Starting phenix.real_space_refine on Fri Aug 22 14:39:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jty_36656/08_2025/8jty_36656.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jty_36656/08_2025/8jty_36656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jty_36656/08_2025/8jty_36656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jty_36656/08_2025/8jty_36656.map" model { file = "/net/cci-nas-00/data/ceres_data/8jty_36656/08_2025/8jty_36656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jty_36656/08_2025/8jty_36656.cif" } resolution = 3.26 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= -0.004 sd= 0.184 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 2785 2.51 5 N 703 2.21 5 O 752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4274 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3366 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 908 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 1.31, per 1000 atoms: 0.31 Number of scatterers: 4274 At special positions: 0 Unit cell: (57.62, 84.28, 126.42, 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 752 8.00 N 703 7.00 C 2785 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " 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: 0.42 Conformation dependent library (CDL) restraints added in 190.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1024 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 5 sheets defined 59.2% alpha, 11.1% 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 21 through 33 Processing helix chain 'A' and resid 37 through 41 Processing helix chain 'A' and resid 54 through 62 removed outlier: 3.568A pdb=" N LEU A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 74 removed outlier: 4.253A pdb=" N ASN A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 141 through 147 removed outlier: 4.768A pdb=" N TRP A 146 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 170 removed outlier: 4.250A pdb=" N GLN A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 163 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 165 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLY A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N TYR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 195 removed outlier: 4.106A pdb=" N LEU A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 228 removed outlier: 3.751A pdb=" N MET A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A 221 " --> pdb=" O TRP A 217 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 232 through 258 removed outlier: 3.580A pdb=" N LEU A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 277 Proline residue: A 271 - end of helix removed outlier: 3.523A pdb=" N LEU A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 338 removed outlier: 3.988A pdb=" N LEU A 337 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE A 338 " --> pdb=" O ALA A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 369 removed outlier: 4.648A pdb=" N ARG A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A 365 " --> pdb=" O TYR A 361 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 366 " --> pdb=" O GLN A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.771A pdb=" N ALA A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 removed outlier: 3.564A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N CYS A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 457 removed outlier: 3.605A pdb=" N ALA A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 447 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 487 removed outlier: 4.456A pdb=" N MET A 467 " --> pdb=" O ASN A 463 " (cutoff:3.500A) Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 494 through 507 removed outlier: 3.790A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 499 " --> pdb=" O PRO A 495 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 507 " --> pdb=" O GLY A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.701A pdb=" N TYR B 31 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 27 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.860A pdb=" N ARG A 90 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY A 119 " --> pdb=" O ARG A 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.850A pdb=" N GLN B 5 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 57 through 59 removed outlier: 3.821A pdb=" N ASN B 58 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR B 50 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 51 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET B 34 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 96 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N CYS B 95 " --> pdb=" O TRP B 112 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP B 112 " --> pdb=" O CYS B 95 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 