Starting phenix.real_space_refine on Thu Jul 2 04:20:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lwd_23545/07_2026/7lwd_23545.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lwd_23545/07_2026/7lwd_23545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lwd_23545/07_2026/7lwd_23545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lwd_23545/07_2026/7lwd_23545.map" model { file = "/net/cci-nas-00/data/ceres_data/7lwd_23545/07_2026/7lwd_23545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lwd_23545/07_2026/7lwd_23545.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lwd_23545/07_2026/7lwd_23545.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lwd_23545/07_2026/7lwd_23545.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 129 atoms to isotropic. 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 4067 2.51 5 N 975 2.21 5 O 1087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 6163 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4319 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 517} Chain: "H" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 101 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3, 68 Unusual residues: {'IXX': 1, 'NAG': 1, 'YG7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 3, 68 Unusual residues: {'IXX': 1, 'NAG': 1, 'YG7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 37 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C08AYG7 A 802 " occ=0.50 ... (64 atoms not shown) pdb=" O02BYG7 A 802 " occ=0.50 Time building chain proxies: 1.39, per 1000 atoms: 0.23 Number of scatterers: 6163 At special positions: 0 Unit cell: (84.888, 73.872, 116.64, 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 1087 8.00 N 975 7.00 C 4067 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=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 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=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 383.8 milliseconds 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1402 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 7 sheets defined 53.2% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.729A pdb=" N PHE A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 112 removed outlier: 5.212A pdb=" N PHE A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix removed outlier: 3.737A pdb=" N GLN A 111 " --> pdb=" O TYR A 107 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 removed outlier: 3.745A pdb=" N MET A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 144 Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 159 through 189 removed outlier: 4.284A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.892A 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 238 through 242 Processing helix chain 'A' and resid 252 through 270 removed outlier: 3.855A pdb=" N CYS A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 262 " --> pdb=" O CYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 286 through 302 removed outlier: 3.762A pdb=" N VAL A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 removed outlier: 4.174A pdb=" N PHE A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 321 removed outlier: 3.756A pdb=" N LEU A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 321 " --> pdb=" O TRP A 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 316 through 321' Processing helix chain 'A' and resid 322 through 338 removed outlier: 4.327A pdb=" N TRP A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 349 Processing helix chain 'A' and resid 360 through 390 removed outlier: 3.512A pdb=" N THR A 364 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 408 Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'A' and resid 424 through 454 removed outlier: 3.844A pdb=" N GLY A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 485 through 494 removed outlier: 4.296A pdb=" N LEU A 491 " --> pdb=" O TYR A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 514 removed outlier: 3.723A pdb=" N LEU A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 530 removed outlier: 3.972A pdb=" N VAL A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 544 removed outlier: 4.483A pdb=" N VAL A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 557 removed outlier: 3.539A pdb=" N LEU A 550 " --> pdb=" O PRO A 546 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE A 556 " --> pdb=" O ILE A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.668A pdb=" N ILE A 576 " --> pdb=" O TYR A 572 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 600 removed outlier: 3.810A pdb=" N ILE A 599 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A 600 " --> pdb=" O ARG A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 611 removed outlier: 4.137A pdb=" N SER A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 51 removed outlier: 3.612A pdb=" N TYR H 50 " --> pdb=" O ARG H 47 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER H 51 " --> pdb=" O PHE H 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 47 through 51' Processing helix chain 'H' and resid 82 through 86 Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.621A pdb=" N SER H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 124 Processing sheet with id=AA1, first strand: chain 'H' and resid 29 through 30 removed outlier: 6.369A pdb=" N GLU H 29 " --> pdb=" O THR H 137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'H' and resid 38 through 42 removed outlier: 3.648A pdb=" N ILE H 39 " --> pdb=" O MET H 100 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR H 88 " --> pdb=" O GLN H 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 78 through 79 removed outlier: 6.914A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL H 112 " --> pdb=" O GLN H 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 24 through 27 removed outlier: 3.545A pdb=" N SER L 27 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR L 94 " --> pdb=" O SER L 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 30 through 31 Processing sheet with id=AA6, first strand: chain 'L' and resid 50 through 51 removed outlier: 3.885A pdb=" N ASN L 51 " --> pdb=" O ILE L 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 77 through 78 removed outlier: 6.536A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N TYR L 73 " --> pdb=" O LEU L 57 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU L 57 " --> pdb=" O TYR L 73 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 926 1.25 - 1.39: 1706 1.39 - 1.53: 3326 1.53 - 1.67: 346 1.67 - 1.81: 49 Bond restraints: 6353 Sorted by residual: bond pdb=" C23AYG7 A 802 " pdb=" O01AYG7 A 802 " ideal model delta sigma weight residual 1.351 1.588 -0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C23BYG7 A 802 " pdb=" O01BYG7 A 802 " ideal model delta sigma weight residual 1.351 1.587 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C21BYG7 A 802 " pdb=" C26BYG7 A 802 " ideal model delta sigma weight residual 1.432 1.224 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C21AYG7 A 802 " pdb=" C26AYG7 A 802 " ideal model delta sigma weight residual 1.432 1.226 0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C26BYG7 A 802 " pdb=" C29BYG7 A 802 " ideal model delta sigma weight residual 1.354 1.171 0.183 2.00e-02 2.50e+03 8.38e+01 ... (remaining 6348 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.98: 8569 3.98 - 7.95: 55 7.95 - 11.93: 23 11.93 - 15.91: 2 15.91 - 19.89: 4 Bond angle restraints: 8653 Sorted by residual: angle pdb=" C26BYG7 A 802 " pdb=" C29BYG7 A 802 " pdb=" O01BYG7 A 802 " ideal model delta sigma weight residual 111.69 131.58 -19.89 3.00e+00 1.11e-01 4.39e+01 angle pdb=" C26AYG7 A 802 " pdb=" C29AYG7 A 802 " pdb=" O01AYG7 A 802 " ideal model delta sigma weight residual 111.69 131.49 -19.80 3.00e+00 1.11e-01 4.36e+01 angle pdb=" C23BYG7 A 802 " pdb=" O01BYG7 A 802 " pdb=" C29BYG7 A 802 " ideal model delta sigma weight residual 106.53 88.85 17.68 3.00e+00 1.11e-01 3.47e+01 angle pdb=" C23AYG7 A 802 " pdb=" O01AYG7 A 802 " pdb=" C29AYG7 A 802 " ideal model delta sigma weight residual 106.53 88.98 17.55 3.00e+00 1.11e-01 3.42e+01 angle pdb=" C GLU L 47 " pdb=" N SER L 48 " pdb=" CA SER L 48 " ideal model delta sigma weight residual 121.70 131.48 -9.78 1.80e+00 3.09e-01 2.95e+01 ... (remaining 8648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.23: 3520 33.23 - 66.46: 67 66.46 - 99.69: 6 99.69 - 132.92: 2 132.92 - 166.15: 2 Dihedral angle restraints: 3597 sinusoidal: 1387 harmonic: 2210 Sorted by residual: dihedral pdb=" CB CYS A 200 " pdb=" SG CYS A 200 " pdb=" SG CYS A 209 " pdb=" CB CYS A 209 " ideal model delta sinusoidal sigma weight residual 93.00 142.29 -49.29 1 1.00e+01 1.00e-02 3.34e+01 dihedral pdb=" C13BYG7 A 802 " pdb=" C14BYG7 A 802 " pdb=" C16BYG7 A 802 " pdb=" C17BYG7 A 802 " ideal model delta sinusoidal sigma weight residual -62.61 103.54 -166.15 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CA GLU L 47 " pdb=" C GLU L 47 " pdb=" N SER L 48 " pdb=" CA SER L 48 " ideal model delta harmonic sigma weight residual 0.00 22.50 -22.50 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 3594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 546 0.031 - 0.061: 283 0.061 - 0.092: 78 0.092 - 0.122: 30 0.122 - 0.153: 1 Chirality restraints: 938 Sorted by residual: chirality pdb=" CA PHE A 380 " pdb=" N PHE A 380 " pdb=" C PHE A 380 " pdb=" CB PHE A 380 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA ILE L 41 " pdb=" N ILE L 41 " pdb=" C ILE L 41 " pdb=" CB ILE L 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA TRP A 103 " pdb=" N TRP A 103 " pdb=" C TRP A 103 " pdb=" CB TRP A 103 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 935 not shown) Planarity restraints: 