A 271 TRP cc_start: 0.7087 (OUTLIER) cc_final: 0.6670 (t60) REVERT: A 548 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.6732 (t80) REVERT: B 82 LYS cc_start: 0.8373 (mmtm) cc_final: 0.7317 (mtmt) outliers start: 32 outliers final: 28 residues processed: 133 average time/residue: 0.0611 time to fit residues: 11.1033 Evaluate side-chains 139 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 204 TRP Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 52 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** C 113 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 = 0.4151 r_free = 0.4151 target = 0.171653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.144450 restraints weight = 8911.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.146868 restraints weight = 6606.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.148558 restraints weight = 5381.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.149516 restraints weight = 4718.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.149930 restraints weight = 4331.880| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6355 Z= 0.145 Angle : 0.668 11.446 8608 Z= 0.324 Chirality : 0.042 0.238 942 Planarity : 0.004 0.032 1047 Dihedral : 4.400 22.242 904 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 5.44 % Allowed : 21.00 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.31), residues: 761 helix: 0.62 (0.28), residues: 352 sheet: -1.27 (0.53), residues: 98 loop : -1.90 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 38 TYR 0.025 0.002 TYR A 385 PHE 0.023 0.001 PHE A 377 TRP 0.012 0.001 TRP C 59 HIS 0.015 0.002 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 6349) covalent geometry : angle 0.66584 / 0.32 ( 8596) SS BOND : bond 0.00328 / 0.16 ( 3) SS BOND : angle 1.86447 / 0.92 ( 6) hydrogen bonds : bond 0.02783 / 1.86 ( 265) hydrogen bonds : angle 4.06964 / 2.73 ( 756) Misc. bond : bond 0.00006 / 0.00 ( 1) link_BETA1-4 : bond 0.00415 / 0.22 ( 1) link_BETA1-4 : angle 1.07327 / 0.57 ( 3) link_NAG-ASN : bond 0.00378 / 0.20 ( 1) link_NAG-ASN : angle 1.03014 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.5476 (mmpt) cc_final: 0.4853 (ptmt) REVERT: A 260 MET cc_start: 0.7903 (tmm) cc_final: 0.7686 (tmt) REVERT: A 271 TRP cc_start: 0.7110 (OUTLIER) cc_final: 0.6635 (t60) REVERT: A 548 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6801 (t80) REVERT: B 82 LYS cc_start: 0.8286 (mmtm) cc_final: 0.7271 (mtmt) outliers start: 35 outliers final: 32 residues processed: 135 average time/residue: 0.0564 time to fit residues: 10.5114 Evaluate side-chains 141 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 204 TRP Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 11 optimal weight: 0.0970 chunk 20 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 0.0470 chunk 67 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.174223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.147054 restraints weight = 8838.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.149857 restraints weight = 6503.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.150846 restraints weight = 5305.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.152764 restraints weight = 4692.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.153019 restraints weight = 4094.477| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6355 Z= 0.127 Angle : 0.680 12.170 8608 Z= 0.325 Chirality : 0.042 0.243 942 Planarity : 0.004 0.044 1047 Dihedral : 4.340 21.828 904 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.82 % Allowed : 21.62 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.31), residues: 761 helix: 0.69 (0.28), residues: 352 sheet: -1.27 (0.53), residues: 98 loop : -1.89 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 47 TYR 0.028 0.001 TYR B 120 PHE 0.023 0.001 PHE A 377 TRP 0.011 0.001 TRP C 59 HIS 0.011 0.002 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 6349) covalent geometry : angle 0.67841 / 0.32 ( 8596) SS BOND : bond 0.00353 / 0.18 ( 3) SS BOND : angle 1.78015 / 0.92 ( 6) hydrogen bonds : bond 0.02659 / 1.76 ( 265) hydrogen bonds : angle 3.98577 / 2.67 ( 756) Misc. bond : bond 0.00011 / 0.01 ( 1) link_BETA1-4 : bond 0.00449 / 0.24 ( 1) link_BETA1-4 : angle 1.08376 / 0.58 ( 3) link_NAG-ASN : bond 0.00398 / 0.21 ( 1) link_NAG-ASN : angle 1.07077 / 0.63 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.5469 (mmpt) cc_final: 0.4868 (ptmt) REVERT: A 260 MET cc_start: 0.7878 (tmm) cc_final: 0.7675 (tmt) REVERT: A 271 TRP cc_start: 0.7093 (OUTLIER) cc_final: 0.6674 (t60) REVERT: A 464 ARG cc_start: 0.7241 (mmp80) cc_final: 0.5285 (tpp-160) REVERT: A 548 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6779 (t80) REVERT: B 82 LYS cc_start: 0.8293 (mmtm) cc_final: 0.7314 (mtmt) outliers start: 31 outliers final: 26 residues processed: 134 average time/residue: 0.0563 time to fit residues: 10.2339 Evaluate side-chains 135 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 204 TRP Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 5 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 67 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 54 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.173597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.146398 restraints weight = 8745.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.148846 restraints weight = 6531.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.150267 restraints weight = 5361.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.151518 restraints weight = 4728.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.152156 restraints weight = 4336.045| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6355 Z= 0.125 Angle : 0.673 12.134 8608 Z= 0.323 Chirality : 0.042 0.247 942 Planarity : 0.004 0.034 1047 Dihedral : 4.297 21.395 904 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.35 % Allowed : 21.93 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.31), residues: 761 helix: 0.73 (0.28), residues: 352 sheet: -1.26 (0.55), residues: 87 loop : -1.91 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 47 TYR 0.027 0.001 TYR B 120 PHE 0.024 0.001 PHE A 586 TRP 0.011 0.001 TRP C 59 HIS 0.011 0.002 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.12 ( 6349) covalent geometry : angle 0.67111 / 0.32 ( 8596) SS BOND : bond 0.00306 / 0.15 ( 3) SS BOND : angle 1.87170 / 0.99 ( 6) hydrogen bonds : bond 0.02601 / 1.72 ( 265) hydrogen bonds : angle 3.96544 / 2.66 ( 756) Misc. bond : bond 0.00011 / 0.01 ( 1) link_BETA1-4 : bond 0.00398 / 0.21 ( 1) link_BETA1-4 : angle 1.04191 / 0.56 ( 3) link_NAG-ASN : bond 0.00412 / 0.22 ( 1) link_NAG-ASN : angle 1.02247 / 0.60 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 938.38 seconds wall clock time: 16 minutes 56.37 seconds (1016.37 seconds total)