Starting phenix.real_space_refine on Sat Aug 23 10:27:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eut_19981/08_2025/9eut_19981_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eut_19981/08_2025/9eut_19981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eut_19981/08_2025/9eut_19981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eut_19981/08_2025/9eut_19981.map" model { file = "/net/cci-nas-00/data/ceres_data/9eut_19981/08_2025/9eut_19981_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eut_19981/08_2025/9eut_19981_neut.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.015 sd= 1.049 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 56 5.16 5 C 7148 2.51 5 N 2082 2.21 5 O 2170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11456 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5685 Classifications: {'peptide': 728} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 690} Chain: "B" Number of atoms: 5685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5685 Classifications: {'peptide': 728} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 690} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.99, per 1000 atoms: 0.26 Number of scatterers: 11456 At special positions: 0 Unit cell: (97.704, 109.296, 159.804, 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 56 16.00 O 2170 8.00 N 2082 7.00 C 7148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 502.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2716 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 14 sheets defined 43.3% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 10 through 14 removed outlier: 3.590A pdb=" N GLU A 13 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP A 14 " --> pdb=" O ASN A 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 10 through 14' Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 60 through 77 Proline residue: A 66 - end of helix Processing helix chain 'A' and resid 122 through 135 Processing helix chain 'A' and resid 139 through 156 removed outlier: 3.562A pdb=" N ASP A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 removed outlier: 3.624A pdb=" N ILE A 195 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 206 removed outlier: 3.638A pdb=" N GLN A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 255 Processing helix chain 'A' and resid 285 through 332 removed outlier: 3.584A pdb=" N GLN A 297 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 345 through 349 removed outlier: 3.519A pdb=" N ALA A 348 " --> pdb=" O GLY A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 382 Processing helix chain 'A' and resid 475 through 498 Processing helix chain 'A' and resid 498 through 529 removed outlier: 3.894A pdb=" N ARG A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASN A 517 " --> pdb=" O HIS A 513 " (cutoff:3.500A) Proline residue: A 518 - end of helix Processing helix chain 'A' and resid 533 through 565 Processing helix chain 'A' and resid 578 through 593 Processing helix chain 'A' and resid 611 through 630 Processing helix chain 'A' and resid 659 through 666 Processing helix chain 'A' and resid 671 through 677 removed outlier: 3.925A pdb=" N ALA A 675 " --> pdb=" O LYS A 671 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 676 " --> pdb=" O ARG A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 698 removed outlier: 4.300A pdb=" N TYR A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 50 Processing helix chain 'B' and resid 60 through 65 Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.651A pdb=" N LEU B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 74 " --> pdb=" O ARG B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 122 through 135 removed outlier: 3.782A pdb=" N ASN B 126 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN B 135 " --> pdb=" O ILE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 156 removed outlier: 3.506A pdb=" N SER B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 196 through 206 Processing helix chain 'B' and resid 244 through 254 Processing helix chain 'B' and resid 285 through 332 removed outlier: 3.512A pdb=" N ILE B 294 " --> pdb=" O MET B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 341 Processing helix chain 'B' and resid 345 through 349 Processing helix chain 'B' and resid 370 through 382 Processing helix chain 'B' and resid 475 through 515 removed outlier: 3.641A pdb=" N LEU B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU B 499 " --> pdb=" O ASN B 495 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 529 removed outlier: 3.558A pdb=" N LEU B 519 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 565 Processing helix chain 'B' and resid 578 through 593 Processing helix chain 'B' and resid 611 through 630 Processing helix chain 'B' and resid 659 through 665 Processing helix chain 'B' and resid 671 through 677 removed outlier: 3.841A pdb=" N ALA B 675 " --> pdb=" O LYS B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 698 removed outlier: 4.548A pdb=" N TYR B 689 " --> pdb=" O GLY B 685 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23 removed outlier: 3.555A