1060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 465 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.59e+00 pdb=" C PHE A 465 " -0.048 2.00e-02 2.50e+03 pdb=" O PHE A 465 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 466 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 103 " 0.014 2.00e-02 2.50e+03 1.14e-02 3.25e+00 pdb=" CG TRP A 103 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 103 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 103 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 103 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 103 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 103 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 103 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 103 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 103 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 287 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A 288 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " 0.020 5.00e-02 4.00e+02 ... (remaining 1057 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 50 2.60 - 3.17: 5503 3.17 - 3.75: 9620 3.75 - 4.32: 13443 4.32 - 4.90: 22109 Nonbonded interactions: 50725 Sorted by model distance: nonbonded pdb=" ND2 ASN A 208 " pdb=" C1 NAG A 803 " model vdw 2.024 3.550 nonbonded pdb=" OG SER A 199 " pdb=" OD2 ASP H 74 " model vdw 2.209 3.040 nonbonded pdb=" ND2 ASN A 208 " pdb=" C2 NAG A 803 " model vdw 2.225 3.550 nonbonded pdb=" OH TYR A 185 " pdb=" OE1 GLN A 254 " model vdw 2.319 3.040 nonbonded pdb=" NE2 GLN H 25 " pdb=" OG1 THR H 134 " model vdw 2.326 3.120 ... (remaining 50720 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=0.50 max=1.00 mean=0.99 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: 5.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.440 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.237 6356 Z= 0.527 Angle : 0.972 19.885 8659 Z= 0.406 Chirality : 0.039 0.153 938 Planarity : 0.004 0.036 1060 Dihedral : 14.882 166.146 2186 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % 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: -4.15 (0.25), residues: 763 helix: -1.97 (0.23), residues: 353 sheet: -4.04 (0.39), residues: 93 loop : -3.15 (0.30), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 69 TYR 0.014 0.001 TYR A 186 PHE 0.024 0.001 PHE A 287 TRP 0.031 0.001 TRP A 103 HIS 0.001 0.000 HIS A 456 Details of bonding type rmsd/Z covalent geometry : bond 0.01059 / 0.53 ( 6353) covalent geometry : angle 0.97237 / 0.41 ( 8653) SS BOND : bond 0.00570 / 0.36 ( 3) SS BOND : angle 0.36361 / 0.17 ( 6) hydrogen bonds : bond 0.15745 / 9.98 ( 265) hydrogen bonds : angle 6.88862 / 4.71 ( 759) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7891 (tpp) cc_final: 0.7537 (tpp) REVERT: A 201 LYS cc_start: 0.6290 (mmtt) cc_final: 0.5828 (tttm) REVERT: A 595 TYR cc_start: 0.7996 (t80) cc_final: 0.7562 (t80) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.0809 time to fit residues: 14.1154 Evaluate side-chains 105 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN A 177 ASN A 368 ASN A 416 ASN L 62 GLN L 78 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.181370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.160397 restraints weight = 7768.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.164289 restraints weight = 4838.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.166902 restraints weight = 3473.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.168673 restraints weight = 2735.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.169891 restraints weight = 2286.862| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3955 r_free = 0.3955 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3955 r_free = 0.3955 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6356 Z= 0.125 Angle : 0.563 9.535 8659 Z= 0.290 Chirality : 0.041 0.150 938 Planarity : 0.004 0.047 1060 Dihedral : 10.793 173.542 869 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.09 % Allowed : 13.18 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.29), residues: 763 helix: -1.00 (0.26), residues: 358 sheet: -3.39 (0.47), residues: 86 loop : -2.52 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 104 TYR 0.016 0.001 TYR A 312 PHE 0.019 0.001 PHE A 586 TRP 0.022 0.001 TRP A 103 HIS 0.001 0.000 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 6353) covalent geometry : angle 0.56220 / 0.29 ( 8653) SS BOND : bond 0.00307 / 0.16 ( 3) SS BOND : angle 1.22146 / 0.59 ( 6) hydrogen bonds : bond 0.03421 / 2.19 ( 265) hydrogen bonds : angle 5.21964 / 3.60 ( 759) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.8237 (t80) cc_final: 0.7996 (t80) REVERT: A 201 LYS cc_start: 0.6500 (mmtt) cc_final: 0.6116 (mmtp) REVERT: A 386 MET cc_start: 0.7637 (mtp) cc_final: 0.7310 (mtp) REVERT: A 392 GLU cc_start: 0.7055 (tm-30) cc_final: 0.6799 (tm-30) REVERT: A 399 LYS cc_start: 0.5714 (mmtt) cc_final: 0.5064 (mptt) REVERT: A 595 TYR cc_start: 0.7962 (t80) cc_final: 0.7609 (t80) outliers start: 7 outliers final: 3 residues processed: 116 average time/residue: 0.0771 time to fit residues: 12.1047 Evaluate side-chains 104 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 27 optimal weight: 0.2980 chunk 72 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.179089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.157961 restraints weight = 7654.