Starting phenix.real_space_refine on Fri Dec 27 10:57:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jty_36656/12_2024/8jty_36656.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jty_36656/12_2024/8jty_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_36656/12_2024/8jty_36656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jty_36656/12_2024/8jty_36656.map" model { file = "/net/cci-nas-00/data/ceres_data/8jty_36656/12_2024/8jty_36656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jty_36656/12_2024/8jty_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 3.28, per 1000 atoms: 0.77 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: 1.36 Conformation dependent library (CDL) restraints added in 602.7 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: 0.49 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: 1.24 Time building geometry restraints manager: 1.27 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.950 Find NCS groups from input model: 0.050 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.830 ------------------------------------------------------------------------------- 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 : 0.515 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1934 time to fit residues: 12.3075 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 : 0.459 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 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 : 0.508 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 56 average time/residue: 0.1651 time to fit residues: 12.2009 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 : 0.474 ------------------------------------------------------------------------------- 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 27 optimal weight: 0.2980 chunk 15 optimal weight: 6.9990 chunk 41 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 chunk 17 optimal weight: 0.0020 chunk 40 optimal weight: 0.9980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4379 Z= 0.146 Angle : 0.484 7.714 5970 Z= 0.248 Chirality : 0.038 0.132 688 Planarity : 0.004 0.055 751 Dihedral : 3.510 13.222 610 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % 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 (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: 1.07 (0.31), residues: 315 sheet: 0.40 (0.75), residues: 53 loop : -2.30 (0.39), residues: 192 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 0.017 0.001 PHE A 275 TYR 0.005 0.001 TYR A 91 ARG 0.002 0.000 ARG A 402 *********************** 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: 10 poor density : 53 time to evaluate : 0.472 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 59 average time/residue: 0.1527 time to fit residues: 11.8246 Evaluate side-chains 56 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 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 49 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 5 optimal weight: 0.0040 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1116 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 : 0.522 7.751 5970 Z= 0.263 Chirality : 0.040 0.224 688 Planarity : 0.004 0.055 751 Dihedral : 3.563 12.836 610 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % 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: -0.19 (0.37), residues: 560 helix: 1.07 (0.31), residues: 316 sheet: 0.41 (0.74), residues: 53 loop : -2.40 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.001 0.000 HIS A 49 PHE 0.018 0.001 PHE A 275 TYR 0.005 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 64 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.418 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 60 average time/residue: 0.1629 time to fit residues: 12.7505 Evaluate side-chains 60 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 44 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1231 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= 0.195 Angle : 0.534 7.806 5970 Z= 0.273 Chirality : 0.040 0.134 688 Planarity : 0.004 0.055 751 Dihedral : 3.644 13.826 610 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.64 % Allowed : 20.45 % 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: -0.22 (0.36), residues: 560 helix: 1.00 (0.31), residues: 317 sheet: 0.57 (0.75), residues: 51 loop : -2.37 (0.39), residues: 192 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 0.016 0.001 PHE A 275 TYR 0.006 0.001 TYR A 91 ARG 0.002 0.000 ARG B 45 *********************** 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 69 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.451 Fit side-chains REVERT: A 144 ASP cc_start: 0.7442 (m-30) cc_final: 0.7100 (m-30) outliers start: 16 outliers final: 10 residues processed: 64 average time/residue: 0.1516 time to fit residues: 12.7715 Evaluate side-chains 61 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 358 SER Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 487 LEU 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 47 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 17 optimal weight: 0.1980 chunk 27 optimal weight: 0.0670 chunk 51 optimal weight: 4.