pdb=" N ALA A 41 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU A 29 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 190 removed outlier: 5.463A pdb=" N VAL A 173 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG A 164 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N TRP A 271 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU A 270 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL A 266 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 362 through 366 removed outlier: 3.688A pdb=" N GLY A 354 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A 417 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE A 424 " --> pdb=" O ARG A 415 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ARG A 415 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N TRP A 426 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ALA A 413 " --> pdb=" O TRP A 426 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ARG A 428 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL A 411 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 433 through 438 Processing sheet with id=AA5, first strand: chain 'A' and resid 446 through 448 Processing sheet with id=AA6, first strand: chain 'A' and resid 574 through 577 Processing sheet with id=AA7, first strand: chain 'A' and resid 598 through 602 Processing sheet with id=AA8, first strand: chain 'B' and resid 22 through 23 removed outlier: 5.682A pdb=" N LEU B 29 " --> pdb=" O SER B 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 189 through 190 removed outlier: 5.547A pdb=" N VAL B 173 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG B 164 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N TRP B 271 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL B 266 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 362 through 366 removed outlier: 6.169A pdb=" N GLY B 422 " --> pdb=" O PHE B 416 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 433 through 437 Processing sheet with id=AB3, first strand: chain 'B' and resid 446 through 448 Processing sheet with id=AB4, first strand: chain 'B' and resid 574 through 577 Processing sheet with id=AB5, first strand: chain 'B' and resid 598 through 602 669 hydrogen bonds defined for protein. 1893 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: 1.41 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2003 1.32 - 1.44: 2981 1.44 - 1.57: 6608 1.57 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 11680 Sorted by residual: bond pdb=" CG1 ILE B 424 " pdb=" CD1 ILE B 424 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.34e+00 bond pdb=" CG1 ILE A 424 " pdb=" CD1 ILE A 424 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.30e+00 bond pdb=" CG1 ILE A 45 " pdb=" CD1 ILE A 45 " ideal model delta sigma weight residual 1.513 1.449 0.064 3.90e-02 6.57e+02 2.69e+00 bond pdb=" CG LEU B 489 " pdb=" CD1 LEU B 489 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.50e+00 bond pdb=" CG1 ILE B 45 " pdb=" CD1 ILE B 45 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.73e+00 ... (remaining 11675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 15187 1.73 - 3.47: 599 3.47 - 5.20: 72 5.20 - 6.94: 9 6.94 - 8.67: 3 Bond angle restraints: 15870 Sorted by residual: angle pdb=" N PRO B 207 " pdb=" CA PRO B 207 " pdb=" C PRO B 207 " ideal model delta sigma weight residual 113.84 118.58 -4.74 1.30e+00 5.92e-01 1.33e+01 angle pdb=" N PRO A 207 " pdb=" CA PRO A 207 " pdb=" C PRO A 207 " ideal model delta sigma weight residual 114.03 117.52 -3.49 1.23e+00 6.61e-01 8.06e+00 angle pdb=" N SER B 177 " pdb=" CA SER B 177 " pdb=" C SER B 177 " ideal model delta sigma weight residual 108.76 104.00 4.76 1.69e+00 3.50e-01 7.93e+00 angle pdb=" N PRO A 25 " pdb=" CA PRO A 25 " pdb=" C PRO A 25 " ideal model delta sigma weight residual 112.47 117.74 -5.27 2.06e+00 2.36e-01 6.54e+00 angle pdb=" CA LEU B 507 " pdb=" CB LEU B 507 " pdb=" CG LEU B 507 " ideal model delta sigma weight residual 116.30 124.97 -8.67 3.50e+00 8.16e-02 6.14e+00 ... (remaining 15865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 6529 16.39 - 32.78: 425 32.78 - 49.16: 111 49.16 - 65.55: 27 65.55 - 81.94: 10 Dihedral angle restraints: 7102 sinusoidal: 2900 harmonic: 4202 Sorted by residual: dihedral pdb=" CA LEU B 273 " pdb=" C LEU B 273 " pdb=" N PHE B 274 " pdb=" CA PHE B 274 " ideal model delta harmonic sigma weight residual 180.00 160.56 19.44 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ARG A 209 " pdb=" C ARG A 209 " pdb=" N LEU A 210 " pdb=" CA LEU A 210 " ideal model delta harmonic sigma weight residual 180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP A 401 " pdb=" CB ASP A 401 " pdb=" CG ASP A 401 " pdb=" OD1 ASP A 401 " ideal model delta sinusoidal sigma weight residual -30.00 -89.13 59.13 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 7099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1136 0.039 - 0.079: 415 0.079 - 0.118: 180 0.118 - 0.158: 46 0.158 - 0.197: 5 Chirality restraints: 1782 Sorted by residual: chirality pdb=" CA PRO A 25 " pdb=" N PRO A 25 " pdb=" C PRO A 25 " pdb=" CB PRO A 25 