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.161860 restraints weight = 4824.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.164216 restraints weight = 3468.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.166103 restraints weight = 2765.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.167112 restraints weight = 2322.408| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3925 r_free = 0.3925 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3925 r_free = 0.3925 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6356 Z= 0.140 Angle : 0.566 9.489 8659 Z= 0.292 Chirality : 0.041 0.158 938 Planarity : 0.004 0.038 1060 Dihedral : 10.671 169.066 869 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.02 % Allowed : 16.43 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.30), residues: 763 helix: -0.60 (0.27), residues: 357 sheet: -3.05 (0.47), residues: 90 loop : -2.23 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 117 TYR 0.017 0.001 TYR A 312 PHE 0.017 0.002 PHE A 380 TRP 0.021 0.001 TRP A 103 HIS 0.001 0.000 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 6353) covalent geometry : angle 0.56585 / 0.29 ( 8653) SS BOND : bond 0.00257 / 0.16 ( 3) SS BOND : angle 1.06092 / 0.51 ( 6) hydrogen bonds : bond 0.03315 / 2.12 ( 265) hydrogen bonds : angle 4.97799 / 3.48 ( 759) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.6912 (mmtt) cc_final: 0.6357 (mmtp) REVERT: A 386 MET cc_start: 0.7622 (mtp) cc_final: 0.7399 (mtp) REVERT: A 399 LYS cc_start: 0.5588 (mmtt) cc_final: 0.4905 (mptt) REVERT: A 595 TYR cc_start: 0.7954 (t80) cc_final: 0.7724 (t80) outliers start: 13 outliers final: 9 residues processed: 112 average time/residue: 0.0690 time to fit residues: 10.7109 Evaluate side-chains 108 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 118 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN A 456 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.180344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.154766 restraints weight = 14558.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.159759 restraints weight = 8017.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.161249 restraints weight = 5326.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.165629 restraints weight = 3915.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.167274 restraints weight = 2747.105| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3884 r_free = 0.3884 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3884 r_free = 0.3884 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6356 Z= 0.173 Angle : 0.582 9.849 8659 Z= 0.300 Chirality : 0.042 0.162 938 Planarity : 0.004 0.034 1060 Dihedral : 10.512 163.606 869 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.95 % Allowed : 18.29 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.30), residues: 763 helix: -0.52 (0.27), residues: 360 sheet: -3.12 (0.49), residues: 77 loop : -2.13 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 47 TYR 0.023 0.002 TYR H 79 PHE 0.018 0.002 PHE A 380 TRP 0.040 0.001 TRP A 103 HIS 0.008 0.001 HIS A 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 6353) covalent geometry : angle 0.58172 / 0.30 ( 8653) SS BOND : bond 0.00295 / 0.18 ( 3) SS BOND : angle 0.82807 / 0.39 ( 6) hydrogen bonds : bond 0.03417 / 2.17 ( 265) hydrogen bonds : angle 4.97570 / 3.48 ( 759) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 145 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7470 (t0) REVERT: A 201 LYS cc_start: 0.7167 (mmtt) cc_final: 0.6368 (tttm) REVERT: A 386 MET cc_start: 0.7661 (mtp) cc_final: 0.7396 (mtp) REVERT: A 392 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6895 (tm-30) REVERT: A 547 LEU cc_start: 0.8807 (tt) cc_final: 0.8596 (tp) REVERT: A 595 TYR cc_start: 0.8043 (t80) cc_final: 0.7750 (t80) REVERT: A 605 LYS cc_start: 0.8449 (tppt) cc_final: 0.8199 (tppt) outliers start: 19 outliers final: 10 residues processed: 117 average time/residue: 0.0597 time to fit residues: 9.7911 Evaluate side-chains 112 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 32 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 456 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.178346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.156236 restraints weight = 8755.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.160428 restraints weight = 5237.