Starting phenix.real_space_refine on Tue Jun 10 08:07:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eut_19981/06_2025/9eut_19981_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eut_19981/06_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_19981/06_2025/9eut_19981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eut_19981/06_2025/9eut_19981.map" model { file = "/net/cci-nas-00/data/ceres_data/9eut_19981/06_2025/9eut_19981_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eut_19981/06_2025/9eut_19981_neut.cif" } resolution = 2.95 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= 0.015 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.05, per 1000 atoms: 0.70 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: 3.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.51 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: 4.25 Time building geometry restraints manager: 3.64 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: 0.05 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: 3.680 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.800 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:17.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.320 ------------------------------------------------------------------------------- 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 (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: -0.11 (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 TRP 0.027 0.004 TRP B 82 HIS 0.010 0.002 HIS B 26 PHE 0.026 0.003 PHE A 416 TYR 0.026 0.006 TYR A 157 ARG 0.028 0.003 ARG B 634 Details of bonding type rmsd hydrogen bonds : bond 0.16703 ( 669) hydrogen bonds : angle 6.98591 ( 1893) covalent geometry : bond 0.00519 (11680) covalent geometry : angle 0.75905 (15870) *********************** 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 : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3462 (mmm) cc_final: 0.2579 (mmm) REVERT: A 380 ARG cc_start: 0.5880 (ttt180) cc_final: 0.5645 (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: 0.6518 (tpt90) outliers start: 7 outliers final: 3 residues processed: 210 average time/residue: 2.2022 time to fit residues: 493.7668 Evaluate side-chains 128 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 1.374 ------------------------------------------------------------------------------- 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 121 optimal weight: 0.2980 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 0.0000 chunk 58 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- 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 128 GLN B 137 HIS B 146 ASN B 277 HIS ** 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 = 0.4716 r_free = 0.4716 target = 0.234586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.169223 restraints weight = 14724.991| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.41 r_work: 0.3843 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11680 Z= 0.161 Angle : 0.639 10.489 15870 Z= 0.320 Chirality : 0.045 0.167 1782 Planarity : 0.005 0.067 2098 Dihedral : 5.870 71.601 1668 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.25 % Allowed : 11.84 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.16 (0.22), residues: 1452 helix: 1.77 (0.20), residues: 577 sheet: 0.69 (0.31), residues: 260 loop : -0.08 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 271 HIS 0.006 0.001 HIS B 26 PHE 0.018 0.002 PHE A 425 TYR 0.022 0.002 TYR B 163 ARG 0.010 0.001 ARG A 504 Details of bonding type rmsd hydrogen bonds : bond 0.04454 ( 669) hydrogen bonds : angle 5.36248 ( 1893) covalent geometry : bond 0.00372 (11680) covalent geometry : angle 0.63917 (15870) *********************** 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 155 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2642 (mmm) cc_final: 0.2257 (mmm) REVERT: A 74 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: A 249 GLU cc_start: 0.8517 (tt0) cc_final: 0.8152 (mm-30) REVERT: A 269 LYS cc_start: 0.8714 (mtmt) cc_final: 0.8507 (ptmm) REVERT: A 380 ARG cc_start: 0.6404 (ttt180) cc_final: 0.5752 (tmm160) REVERT: A 484 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7750 (tttp) REVERT: B 321 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6757 (tpt90) REVERT: B 501 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7331 (t70) outliers start: 28 outliers final: 7 residues processed: 143 average time/residue: 1.3888 time to fit residues: 214.3528 Evaluate side-chains 117 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 484 LYS Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 613 ASP 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 24 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 37 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 135 GLN A 376 ASN B 11 ASN B 61 GLN B 126 ASN ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.234832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.170064 restraints weight = 15105.462| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.52 r_work: 0.3800 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11680 Z= 0.153 Angle : 0.601 10.360 15870 Z= 0.300 Chirality : 0.044 0.157 1782 Planarity : 0.004 0.049 2098 Dihedral : 5.591 61.460 1662 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.09 % Allowed : 13.37 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.45 (0.22), residues: 1452 helix: 2.12 (0.20), residues: 579 sheet: 0.83 (0.32), residues: 271 loop : -0.07 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 271 HIS 0.006 0.001 HIS B 26 PHE 0.028 0.002 PHE B 222 TYR 0.021 0.002 TYR B 163 ARG 0.006 0.000 ARG A 701 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 669) hydrogen bonds : angle 5.04767 ( 1893) covalent geometry : bond 0.00355 (11680) covalent