Starting phenix.real_space_refine on Thu Mar 6 00:58:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jty_36656/03_2025/8jty_36656.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jty_36656/03_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_36656/03_2025/8jty_36656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jty_36656/03_2025/8jty_36656.map" model { file = "/net/cci-nas-00/data/ceres_data/8jty_36656/03_2025/8jty_36656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jty_36656/03_2025/8jty_36656.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'ASP:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} 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: 3.53, per 1000 atoms: 0.83 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: 1.07 Conformation dependent library (CDL) restraints added in 547.1 milliseconds 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: 0.52 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: 1.10 Time building geometry restraints manager: 1.30 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.240 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.500 ------------------------------------------------------------------------------- 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 4379 Z= 0.191 Angle : 0.547 8.455 5970 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP A 261 HIS 0.001 0.001 HIS A 367 PHE 0.014 0.001 PHE A 275 TYR 0.007 0.001 TYR A 91 ARG 0.002 0.000 ARG B 45 *********************** 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 : 0.402 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1819 time to fit residues: 11.4564 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 : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 14 optimal weight: 0.0870 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 49 optimal weight: 0.0470 overall best weight: 0.4256 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.202129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.148682 restraints weight = 4639.079| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 3.49 r_work: 0.3506 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4379 Z= 0.156 Angle : 0.501 8.112 5970 Z= 0.258 Chirality : 0.039 0.131 688 Planarity : 0.004 0.055 751 Dihedral : 3.659 13.655 610 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.05 % Allowed : 21.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.36), residues: 560 helix: 0.89 (0.31), residues: 314 sheet: 0.58 (0.77), residues: 53 loop : -2.31 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.001 0.000 HIS A 367 PHE 0.016 0.001 PHE A 275 TYR 0.006 0.001 TYR A 91 ARG 0.002 0.000 ARG A 89 *********************** 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 58 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.491 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 56 average time/residue: 0.1540 time to fit residues: 11.3251 Evaluate side-chains 53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 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 20 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.193738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.141448 restraints weight = 4656.964| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.95 r_work: 0.3448 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4379 Z= 0.351 Angle : 0.638 6.662 5970 Z= 0.331 Chirality : 0.044 0.154 688 Planarity : 0.004 0.053 751 Dihedral : 4.117 17.053 610 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.95 % Allowed : 20.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.36), residues: 560 helix: 0.49 (0.30), residues: 317 sheet: 0.64 (0.77), residues: 51 loop : -2.58 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.020 0.002 PHE A 151 TYR 0.009 0.001 TYR A 91 ARG 0.003 0.000 ARG B 45 *********************** 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 63 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.380 Fit side-chains REVERT: A 239 MET cc_start: 0.6968 (mmp) cc_final: 0.6543 (mmt) outliers start: 13 outliers final: 6 residues processed: 59 average time/residue: 0.1488 time to fit residues: 11.5734 Evaluate side-chains 53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 5 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.199459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.146547 restraints weight = 4671.910| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.37 r_work: 0.3505 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4379 Z= 0.153 Angle : 0.513 8.079 5970 Z= 0.261 Chirality : 0.039 0.131 688 Planarity : 0.004 0.055 751 Dihedral : 3.721 13.874 610 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.64 % Allowed : 19.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.36), residues: 560 helix: 0.96 (0.31), residues: 315 sheet: 0.53 (0.76), residues: 51 loop : -2.45 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.001 0.000 HIS A 49 PHE 0.018 0.001 PHE A 275 TYR 0.004 0.001 TYR A 91 ARG 0.002 0.000 ARG A 402 *********************** 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 63 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.403 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 59 average time/residue: 0.1439 time to fit residues: 11.1219 Evaluate side-chains 56 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 128 ASP 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 A residue 501 VAL 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 50 optimal weight: 4.9990 chunk 4 optimal weight: 0.0050 chunk 25 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.196140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.143385 restraints weight = 4686.763| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.83 r_work: 0.3420 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4379 Z= 0.226 Angle : 0.568 7.097 5970 Z= 0.288 Chirality : 0.041 0.140 688 Planarity : 0.004 0.055 751 Dihedral : 3.834 14.848 610 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.95 % Allowed : 21.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.36), residues: 560 helix: 0.85 (0.31), residues: 316 sheet: 0.56 (0.75), residues: 51 loop : -2.46 (0.38), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.016 0.001 PHE A 275 TYR 0.006 0.001 TYR A 91 ARG 0.002 0.000 ARG A 399 *********************** 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 63 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.370 Fit side-chains REVERT: A 144 ASP cc_start: 0.7023 (m-30) cc_final: 0.6709 (m-30) outliers start: 13 outliers final: 9 residues processed: 60 average time/residue: 0.1608 time to fit residues: 12.7478 Evaluate side-chains 58 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 140 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 36 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 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 = 0.4183 r_free = 0.4183 target = 0.197244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.144643 restraints weight = 4656.506| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 3.17 r_work: 0.3483 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4379 