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.73e-01 chirality pdb=" CA PRO B 25 " pdb=" N PRO B 25 " pdb=" C PRO B 25 " pdb=" CB PRO B 25 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.89e-01 chirality pdb=" CB ILE A 112 " pdb=" CA ILE A 112 " pdb=" CG1 ILE A 112 " pdb=" CG2 ILE A 112 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.62e-01 ... (remaining 1779 not shown) Planarity restraints: 2098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 178 " -0.315 9.50e-02 1.11e+02 1.42e-01 1.46e+01 pdb=" NE ARG A 178 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 178 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG A 178 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 178 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 152 " 0.288 9.50e-02 1.11e+02 1.30e-01 1.22e+01 pdb=" NE ARG B 152 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG B 152 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG B 152 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG B 152 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 634 " 0.272 9.50e-02 1.11e+02 1.23e-01 1.18e+01 pdb=" NE ARG B 634 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG B 634 " 0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG B 634 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG B 634 " 0.000 2.00e-02 2.50e+03 ... (remaining 2095 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 293 2.71 - 3.25: 11216 3.25 - 3.80: 17786 3.80 - 4.35: 22994 4.35 - 4.90: 39248 Nonbonded interactions: 91537 Sorted by model distance: nonbonded pdb=" NH1 ARG A 178 " pdb=" O LEU A 182 " model vdw 2.158 3.120 nonbonded pdb=" NE1 TRP B 437 " pdb=" OE1 GLU B 465 " model vdw 2.250 3.120 nonbonded pdb=" OH TYR B 203 " pdb=" O2B LBV B2000 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR A 203 " pdb=" O2B LBV A2000 " model vdw 2.262 3.040 nonbonded pdb=" OE2 GLU B 109 " pdb=" OG SER B 238 " model vdw 2.269 3.040 ... (remaining 91532 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 4.840 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.690 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.005 0.071 11680 Z= 0.217 Angle : 0.759 8.672 15870 Z= 0.428 Chirality : 0.049 0.197 1782 Planarity : 0.011 0.142 2098 Dihedral : 12.335 81.940 4386 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.56 % Allowed : 4.03 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.20), residues: 1452 helix: 0.43 (0.20), residues: 562 sheet: 0.41 (0.30), residues: 275 loop : -0.65 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.003 ARG B 634 TYR 0.026 0.006 TYR A 157 PHE 0.026 0.003 PHE A 416 TRP 0.027 0.004 TRP B 82 HIS 0.010 0.002 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00519 (11680) covalent geometry : angle 0.75905 (15870) hydrogen bonds : bond 0.16703 ( 669) hydrogen bonds : angle 6.98591 ( 1893) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 205 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3462 (mmm) cc_final: 0.2582 (mmm) REVERT: A 380 ARG cc_start: 0.5880 (ttt180) cc_final: 0.5646 (tmm160) REVERT: B 1 MET cc_start: -0.1151 (mmm) cc_final: -0.1473 (mmm) REVERT: B 71 MET cc_start: 0.7860 (ttp) cc_final: 0.7577 (ttp) REVERT: B 321 ARG cc_start: 0.6820 (mmm160) cc_final: 0.6517 (tpt90) outliers start: 7 outliers final: 3 residues processed: 210 average time/residue: 0.6734 time to fit residues: 150.4340 Evaluate side-chains 127 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 686 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 541 GLN B 61 GLN B 128 GLN B 137 HIS B 146 ASN ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.235991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.172555 restraints weight = 14995.196| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.66 r_work: 0.3777 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11680 Z= 0.156 Angle : 0.641 11.044 15870 Z= 0.318 Chirality : 0.045 0.166 1782 Planarity : 0.005 0.081 2098 Dihedral : 5.920 72.749 1668 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.42 % Allowed : 11.84 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.22), residues: 1452 helix: 1.80 (0.20), residues: 578 sheet: 0.69 (0.31), residues: 261 loop : -0.06 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 701 TYR 0.023 0.002 TYR B 163 PHE 0.018 0.002 PHE A 425 TRP 0.014 0.002 TRP A 271 HIS 0.005 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00359 (11680) covalent geometry : angle 0.64051 (15870) hydrogen bonds : bond 0.04274 ( 669) hydrogen bonds : angle 5.32274 ( 1893) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2618 (mmm) cc_final: 0.2236 (mmm) REVERT: A 74 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: A 269 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8310 (ptmm) REVERT: A 380 ARG cc_start: 0.6375 (ttt180) cc_final: 0.5775 (tmm160) REVERT: B 321 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6599 (tpt90) REVERT: B 501 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7208 (t70) outliers start: 30 outliers final: 8 residues processed: 145 average time/residue: 0.5825 time to fit residues: 91.0740 Evaluate side-chains 118 