geometry : angle 0.60108 (15870) *********************** 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 149 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 1.283 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: 0.2757 (mmm) cc_final: 0.2305 (mmm) REVERT: A 74 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: A 249 GLU cc_start: 0.8222 (tt0) cc_final: 0.7990 (mm-30) REVERT: A 380 ARG cc_start: 0.6421 (ttt180) cc_final: 0.5928 (tmm160) REVERT: A 492 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7928 (tt) REVERT: B 418 ARG cc_start: 0.7564 (ttt180) cc_final: 0.6697 (tpm170) outliers start: 26 outliers final: 10 residues processed: 139 average time/residue: 1.3363 time to fit residues: 200.2717 Evaluate side-chains 116 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 1.351 ------------------------------------------------------------------------------- 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 492 LEU 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 64 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 321 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 33 optimal weight: 0.4980 chunk 114 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 25 optimal weight: 0.0970 chunk 54 optimal weight: 20.0000 chunk 74 optimal weight: 0.0970 chunk 120 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS 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 = 0.4600 r_free = 0.4600 target = 0.229370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 120)---------------| | r_work = 0.3945 r_free = 0.3945 target = 0.168162 restraints weight = 15066.656| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.38 r_work: 0.3767 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11680 Z= 0.118 Angle : 0.575 10.914 15870 Z= 0.280 Chirality : 0.043 0.158 1782 Planarity : 0.004 0.045 2098 Dihedral : 5.453 53.514 1662 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.42 % Allowed : 13.69 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.58 (0.22), residues: 1452 helix: 2.32 (0.20), residues: 585 sheet: 0.87 (0.32), residues: 271 loop : -0.11 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 426 HIS 0.004 0.001 HIS B 26 PHE 0.021 0.002 PHE B 222 TYR 0.019 0.001 TYR A 250 ARG 0.004 0.000 ARG A 504 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 669) hydrogen bonds : angle 4.80677 ( 1893) covalent geometry : bond 0.00263 (11680) covalent geometry : angle 0.57536 (15870) *********************** 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 145 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2797 (mmm) cc_final: 0.2212 (mmm) REVERT: A 74 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: A 249 GLU cc_start: 0.8264 (tt0) cc_final: 0.8053 (mm-30) REVERT: A 380 ARG cc_start: 0.6518 (ttt180) cc_final: 0.5993 (tmm160) REVERT: A 492 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8042 (tt) REVERT: A 541 GLN cc_start: 0.8813 (mm110) cc_final: 0.8606 (pp30) REVERT: A 550 MET cc_start: 0.4112 (mtt) cc_final: 0.3904 (mtt) outliers start: 30 outliers final: 11 residues processed: 130 average time/residue: 1.2816 time to fit residues: 180.7336 Evaluate side-chains 113 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 613 ASP 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 93 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 90 optimal weight: 0.0010 chunk 26 optimal weight: 0.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4594 r_free = 0.4594 target = 0.228464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3950 r_free = 0.3950 target = 0.167922 restraints weight = 14842.941| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.80 r_work: 0.3749 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11680 Z= 0.133 Angle : 0.590 11.770 15870 Z= 0.284 Chirality : 0.043 0.169 1782 Planarity : 0.004 0.048 2098 Dihedral : 5.383 52.763 1662 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.42 % Allowed : 14.01 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.63 (0.22), residues: 1452 helix: 2.40 (0.20), residues: 586 sheet: 0.86 (0.32), residues: 274 loop : -0.13 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 423 HIS 0.005 0.001 HIS B 26 PHE 0.018 0.002 PHE B 222 TYR 0.021 0.002 TYR B 163 ARG 0.011 0.000 ARG A 614 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 669) hydrogen bonds : angle 4.77217 ( 1893) covalent geometry : bond 0.00308 (11680) covalent geometry : angle 0.58990 (15870) *********************** 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 : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2971 (mmm) cc_final: 0.2278 (mmm) REVERT: A 74 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: A 249 GLU cc_start: 0.8273 (tt0) cc_final: 0.8040 (mm-30) REVERT: A 380 ARG cc_start: 0.6548 (ttt180) cc_final: 0.5950 (tmm160) REVERT: A 492 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7959 (tt) REVERT: A 614 ARG cc_start: 0.8928 (mmp80) cc_final: 0.8680 (mmt180) outliers start: 30 outliers final: 12 residues processed: 131 average time/residue: 1.1989 time to fit residues: 170.9515 Evaluate side-chains 119 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 69 LEU 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 492 LEU Chi-restraints excluded: chain A residue 531 SER 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 Chi-restraints excluded: chain B residue 283 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 125 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 135 optimal weight: 0.0070 chunk 41 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 106 optimal weight: 0.4980 chunk 50 optimal weight: 10.0000 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 146 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.230692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3964 