Z= 0.197 Angle : 0.537 7.421 5970 Z= 0.275 Chirality : 0.040 0.135 688 Planarity : 0.004 0.056 751 Dihedral : 3.792 14.376 610 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.36), residues: 560 helix: 0.92 (0.31), residues: 316 sheet: 0.32 (0.74), residues: 53 loop : -2.45 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 261 HIS 0.001 0.001 HIS A 49 PHE 0.016 0.001 PHE A 275 TYR 0.005 0.001 TYR A 91 ARG 0.002 0.000 ARG B 45 *********************** 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 60 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.367 Fit side-chains REVERT: A 144 ASP cc_start: 0.7100 (m-30) cc_final: 0.6814 (m-30) outliers start: 11 outliers final: 9 residues processed: 56 average time/residue: 0.2445 time to fit residues: 17.5456 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 : 0.476 ------------------------------------------------------------------------------- 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 140 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 26 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 1 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.0060 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.200901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148545 restraints weight = 4639.400| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 3.27 r_work: 0.3528 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4379 Z= 0.148 Angle : 0.501 7.684 5970 Z= 0.255 Chirality : 0.038 0.128 688 Planarity : 0.004 0.058 751 Dihedral : 3.585 13.507 610 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.50 % Allowed : 21.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.37), residues: 560 helix: 1.13 (0.31), residues: 316 sheet: 0.28 (0.73), residues: 53 loop : -2.39 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 261 HIS 0.001 0.000 HIS A 367 PHE 0.016 0.001 PHE A 275 TYR 0.004 0.001 TYR A 457 ARG 0.001 0.000 ARG A 399 *********************** 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 58 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.455 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 55 average time/residue: 0.1864 time to fit residues: 13.2864 Evaluate side-chains 52 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 B residue 46 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 45 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 46 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4182 r_free = 0.4182 target = 0.197068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.143611 restraints weight = 4536.520| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.72 r_work: 0.3445 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 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 0.035 4379 Z= 0.201 Angle : 0.538 7.551 5970 Z= 0.276 Chirality : 0.040 0.136 688 Planarity : 0.004 0.057 751 Dihedral : 3.692 14.100 610 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.36), residues: 560 helix: 1.04 (0.31), residues: 316 sheet: 0.27 (0.73), residues: 53 loop : -2.42 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.001 0.000 HIS A 49 PHE 0.016 0.001 PHE A 275 TYR 0.007 0.001 TYR A 240 ARG 0.002 0.000 ARG A 439 *********************** 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 61 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.376 Fit side-chains REVERT: A 144 ASP cc_start: 0.7006 (m-30) cc_final: 0.6641 (m-30) outliers start: 11 outliers final: 9 residues processed: 58 average time/residue: 0.1534 time to fit residues: 11.7132 Evaluate side-chains 58 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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 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 10 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 0.0770 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.200792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.148092 restraints weight = 4675.267| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 3.48 r_work: 0.3519 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4379 Z= 0.153 Angle : 0.507 7.712 5970 Z= 0.260 Chirality : 0.038 0.128 688 Planarity : 0.004 0.059 751 Dihedral : 3.569 13.606 610 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.27 % Allowed : 22.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.36), residues: 560 helix: 1.24 (0.32), residues: 310 sheet: 0.20 (0.72), residues: 53 loop : -2.36 (0.38), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.001 0.000 HIS A 367 PHE 0.016 0.001 PHE A 275 TYR 0.006 0.001 TYR A 240 ARG 0.001 0.000 ARG A 439 *********************** 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 57 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.433 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 54 average time/residue: 0.1537 time to fit residues: 10.9080 Evaluate side-chains 53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 B residue 46 GLU Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 50 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.198981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.146382 restraints weight = 4566.906| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 3.31 r_work: 0.3502 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4379 Z= 0.175 Angle : 0.524 8.025 5970 Z= 0.268 Chirality : 0.039 0.128 688 Planarity : 0.004 0.058 751 Dihedral : 3.607 13.572 610 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.59 % Allowed : 23.18 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.36), residues: 560 helix: 1.19 (0.31), residues: 310 sheet: 0.17 (0.73), residues: 53 loop : -2.36 (0.38), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.001 0.000 HIS A 49 PHE 0.015 0.001 PHE A 275 TYR 0.007 0.001 TYR A 240 ARG 0.001 0.000 ARG A 439 ********************** 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 52 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.466 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 49 average time/residue: 0.1571 time to fit residues: 10.1110 Evaluate side-chains 52 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 B residue 46 GLU Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 0.0970 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.4202 r_free = 0.4202 target = 0.199333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.145698 restraints weight = 4620.144| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 3.53 r_work: 0.3489 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4379 Z= 0.173 Angle : 0.529 8.005 5970 Z= 0.270 Chirality : 0.039 0.130 688 Planarity : 0.004 0.058 751 Dihedral : 3.609 13.590 610 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.27 % Allowed : 22.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.36), residues: 560 helix: 1.19 (0.31), residues: 310 sheet: 0.16 (0.72), residues: 53 loop : -2.36 (0.38), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 261 HIS 0.001 0.000 HIS A 49 PHE 0.015 0.001 PHE A 275 TYR 0.007 0.001 TYR A 240 ARG 0.001 0.000 ARG A 439 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2605.90 seconds wall clock time: 46 minutes 52.32 seconds (2812.32 seconds total)