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 269 LYS Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 501 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 21 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 96 optimal weight: 0.0010 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 22 optimal weight: 0.0020 chunk 3 optimal weight: 0.5980 chunk 68 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN B 61 GLN B 93 HIS B 126 ASN ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.236256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.172950 restraints weight = 15220.346| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.34 r_work: 0.3825 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11680 Z= 0.121 Angle : 0.586 10.340 15870 Z= 0.287 Chirality : 0.043 0.159 1782 Planarity : 0.004 0.059 2098 Dihedral : 5.530 62.741 1662 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.61 % Allowed : 13.69 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.22), residues: 1452 helix: 2.23 (0.20), residues: 578 sheet: 0.95 (0.32), residues: 267 loop : -0.01 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 614 TYR 0.019 0.001 TYR B 163 PHE 0.025 0.002 PHE B 222 TRP 0.011 0.001 TRP A 271 HIS 0.004 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00273 (11680) covalent geometry : angle 0.58573 (15870) hydrogen bonds : bond 0.03792 ( 669) hydrogen bonds : angle 4.95904 ( 1893) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2831 (mmm) cc_final: 0.2293 (mmm) REVERT: A 74 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: A 249 GLU cc_start: 0.8226 (tt0) cc_final: 0.7996 (mm-30) REVERT: A 380 ARG cc_start: 0.6401 (ttt180) cc_final: 0.5955 (tmm160) REVERT: A 492 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7922 (tt) REVERT: B 418 ARG cc_start: 0.7551 (ttt180) cc_final: 0.6695 (tpm170) outliers start: 20 outliers final: 7 residues processed: 136 average time/residue: 0.5797 time to fit residues: 84.6626 Evaluate side-chains 116 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 184 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 120 optimal weight: 0.5980 chunk 134 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 129 optimal weight: 0.0170 chunk 83 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN B 61 GLN B 580 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.228324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.179395 restraints weight = 15154.988| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 1.80 r_work: 0.3819 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11680 Z= 0.138 Angle : 0.590 10.607 15870 Z= 0.288 Chirality : 0.044 0.153 1782 Planarity : 0.004 0.038 2098 Dihedral : 5.433 52.048 1662 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.09 % Allowed : 13.77 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.22), residues: 1452 helix: 2.34 (0.20), residues: 585 sheet: 0.79 (0.32), residues: 272 loop : -0.10 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 614 TYR 0.021 0.002 TYR B 163 PHE 0.020 0.002 PHE B 222 TRP 0.011 0.002 TRP B 423 HIS 0.006 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00318 (11680) covalent geometry : angle 0.59011 (15870) hydrogen bonds : bond 0.03727 ( 669) hydrogen bonds : angle 4.85542 ( 1893) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3235 (mmm) cc_final: 0.2364 (mmm) REVERT: A 74 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: A 492 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8040 (tt) outliers start: 26 outliers final: 10 residues processed: 128 average time/residue: 0.5930 time to fit residues: 82.1232 Evaluate side-chains 113 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 283 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 114 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.231244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.167184 restraints weight = 15061.985| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.54 r_work: 0.3733 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 11680 Z= 0.266 Angle : 0.696 11.008 15870 Z= 0.342 Chirality : 0.048 0.162 1782 Planarity : 0.005 0.046 2098 Dihedral : 5.938 58.113 1662 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.42 % Allowed : 14.49 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.22), residues: 1452 helix: 2.19 (0.21), residues: 584 sheet: 0.60 (0.32), residues: 273 loop : -0.32 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 380 TYR 0.027 0.002 TYR B 163 PHE 0.025 0.003 PHE A 416 TRP 0.016 0.002 TRP B 423 HIS 0.011 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00641 (11680) covalent geometry : angle 0.69605 (15870) hydrogen bonds : bond 0.04349 ( 669) hydrogen bonds : angle 5.12493 ( 1893) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2810 (mmm) cc_final: 0.2288 (mmm) REVERT: A 74 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: A 419 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7478 (mt0) REVERT: A 492 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8028 (tt) outliers start: 30 outliers final: 9 residues processed: 130 average time/residue: 0.4835 time to fit