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.163223 restraints weight = 3674.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.165010 restraints weight = 2850.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.166431 restraints weight = 2382.993| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3923 r_free = 0.3923 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3923 r_free = 0.3923 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6356 Z= 0.141 Angle : 0.565 9.758 8659 Z= 0.293 Chirality : 0.041 0.225 938 Planarity : 0.004 0.037 1060 Dihedral : 10.319 162.080 869 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.26 % Allowed : 19.84 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.30), residues: 763 helix: -0.36 (0.27), residues: 358 sheet: -2.95 (0.49), residues: 77 loop : -1.95 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 47 TYR 0.016 0.001 TYR H 79 PHE 0.019 0.001 PHE A 380 TRP 0.028 0.001 TRP A 103 HIS 0.008 0.001 HIS A 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 6353) covalent geometry : angle 0.56539 / 0.29 ( 8653) SS BOND : bond 0.00180 / 0.11 ( 3) SS BOND : angle 0.68359 / 0.31 ( 6) hydrogen bonds : bond 0.03255 / 2.07 ( 265) hydrogen bonds : angle 4.86017 / 3.40 ( 759) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7154 (mmtt) cc_final: 0.6547 (mmtp) REVERT: A 547 LEU cc_start: 0.8794 (tt) cc_final: 0.8567 (tp) REVERT: A 595 TYR cc_start: 0.7986 (t80) cc_final: 0.7666 (t80) REVERT: A 605 LYS cc_start: 0.8369 (tppt) cc_final: 0.8160 (tppt) REVERT: H 37 VAL cc_start: 0.8967 (p) cc_final: 0.8674 (m) REVERT: H 50 TYR cc_start: 0.8063 (m-80) cc_final: 0.7804 (m-80) outliers start: 21 outliers final: 13 residues processed: 116 average time/residue: 0.0658 time to fit residues: 10.7372 Evaluate side-chains 113 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 118 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 7 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 69 optimal weight: 0.0970 chunk 13 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 456 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.172724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.150622 restraints weight = 8012.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.154273 restraints weight = 5088.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.156946 restraints weight = 3758.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.158707 restraints weight = 2994.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.159647 restraints weight = 2535.111| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3849 r_free = 0.3849 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3849 r_free = 0.3849 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6356 Z= 0.126 Angle : 0.551 9.643 8659 Z= 0.286 Chirality : 0.040 0.167 938 Planarity : 0.004 0.034 1060 Dihedral : 10.264 161.926 869 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.26 % Allowed : 20.78 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % 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: -1.72 (0.30), residues: 763 helix: -0.18 (0.28), residues: 352 sheet: -2.78 (0.50), residues: 76 loop : -1.72 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 47 TYR 0.017 0.001 TYR A 134 PHE 0.019 0.001 PHE A 380 TRP 0.024 0.001 TRP A 103 HIS 0.008 0.001 HIS A 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 6353) covalent geometry : angle 0.55122 / 0.29 ( 8653) SS BOND : bond 0.00193 / 0.12 ( 3) SS BOND : angle 0.63822 / 0.30 ( 6) hydrogen bonds : bond 0.03178 / 2.03 ( 265) hydrogen bonds : angle 4.80141 / 3.36 ( 759) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7135 (mmtt) cc_final: 0.6504 (mmtp) REVERT: A 544 ILE cc_start: 0.9171 (mm) cc_final: 0.8896 (mt) REVERT: A 547 LEU cc_start: 0.8819 (tt) cc_final: 0.8598 (tp) REVERT: A 595 TYR cc_start: 0.8008 (t80) cc_final: 0.7681 (t80) REVERT: A 605 LYS cc_start: 0.8422 (tppt) cc_final: 0.8197 (tppt) REVERT: H 37 VAL cc_start: 0.8950 (p) cc_final: 0.8655 (m) outliers start: 21 outliers final: 17 residues processed: 112 average time/residue: 0.0578 time to fit residues: 9.3653 Evaluate side-chains 114 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 ASN A 456 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.169656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.144664 restraints weight = 11459.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.150075 restraints weight = 6893.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.153054 restraints weight = 4493.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.156748 restraints weight = 3282.