97 " --> pdb=" O ILE B 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 59 removed outlier: 3.821A pdb=" N ASN B 58 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR B 50 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 51 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET B 34 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 96 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 91 " --> pdb=" O VAL B 118 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 615 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.61 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1342 1.34 - 1.46: 1033 1.46 - 1.58: 1953 1.58 - 1.70: 0 1.70 - 1.81: 51 Bond restraints: 4379 Sorted by residual: bond pdb=" CD2 TRP A 125 " pdb=" CE2 TRP A 125 " ideal model delta sigma weight residual 1.409 1.464 -0.055 1.70e-02 3.46e+03 1.04e+01 bond pdb=" CA TRP A 64 " pdb=" C TRP A 64 " ideal model delta sigma weight residual 1.524 1.497 0.026 1.27e-02 6.20e+03 4.34e+00 bond pdb=" CG TRP A 125 " pdb=" CD2 TRP A 125 " ideal model delta sigma weight residual 1.433 1.469 -0.036 1.80e-02 3.09e+03 3.93e+00 bond pdb=" NE1 TRP A 125 " pdb=" CE2 TRP A 125 " ideal model delta sigma weight residual 1.370 1.350 0.020 1.10e-02 8.26e+03 3.22e+00 bond pdb=" CA TRP A 125 " pdb=" C TRP A 125 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.34e-02 5.57e+03 2.97e+00 ... (remaining 4374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 5863 1.69 - 3.38: 85 3.38 - 5.07: 17 5.07 - 6.76: 3 6.76 - 8.45: 2 Bond angle restraints: 5970 Sorted by residual: angle pdb=" C SER A 65 " pdb=" N PRO A 66 " pdb=" CA PRO A 66 " ideal model delta sigma weight residual 119.32 114.35 4.97 1.14e+00 7.69e-01 1.90e+01 angle pdb=" N ASP A 398 " pdb=" CA ASP A 398 " pdb=" CB ASP A 398 " ideal model delta sigma weight residual 114.17 109.80 4.37 1.14e+00 7.69e-01 1.47e+01 angle pdb=" N ALA A 143 " pdb=" CA ALA A 143 " pdb=" C ALA A 143 " ideal model delta sigma weight residual 112.87 117.41 -4.54 1.20e+00 6.94e-01 1.43e+01 angle pdb=" N LEU A 70 " pdb=" CA LEU A 70 " pdb=" C LEU A 70 " ideal model delta sigma weight residual 110.97 106.92 4.05 1.09e+00 8.42e-01 1.38e+01 angle pdb=" N TRP A 125 " pdb=" CA TRP A 125 " pdb=" C TRP A 125 " ideal model delta sigma weight residual 110.80 117.12 -6.32 2.13e+00 2.20e-01 8.80e+00 ... (remaining 5965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 2203 17.80 - 35.59: 243 35.59 - 53.39: 81 53.39 - 71.18: 5 71.18 - 88.98: 7 Dihedral angle restraints: 2539 sinusoidal: 929 harmonic: 1610 Sorted by residual: dihedral pdb=" CB CYS A 62 " pdb=" SG CYS A 62 " pdb=" SG CYS A 102 " pdb=" CB CYS A 102 " ideal model delta sinusoidal sigma weight residual -86.00 -127.01 41.01 1 1.00e+01 1.00e-02 2.36e+01 dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual -86.00 -117.68 31.68 1 1.00e+01 1.00e-02 1.43e+01 dihedral pdb=" CA ASN A 453 " pdb=" CB ASN A 453 " pdb=" CG ASN A 453 " pdb=" OD1 ASN A 453 " ideal model delta sinusoidal sigma weight residual 120.00 -166.22 -73.78 2 2.00e+01 2.50e-03 1.11e+01 ... (remaining 2536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 455 0.033 - 0.066: 172 0.066 - 0.100: 36 0.100 - 0.133: 22 0.133 - 0.166: 3 Chirality restraints: 688 Sorted by residual: chirality pdb=" CA TRP A 125 " pdb=" N TRP A 125 " pdb=" C TRP A 125 " pdb=" CB TRP A 125 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CA ALA A 143 " pdb=" N ALA A 143 " pdb=" C ALA A 143 " pdb=" CB ALA A 143 " both_signs ideal model delta sigma weight residual False 2.48 2.34 0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CB THR A 45 " pdb=" CA THR A 45 " pdb=" OG1 THR A 45 " pdb=" CG2 THR A 45 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 685 not shown) Planarity restraints: 751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO A 271 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 398 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C ASP A 398 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP A 398 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG A 399 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 37 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.78e+00 pdb=" C VAL A 37 " -0.023 2.00e-02 2.50e+03 pdb=" O VAL A 37 " 0.008 2.00e-02 2.50e+03 pdb=" N GLY A 38 " 0.008 2.00e-02 2.50e+03 ... (remaining 748 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 563 2.75 - 3.29: 3887 3.29 - 3.83: 6527 3.83 - 4.36: 6841 4.36 - 4.90: 12819 Nonbonded interactions: 30637 Sorted by model distance: nonbonded pdb=" O GLY A 476 " pdb=" OG1 THR A 480 " model vdw 2.217 3.040 nonbonded pdb=" OG SER B 7 " pdb=" OG SER B 21 " model vdw 2.300 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O TRP B 106 " model vdw 2.338 3.040 nonbonded pdb=" OG SER A 52 " pdb=" NH2 ARG A 90 " model vdw 2.351 3.120 nonbonded pdb=" N GLU B 32 " pdb=" OE1 GLU B 32 " model vdw 2.361 3.120 ... (remaining 30632 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.240 Find NCS groups from input model: 0.010 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 8.