residues: 68.5663 Evaluate side-chains 119 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 184 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 53 optimal weight: 20.0000 chunk 135 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 chunk 94 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.226221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.177065 restraints weight = 14986.030| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 1.82 r_work: 0.3787 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11680 Z= 0.155 Angle : 0.617 12.752 15870 Z= 0.300 Chirality : 0.044 0.154 1782 Planarity : 0.004 0.036 2098 Dihedral : 5.671 54.428 1662 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.85 % Allowed : 15.62 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.22), residues: 1452 helix: 2.33 (0.21), residues: 585 sheet: 0.59 (0.32), residues: 275 loop : -0.28 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 506 TYR 0.023 0.002 TYR A 250 PHE 0.020 0.002 PHE B 222 TRP 0.013 0.002 TRP A 426 HIS 0.006 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00362 (11680) covalent geometry : angle 0.61690 (15870) hydrogen bonds : bond 0.03820 ( 669) hydrogen bonds : angle 4.91655 ( 1893) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3232 (mmm) cc_final: 0.2398 (mmm) REVERT: A 74 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: A 492 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8078 (tt) outliers start: 23 outliers final: 12 residues processed: 129 average time/residue: 0.6272 time to fit residues: 87.8050 Evaluate side-chains 117 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 276 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 39 optimal weight: 0.8980 chunk 140 optimal weight: 0.0370 chunk 84 optimal weight: 0.7980 chunk 119 optimal weight: 0.4980 chunk 118 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 92 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS B 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.229460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.165678 restraints weight = 15003.981| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.26 r_work: 0.3756 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11680 Z= 0.121 Angle : 0.605 17.811 15870 Z= 0.290 Chirality : 0.043 0.168 1782 Planarity : 0.004 0.053 2098 Dihedral : 5.527 54.559 1662 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.61 % Allowed : 16.34 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.22), residues: 1452 helix: 2.45 (0.21), residues: 585 sheet: 0.63 (0.32), residues: 275 loop : -0.20 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 506 TYR 0.020 0.001 TYR A 250 PHE 0.018 0.002 PHE B 222 TRP 0.012 0.001 TRP A 426 HIS 0.004 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00275 (11680) covalent geometry : angle 0.60453 (15870) hydrogen bonds : bond 0.03553 ( 669) hydrogen bonds : angle 4.78825 ( 1893) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2931 (mmm) cc_final: 0.2309 (mmm) REVERT: A 74 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: A 380 ARG cc_start: 0.6274 (tpp80) cc_final: 0.5215 (tmm160) REVERT: A 492 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7879 (tt) outliers start: 20 outliers final: 11 residues processed: 125 average time/residue: 0.5419 time to fit residues: 73.7999 Evaluate side-chains 119 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 184 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 128 optimal weight: 6.9990 chunk 39 optimal weight: 0.0070 chunk 34 optimal weight: 0.6980 chunk 139 optimal weight: 7.9990 chunk 56 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 93 optimal weight: 0.0050 chunk 30 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.0270 overall best weight: 0.3470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.229926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3979 r_free = 0.3979 target = 0.170064 restraints weight = 15120.178| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.26 r_work: 0.3784 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11680 Z= 0.106 Angle : 0.585 15.963 15870 Z= 0.280 Chirality : 0.043 0.159 1782 Planarity : 0.004 0.069 2098 Dihedral : 5.379 58.545 1662 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.29 % Allowed : 17.15 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.22), residues: 1452 helix: 2.56 (0.21), residues: 586 sheet: 0.68 (0.32), residues: 274 loop : -0.08 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 380 TYR 0.018 0.001 TYR A 250 PHE 0.017 0.002 PHE B 222 TRP 0.011 0.001 TRP B 395 HIS 0.004 0.001 HIS A 26 Details of bonding type rmsd covalent geometry : bond 0.00236 (11680) covalent geometry : angle 0.58516 (15870) hydrogen bonds : bond 0.03335 ( 669) hydrogen bonds : angle 4.63014 ( 1893) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2958 (mmm) cc_final: 0.2278 (mmm) REVERT: A 74 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: A 150 GLU cc_start: 0.8290 (tp30) cc_final: 0.8032 (tp30) REVERT: A 183 GLU cc_start: 0.7893 (tp30) cc_final: 0.7670 (mm-30) REVERT: A 380 ARG cc_start: 0.6270 (tpp80) cc_final: 