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.156975 restraints weight = 2557.357| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6356 Z= 0.163 Angle : 0.582 9.812 8659 Z= 0.302 Chirality : 0.042 0.276 938 Planarity : 0.004 0.033 1060 Dihedral : 10.226 158.870 869 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.41 % Allowed : 21.40 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % 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: -1.77 (0.30), residues: 763 helix: -0.25 (0.27), residues: 353 sheet: -2.90 (0.50), residues: 70 loop : -1.72 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 47 TYR 0.018 0.002 TYR A 134 PHE 0.021 0.001 PHE A 380 TRP 0.021 0.001 TRP A 103 HIS 0.008 0.001 HIS A 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 6353) covalent geometry : angle 0.58230 / 0.30 ( 8653) SS BOND : bond 0.00238 / 0.15 ( 3) SS BOND : angle 0.68757 / 0.31 ( 6) hydrogen bonds : bond 0.03347 / 2.13 ( 265) hydrogen bonds : angle 4.83159 / 3.38 ( 759) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8424 (t80) cc_final: 0.8061 (t80) REVERT: A 201 LYS cc_start: 0.7291 (mmtt) cc_final: 0.6609 (mmtp) REVERT: A 547 LEU cc_start: 0.8819 (tt) cc_final: 0.8598 (tp) REVERT: A 595 TYR cc_start: 0.8027 (t80) cc_final: 0.7759 (t80) REVERT: A 605 LYS cc_start: 0.8465 (tppt) cc_final: 0.8224 (tppt) REVERT: A 610 LYS cc_start: 0.9139 (tptp) cc_final: 0.8935 (tptt) REVERT: H 37 VAL cc_start: 0.8977 (p) cc_final: 0.8692 (m) outliers start: 22 outliers final: 15 residues processed: 114 average time/residue: 0.0585 time to fit residues: 9.4963 Evaluate side-chains 119 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 12 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 0.0270 chunk 42 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.173495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.149609 restraints weight = 10287.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.153914 restraints weight = 5943.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.157016 restraints weight = 4148.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.159064 restraints weight = 3199.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.160348 restraints weight = 2655.599| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6356 Z= 0.128 Angle : 0.569 10.436 8659 Z= 0.296 Chirality : 0.041 0.237 938 Planarity : 0.004 0.033 1060 Dihedral : 10.192 159.116 869 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.79 % Allowed : 22.95 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % 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: -1.64 (0.30), residues: 763 helix: -0.17 (0.28), residues: 356 sheet: -2.77 (0.50), residues: 70 loop : -1.64 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 47 TYR 0.027 0.001 TYR H 79 PHE 0.019 0.001 PHE A 380 TRP 0.020 0.001 TRP A 103 HIS 0.002 0.000 HIS L 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 6353) covalent geometry : angle 0.56860 / 0.30 ( 8653) SS BOND : bond 0.00197 / 0.12 ( 3) SS BOND : angle 0.52692 / 0.25 ( 6) hydrogen bonds : bond 0.03174 / 2.03 ( 265) hydrogen bonds : angle 4.73906 / 3.31 ( 759) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7254 (mmtt) cc_final: 0.6578 (mmtp) REVERT: A 386 MET cc_start: 0.7471 (mtp) cc_final: 0.7219 (mtp) REVERT: A 547 LEU cc_start: 0.8809 (tt) cc_final: 0.8585 (tp) REVERT: A 595 TYR cc_start: 0.7978 (t80) cc_final: 0.7715 (t80) REVERT: A 605 LYS cc_start: 0.8441 (tppt) cc_final: 0.8224 (tppt) REVERT: H 37 VAL cc_start: 0.8954 (p) cc_final: 0.8666 (m) REVERT: L 66 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7288 (mt0) outliers start: 18 outliers final: 15 residues processed: 111 average time/residue: 0.0651 time to fit residues: 10.4232 Evaluate side-chains 111 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 53 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 73 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.174257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.152396 restraints weight = 7925.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.156195 restraints weight = 5056.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.158781 restraints weight = 3682.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.160397 restraints weight = 2932.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.161700 restraints weight = 2501.339| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3868 r_free = 0.3868 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3868 r_free = 0.3868 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6356 Z= 0.127 Angle : 0.564 9.621 8659 Z= 0.294 Chirality : 0.041 0.211 938 Planarity : 0.004 0.032 1060 Dihedral : 10.167 158.995 869 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.48 % Allowed : 22.64 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % 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: -1.53 (0.30), residues: 763 helix: -0.10 (0.28), residues: 356 sheet: -2.57 (0.50), residues: 70 loop : -1.60 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 538 TYR 0.025 0.002 TYR H 79 PHE 0.019 0.001 PHE A 380 TRP 0.020 0.001 TRP