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1297 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= 0.164 Angle : 0.505 8.057 5970 Z= 0.257 Chirality : 0.039 0.127 688 Planarity : 0.004 0.055 751 Dihedral : 3.564 13.056 610 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.64 % Allowed : 20.68 % 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 (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: -0.13 (0.37), residues: 560 helix: 1.13 (0.31), residues: 316 sheet: 0.53 (0.75), residues: 51 loop : -2.39 (0.39), residues: 193 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 0.004 0.001 TYR A 457 ARG 0.001 0.000 ARG A 402 *********************** 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 66 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.424 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 62 average time/residue: 0.1595 time to fit residues: 13.0744 Evaluate side-chains 59 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 358 SER Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 487 LEU 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 5 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4379 Z= 0.259 Angle : 0.579 7.096 5970 Z= 0.297 Chirality : 0.041 0.137 688 Planarity : 0.004 0.054 751 Dihedral : 3.848 15.211 610 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.41 % Allowed : 20.45 % 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: -0.41 (0.36), residues: 560 helix: 0.84 (0.31), residues: 317 sheet: 0.58 (0.74), residues: 51 loop : -2.46 (0.39), residues: 192 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 0.007 0.001 TYR A 240 ARG 0.003 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 63 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.478 Fit side-chains REVERT: A 144 ASP cc_start: 0.7482 (m-30) cc_final: 0.7148 (m-30) outliers start: 15 outliers final: 11 residues processed: 59 average time/residue: 0.1605 time to fit residues: 12.4022 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 : 0.454 ------------------------------------------------------------------------------- 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 269 SER Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 358 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 41 optimal weight: 0.4980 chunk 48 optimal weight: 0.4980 chunk 50 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4379 Z= 0.170 Angle : 0.524 7.819 5970 Z= 0.266 Chirality : 0.039 0.129 688 Planarity : 0.004 0.055 751 Dihedral : 3.671 13.528 610 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % 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: -0.25 (0.36), residues: 560 helix: 1.03 (0.31), residues: 316 sheet: 0.31 (0.73), residues: 53 loop : -2.43 (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 0.017 0.001 PHE A 275 TYR 0.005 0.001 TYR A 457 ARG 0.001 0.000 ARG B 45 *********************** 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: 13 poor density : 48 time to evaluate : 0.441 Fit side-chains REVERT: A 144 ASP cc_start: 0.7392 (m-30) cc_final: 0.7041 (m-30) REVERT: A 239 MET cc_start: 0.7081 (mmp) cc_final: 0.6445 (mmt) outliers start: 13 outliers final: 10 residues processed: 57 average time/residue: 0.1574 time to fit residues: 11.7586 Evaluate side-chains 56 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 358 SER 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 50 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1440 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= 0.201 Angle : 0.545 7.719 5970 Z= 0.277 Chirality : 0.040 0.132 688 Planarity : 0.004 0.054 751 Dihedral : 3.717 14.206 610 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.73 % Allowed : 21.36 % 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: -0.32 (0.36), residues: 560 helix: 0.96 (0.31), residues: 317 sheet: 0.18 (0.72), residues: 54 loop : -2.42 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 261 HIS 0.001 0.000 HIS A 49 PHE 0.016 0.001 PHE A 275 TYR 0.008 0.001 TYR A 240 ARG 0.002 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 61 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.460 Fit side-chains REVERT: A 144 ASP cc_start: 0.7430 (m-30) cc_final: 0.7085 (m-30) REVERT: A 239 MET cc_start: 0.7098 (mmp) cc_final: 0.6427 (mmt) outliers start: 12 outliers final: 11 residues processed: 58 average time/residue: 0.1655 time to fit residues: 12.6305 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 : 0.477 ------------------------------------------------------------------------------- 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 269 SER Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 358 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1467 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= 0.184 Angle : 0.540 7.832 5970 Z= 0.274 Chirality : 0.039 0.130 688 Planarity : 0.004 0.055 751 Dihedral : 3.687 13.826 610 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % 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: -0.27 (0.36), residues: 560 helix: 1.03 (0.31), residues: 316 sheet: 0.19 (0.72), residues: 54 loop : -2.44 (0.39), residues: 190 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 0.008 0.001 TYR A 240 ARG 0.002 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 56 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.433 Fit side-chains REVERT: A 144 ASP cc_start: 0.7413 (m-30) cc_final: 0.7067 (m-30) outliers start: 11 outliers final: 10 residues processed: 53 average time/residue: 0.1606 time to fit residues: 11.1147 Evaluate side-chains 55 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 358 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.197849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.144302 restraints weight = 4604.976| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 3.73 r_work: 0.3463 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 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 0.036 4379 Z= 0.187 Angle : 0.542 7.680 5970 Z= 0.277 Chirality : 0.039 0.128 688 Planarity : 0.004 0.055 751 Dihedral : 3.688 13.844 610 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % 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: -0.28 (0.36), residues: 560 helix: 1.00 (0.31), residues: 317 sheet: 0.21 (0.72), residues: 54 loop : -2.44 (0.39), residues: 189 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 0.009 0.001 TYR A 240 ARG 0.002 0.000 ARG A 439 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1278.31 seconds wall clock time: 23 minutes 43.89 seconds (1423.89 seconds total)