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4383 Z= 0.153 Angle : 0.547 8.455 5978 Z= 0.301 Chirality : 0.040 0.166 688 Planarity : 0.004 0.057 751 Dihedral : 16.261 88.975 1503 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 23.41 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.36), residues: 560 helix: 0.66 (0.31), residues: 305 sheet: 0.52 (0.78), residues: 53 loop : -2.26 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 45 TYR 0.007 0.001 TYR A 91 PHE 0.014 0.001 PHE A 275 TRP 0.011 0.001 TRP A 261 HIS 0.001 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4379) covalent geometry : angle 0.54729 ( 5970) SS BOND : bond 0.00141 ( 4) SS BOND : angle 0.38073 ( 8) hydrogen bonds : bond 0.17740 ( 213) hydrogen bonds : angle 5.33046 ( 615) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.159 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0859 time to fit residues: 5.3848 Evaluate side-chains 48 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.0170 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 0.0060 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.3034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.203908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.150573 restraints weight = 4640.873| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 3.46 r_work: 0.3535 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4383 Z= 0.106 Angle : 0.493 8.177 5978 Z= 0.253 Chirality : 0.038 0.136 688 Planarity : 0.004 0.055 751 Dihedral : 3.633 13.644 610 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.05 % Allowed : 21.36 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.36), residues: 560 helix: 0.93 (0.31), residues: 314 sheet: 0.61 (0.77), residues: 53 loop : -2.31 (0.38), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 402 TYR 0.006 0.001 TYR A 91 PHE 0.016 0.001 PHE A 275 TRP 0.010 0.001 TRP A 261 HIS 0.001 0.000 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 4379) covalent geometry : angle 0.49240 ( 5970) SS BOND : bond 0.00079 ( 4) SS BOND : angle 0.66634 ( 8) hydrogen bonds : bond 0.04281 ( 213) hydrogen bonds : angle 3.77811 ( 615) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.151 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 57 average time/residue: 0.0692 time to fit residues: 5.1672 Evaluate side-chains 54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 8 optimal weight: 0.0030 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.201489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.148390 restraints weight = 4616.009| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 3.01 r_work: 0.3545 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4383 Z= 0.113 Angle : 0.504 7.666 5978 Z= 0.257 Chirality : 0.039 0.162 688 Planarity : 0.004 0.055 751 Dihedral : 3.568 13.096 610 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.27 % Allowed : 21.36 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.36), residues: 560 helix: 1.05 (0.31), residues: 316 sheet: 0.49 (0.76), residues: 53 loop : -2.39 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 402 TYR 0.005 0.001 TYR A 91 PHE 0.017 0.001 PHE A 275 TRP 0.012 0.001 TRP A 261 HIS 0.001 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 4379) covalent geometry : angle 0.50298 ( 5970) SS BOND : bond 0.00219 ( 4) SS BOND : angle 0.81972 ( 8) hydrogen bonds : bond 0.04583 ( 213) hydrogen bonds : angle 3.72985 ( 615) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.175 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 60 average time/residue: 0.0630 time to fit residues: 4.9959 Evaluate side-chains 55 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 0.0670 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.201238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.148189 restraints weight = 4600.763| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.02 r_work: 0.3542 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4383 Z= 0.113 Angle : 0.512 7.727 5978 Z= 0.258 Chirality : 0.039 0.129 688 Planarity : 0.004 0.055 751 Dihedral : 3.549 12.836 610 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.18 % Allowed : 20.91 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.37), residues: 560 helix: 1.10 (0.31), residues: 316 sheet: 0.33 (0.74), residues: 53 loop : -2.41 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 402 TYR 0.005 0.001 TYR A 91 PHE 0.018 0.001 PHE A 275 TRP 0.011 0.001 TRP A 261 HIS 0.001 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 4379) covalent geometry : angle 0.51143 ( 5970) SS BOND : bond 0.00084 ( 4) SS BOND : angle 0.60767 ( 8) hydrogen bonds : bond 0.04458 ( 213) hydrogen bonds : angle 3.64553 ( 615) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.145 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 62 average time/residue: 0.0632 time to fit residues: 5.1879 Evaluate side-chains 61 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.192424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.138581 restraints weight = 4746.205| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 3.30 r_work: 0.3394 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 4383 Z= 0.267 Angle : 0.701 7.742 5978 Z= 0.362 Chirality : 0.046 0.146 688 Planarity : 0.005 0.051 751 Dihedral : 4.249 18.199 610 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.09 % Allowed : 19.77 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.35), residues: 560 helix: 0.36 (0.30), residues: 318 sheet: 0.61 (0.76), residues: 51 loop : -2.65 (0.38), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 45 TYR 0.011 0.002 TYR B 37 PHE 0.019 0.002 PHE A 151 TRP 0.014 0.002 TRP A 261 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00657 ( 4379) covalent geometry : angle 0.70110 ( 5970) SS BOND : bond 0.00253 ( 4) SS BOND : angle 0.75663 ( 8) hydrogen bonds : bond 0.08220 ( 213) hydrogen bonds : angle 4.52324 ( 615) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.148 Fit side-chains REVERT: A 90 ARG cc_start: 0.7604 (ptm-80) cc_final: 0.7186 (ptt90) REVERT: A 144 ASP cc_start: 0.7356 (m-30) cc_final: 0.7089 (m-30) REVERT: A 172 ARG cc_start: 0.7079 (tpt90) cc_final: 0.6848 (tpp80) REVERT: A 240 TYR cc_start: 0.7174 (OUTLIER) cc_final: 0.6848 (m-80) outliers start: 18 outliers final: 10 residues processed: 66 average time/residue: 0.0888 time to fit residues: 7.2129 Evaluate side-chains 61 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 50 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.197770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.150800 restraints weight = 4695.500| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.93 r_work: 0.3471 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4383 Z= 0.133 Angle : 0.544 7.191 5978 Z= 0.280 Chirality : 0.040 0.134 688 Planarity : 0.004 0.054 751 Dihedral : 3.923 15.419 610 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.41 % Allowed : 21.14 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.36), residues: 560 helix: 0.73 (0.31), residues: 317 sheet: 0.48 (0.75), residues: 51 loop : -2.57 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 89 TYR 0.005 0.001 TYR A 240 PHE 0.016 0.001 PHE A 275 TRP 0.014 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4379) covalent geometry : angle 0.54405 ( 5970) SS BOND : bond 0.00075 ( 4) SS BOND : angle 0.59127 ( 8) hydrogen bonds : bond 0.05408 ( 213) hydrogen bonds : angle 3.95314 ( 615) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.166 Fit side-chains REVERT: A 144 ASP cc_start: 0.7419 (m-30) cc_final: 0.7134 (m-30) outliers start: 15 outliers final: 11 residues processed: 58 average time/residue: 0.0689 time to fit residues: 5.2647 Evaluate side-chains 59 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.0270 chunk 33 optimal weight: 0.3980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.200903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.148457 restraints weight = 4694.654| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.98 r_work: 0.3547 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4383 Z= 0.106 Angle : 0.509 7.692 5978 Z= 0.259 Chirality : 0.038 0.128 688 Planarity : 0.004 0.058 751 Dihedral : 3.638 13.656 610 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.50 % Allowed : 21.59 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.37), residues: 560 helix: 1.08 (0.31), residues: 316 sheet: 0.20 (0.73), residues: 53 loop : -2.47 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 89 TYR 0.005 0.001 TYR A 457 PHE 0.016 0.001 PHE A 275 TRP 0.014 0.001 TRP A 261 HIS 0.001 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 4379) covalent geometry : angle 0.50865 ( 5970) SS BOND : bond 0.00052 ( 4) SS BOND : angle 0.51059 ( 8) hydrogen bonds : bond 0.04025 ( 213) hydrogen bonds : angle 3.59171 ( 615) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.154 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 56 average time/residue: 0.0751 time to fit residues: 5.4354 Evaluate side-chains 54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.194353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.144280 restraints weight = 4641.940| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.19 r_work: 0.3394 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4383 Z= 0.162 Angle : 0.575 7.463 5978 Z= 0.295 Chirality : 0.041 0.141 688 Planarity : 0.004 0.056 751 Dihedral : 3.859 15.374 610 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.73 % Allowed : 21.59 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.36), residues: 560 helix: 0.84 (0.31), residues: 317 sheet: 0.17 (0.73), residues: 53 loop : -2.52 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 89 TYR 0.010 0.001 TYR A 240 PHE 0.016 0.001 PHE A 275 TRP 0.013 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 4379) covalent geometry : angle 0.57517 ( 5970) SS BOND : bond 0.00109 ( 4) SS BOND : angle 0.54689 ( 8) hydrogen bonds : bond 0.05897 ( 213) hydrogen bonds : angle 3.94626 ( 615) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.189 Fit side-chains REVERT: A 144 ASP cc_start: 0.7439 (m-30) cc_final: 0.7180 (m-30) outliers start: 12 outliers final: 9 residues processed: 57 average time/residue: 0.0761 time to fit residues: 5.7122 Evaluate side-chains 57 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 29 optimal weight: 0.0470 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 30.0000 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.199028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.145445 restraints weight = 4690.363| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 3.41 r_work: 0.3497 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4383 Z= 0.113 Angle : 0.520 7.648 5978 Z= 0.266 Chirality : 0.039 0.128 688 Planarity : 0.004 0.057 751 Dihedral : 3.676 13.808 610 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.50 % Allowed : 21.82 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.36), residues: 560 helix: 1.05 (0.31), residues: 316 sheet: 0.15 (0.73), residues: 53 loop : -2.48 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 89 TYR 0.006 0.001 TYR A 240 PHE 0.017 0.001 PHE A 275 TRP 0.013 0.001 TRP A 261 HIS 0.001 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 4379) covalent geometry : angle 0.51992 ( 5970) SS BOND : bond 0.00067 ( 4) SS BOND : angle 0.46307 ( 8) hydrogen bonds : bond 0.04400 ( 213) hydrogen bonds : angle 3.65787 ( 615) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.152 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 54 average time/residue: 0.0717 time to fit residues: 5.0630 Evaluate side-chains 55 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 31 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 26 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.200121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.147634 restraints weight = 4694.953| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.22 r_work: 0.3520 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4383 Z= 0.111 Angle : 0.516 7.894 5978 Z= 0.264 Chirality : 0.038 0.131 688 Planarity : 0.004 0.060 751 Dihedral : 3.574 13.502 610 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.05 % Allowed : 22.27 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.37), residues: 560 helix: 1.14 (0.31), residues: 316 sheet: 0.11 (0.72), residues: 53 loop : -2.46 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 89 TYR 0.007 0.001 TYR A 240 PHE 0.016 0.001 PHE A 275 TRP 0.014 0.001 TRP A 261 HIS 0.001 0.000 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 4379) covalent geometry : angle 0.51564 ( 5970) SS BOND : bond 0.00057 ( 4) SS BOND : angle 0.43842 ( 8) hydrogen bonds : bond 0.04202 ( 213) hydrogen bonds : angle 3.57403 ( 615) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.175 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 53 average time/residue: 0.0788 time to fit residues: 5.4302 Evaluate side-chains 55 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 48 optimal weight: 0.1980 chunk 49 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 5 optimal weight: 0.0070 chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.200643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.147424 restraints weight = 4636.025| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 3.57 r_work: 0.3513 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4383 Z= 0.108 Angle : 0.510 7.797 5978 Z= 0.261 Chirality : 0.038 0.128 688 Planarity : 0.004 0.059 751 Dihedral : 3.538 13.493 610 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.82 % Allowed : 22.50 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.37), residues: 560 helix: 1.26 (0.32), residues: 310 sheet: 0.08 (0.71), residues: 53 loop : -2.37 (0.38), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 89 TYR 0.006 0.001 TYR A 240 PHE 0.016 0.001 PHE A 275 TRP 0.013 0.001 TRP A 261 HIS 0.001 0.000 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 4379) covalent geometry : angle 0.50974 ( 5970) SS BOND : bond 0.00060 ( 4) SS BOND : angle 0.41074 ( 8) hydrogen bonds : bond 0.04051 ( 213) hydrogen bonds : angle 3.52193 ( 615) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1376.55 seconds wall clock time: 24 minutes 12.21 seconds (1452.21 seconds total)