A 103 HIS 0.002 0.000 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 6353) covalent geometry : angle 0.56390 / 0.29 ( 8653) SS BOND : bond 0.00364 / 0.23 ( 3) SS BOND : angle 0.58507 / 0.27 ( 6) hydrogen bonds : bond 0.03151 / 2.02 ( 265) hydrogen bonds : angle 4.69417 / 3.29 ( 759) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7249 (mmtt) cc_final: 0.6685 (mmmt) REVERT: A 393 ASP cc_start: 0.7291 (m-30) cc_final: 0.6994 (p0) REVERT: A 544 ILE cc_start: 0.9169 (mm) cc_final: 0.8877 (mt) REVERT: A 547 LEU cc_start: 0.8790 (tt) cc_final: 0.8563 (tp) REVERT: A 595 TYR cc_start: 0.7966 (t80) cc_final: 0.7693 (t80) REVERT: H 37 VAL cc_start: 0.8942 (p) cc_final: 0.8652 (m) REVERT: L 66 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7292 (mt0) outliers start: 16 outliers final: 14 residues processed: 109 average time/residue: 0.0617 time to fit residues: 9.8472 Evaluate side-chains 111 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 28 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 0.1980 chunk 70 optimal weight: 0.0870 chunk 34 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.175772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.153381 restraints weight = 8465.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.157466 restraints weight = 5240.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.160077 restraints weight = 3755.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.161779 restraints weight = 2987.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.163174 restraints weight = 2530.143| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3883 r_free = 0.3883 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3883 r_free = 0.3883 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6356 Z= 0.116 Angle : 0.557 9.569 8659 Z= 0.291 Chirality : 0.040 0.191 938 Planarity : 0.004 0.032 1060 Dihedral : 10.113 159.872 869 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.64 % Allowed : 22.64 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % 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: -1.46 (0.30), residues: 763 helix: -0.02 (0.28), residues: 357 sheet: -2.46 (0.49), residues: 73 loop : -1.61 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 523 TYR 0.024 0.001 TYR H 79 PHE 0.018 0.001 PHE A 380 TRP 0.020 0.001 TRP A 103 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 6353) covalent geometry : angle 0.55729 / 0.29 ( 8653) SS BOND : bond 0.00193 / 0.12 ( 3) SS BOND : angle 0.58439 / 0.27 ( 6) hydrogen bonds : bond 0.03050 / 1.96 ( 265) hydrogen bonds : angle 4.60020 / 3.22 ( 759) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7147 (mmtt) cc_final: 0.6610 (mmmt) REVERT: A 544 ILE cc_start: 0.9144 (mm) cc_final: 0.8884 (mt) REVERT: A 595 TYR cc_start: 0.7913 (t80) cc_final: 0.7622 (t80) REVERT: H 37 VAL cc_start: 0.8933 (p) cc_final: 0.8643 (m) REVERT: L 66 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7267 (mt0) outliers start: 17 outliers final: 14 residues processed: 110 average time/residue: 0.0678 time to fit residues: 10.6132 Evaluate side-chains 110 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.0980 chunk 50 optimal weight: 0.1980 chunk 57 optimal weight: 0.7980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.174842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.150698 restraints weight = 10281.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155155 restraints weight = 6018.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.158245 restraints weight = 4171.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.160296 restraints weight = 3213.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.161439 restraints weight = 2665.952| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3862 r_free = 0.3862 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3862 r_free = 0.3862 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6356 Z= 0.132 Angle : 0.598 11.767 8659 Z= 0.306 Chirality : 0.041 0.258 938 Planarity : 0.004 0.032 1060 Dihedral : 10.052 159.237 869 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.79 % Allowed : 23.10 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % 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: -1.50 (0.30), residues: 763 helix: -0.06 (0.28), residues: 358 sheet: -2.44 (0.49), residues: 73 loop : -1.63 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 117 TYR 0.032 0.002 TYR H 50 PHE 0.032 0.002 PHE A 440 TRP 0.020 0.001 TRP A 103 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 6353) covalent geometry : angle 0.59787 / 0.31 ( 8653) SS BOND : bond 0.00138 / 0.08 ( 3) SS BOND : angle 0.49425 / 0.24 ( 6) hydrogen bonds : bond 0.03092 / 1.99 ( 265) hydrogen bonds : angle 4.62157 / 3.24 ( 759) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1354.86 seconds wall clock time: 24 minutes 15.08 seconds (1455.08 seconds total)