0.5281 (tmm160) outliers start: 16 outliers final: 8 residues processed: 129 average time/residue: 0.6033 time to fit residues: 84.6043 Evaluate side-chains 113 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 184 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 28 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 131 optimal weight: 7.9990 chunk 120 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 141 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 72 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.229349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.3916 r_free = 0.3916 target = 0.163848 restraints weight = 14913.334| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.44 r_work: 0.3741 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11680 Z= 0.140 Angle : 0.617 15.431 15870 Z= 0.295 Chirality : 0.044 0.194 1782 Planarity : 0.005 0.067 2098 Dihedral : 5.439 54.787 1662 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.21 % Allowed : 17.63 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.22), residues: 1452 helix: 2.48 (0.21), residues: 587 sheet: 0.60 (0.32), residues: 275 loop : -0.11 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 380 TYR 0.021 0.002 TYR A 250 PHE 0.019 0.002 PHE A 123 TRP 0.011 0.001 TRP B 426 HIS 0.005 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00328 (11680) covalent geometry : angle 0.61659 (15870) hydrogen bonds : bond 0.03546 ( 669) hydrogen bonds : angle 4.69616 ( 1893) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2779 (mmm) cc_final: 0.2222 (mmm) REVERT: A 74 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: A 380 ARG cc_start: 0.6265 (tpp80) cc_final: 0.5262 (tmm160) REVERT: A 614 ARG cc_start: 0.8639 (mmt-90) cc_final: 0.8378 (mpt180) outliers start: 15 outliers final: 8 residues processed: 119 average time/residue: 0.5440 time to fit residues: 70.4486 Evaluate side-chains 113 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 390 TYR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 184 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 119 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 120 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 83 optimal weight: 0.0470 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.230377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.171572 restraints weight = 15052.088| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.44 r_work: 0.3782 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11680 Z= 0.118 Angle : 0.607 15.602 15870 Z= 0.291 Chirality : 0.043 0.190 1782 Planarity : 0.004 0.062 2098 Dihedral : 5.407 56.900 1662 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.97 % Allowed : 18.20 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.22), residues: 1452 helix: 2.42 (0.21), residues: 593 sheet: 0.60 (0.32), residues: 279 loop : -0.07 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 380 TYR 0.019 0.001 TYR A 250 PHE 0.024 0.002 PHE A 123 TRP 0.026 0.002 TRP B 426 HIS 0.004 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00271 (11680) covalent geometry : angle 0.60690 (15870) hydrogen bonds : bond 0.03436 ( 669) hydrogen bonds : angle 4.63879 ( 1893) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2714 (mmm) cc_final: 0.2118 (mmm) REVERT: A 74 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: A 104 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7292 (pp20) REVERT: A 321 ARG cc_start: 0.6769 (mtp-110) cc_final: 0.6185 (ttt180) REVERT: A 380 ARG cc_start: 0.6263 (tpp80) cc_final: 0.5285 (tmm160) outliers start: 12 outliers final: 7 residues processed: 120 average time/residue: 0.5414 time to fit residues: 70.9357 Evaluate side-chains 114 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 184 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 111 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 30.0000 chunk 106 optimal weight: 0.0570 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN B 470 HIS ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.228828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3924 r_free = 0.3924 target = 0.166017 restraints weight = 15010.099| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.80 r_work: 0.3712 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11680 Z= 0.158 Angle : 0.626 14.925 15870 Z= 0.303 Chirality : 0.045 0.190 1782 Planarity : 0.005 0.060 2098 Dihedral : 5.487 54.780 1662 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.72 % Allowed : 18.52 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.22), residues: 1452 helix: 2.37 (0.21), residues: 591 sheet: 0.56 (0.32), residues: 279 loop : -0.14 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 380 TYR 0.022 0.002 TYR A 250 PHE 0.026 0.002 PHE A 123 TRP 0.016 0.002 TRP B 426 HIS 0.006 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00377 (11680) covalent geometry : angle 0.62618 (15870) hydrogen bonds : bond 0.03688 ( 669) hydrogen bonds : angle 4.73455 ( 1893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4509.32 seconds wall clock time: 77 minutes 19.71 seconds (4639.71 seconds total)