r_free = 0.3964 target = 0.168490 restraints weight = 15107.051| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.31 r_work: 0.3786 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11680 Z= 0.118 Angle : 0.586 13.206 15870 Z= 0.281 Chirality : 0.043 0.156 1782 Planarity : 0.004 0.048 2098 Dihedral : 5.330 54.809 1662 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.85 % Allowed : 14.98 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.69 (0.22), residues: 1452 helix: 2.45 (0.20), residues: 586 sheet: 0.84 (0.32), residues: 274 loop : -0.06 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 395 HIS 0.005 0.001 HIS B 26 PHE 0.017 0.002 PHE B 222 TYR 0.021 0.001 TYR A 250 ARG 0.010 0.000 ARG B 380 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 669) hydrogen bonds : angle 4.70832 ( 1893) covalent geometry : bond 0.00268 (11680) covalent geometry : angle 0.58551 (15870) *********************** 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 143 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2835 (mmm) cc_final: 0.2217 (mmm) REVERT: A 74 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: A 249 GLU cc_start: 0.8283 (tt0) cc_final: 0.7982 (mm-30) REVERT: A 380 ARG cc_start: 0.6566 (ttt180) cc_final: 0.5906 (tmm160) REVERT: A 419 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7627 (mt0) REVERT: A 492 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7843 (tt) REVERT: A 614 ARG cc_start: 0.8914 (mmp80) cc_final: 0.8650 (mmp80) outliers start: 23 outliers final: 11 residues processed: 137 average time/residue: 1.2089 time to fit residues: 180.1270 Evaluate side-chains 123 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 69 LEU 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 419 GLN 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 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 283 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 28 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 38 optimal weight: 0.1980 chunk 93 optimal weight: 0.0470 chunk 64 optimal weight: 4.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.231236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.169821 restraints weight = 15266.468| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.30 r_work: 0.3782 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11680 Z= 0.110 Angle : 0.605 17.836 15870 Z= 0.284 Chirality : 0.043 0.156 1782 Planarity : 0.004 0.038 2098 Dihedral : 5.266 57.296 1662 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.61 % Allowed : 15.78 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.75 (0.22), residues: 1452 helix: 2.54 (0.20), residues: 586 sheet: 0.76 (0.32), residues: 274 loop : -0.01 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 395 HIS 0.004 0.001 HIS B 26 PHE 0.015 0.002 PHE B 222 TYR 0.018 0.001 TYR B 163 ARG 0.007 0.000 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 669) hydrogen bonds : angle 4.62414 ( 1893) covalent geometry : bond 0.00249 (11680) covalent geometry : angle 0.60496 (15870) *********************** 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 135 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2835 (mmm) cc_final: 0.2186 (mmm) REVERT: A 74 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: A 249 GLU cc_start: 0.8286 (tt0) cc_final: 0.8032 (mm-30) REVERT: A 380 ARG cc_start: 0.6467 (ttt180) cc_final: 0.6252 (tpp80) REVERT: A 436 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7575 (ttp-170) REVERT: A 492 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7919 (tt) REVERT: A 503 MET cc_start: 0.8542 (ppp) cc_final: 0.8248 (ppp) REVERT: B 113 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.6183 (mtm-85) outliers start: 20 outliers final: 13 residues processed: 129 average time/residue: 1.2693 time to fit residues: 177.7205 Evaluate side-chains 127 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 69 LEU 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 390 TYR Chi-restraints excluded: chain A residue 436 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 283 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 93 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 72 optimal weight: 20.0000 chunk 138 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 38 optimal weight: 0.4980 chunk 118 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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 = 0.229584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.180169 restraints weight = 15108.477| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 1.88 r_work: 0.3807 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11680 Z= 0.150 Angle : 0.627 15.412 15870 Z= 0.298 Chirality : 0.044 0.161 1782 Planarity : 0.004 0.038 2098 Dihedral : 5.352 54.371 1662 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.45 % Allowed : 16.51 % 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 (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: 1.63 (0.22), residues: 1452 helix: 2.47 (0.20), residues: 586 sheet: 0.60 (0.32), residues: 275 loop : -0.06 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 423 HIS 0.006 0.001 HIS B 26 PHE 0.018 0.002 PHE B 425 TYR 0.022 0.002 TYR B 163 ARG 0.010 0.000 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 669) hydrogen bonds : angle 4.75112 ( 1893) covalent geometry : bond 0.00354 (11680) covalent geometry : angle 0.62730 (15870) *********************** 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 127 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 1.285 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: 0.3204 (mmm) cc_final: 0.2323 (mmm) REVERT: A 74 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: A 249 GLU cc_start: 0.8282 (tt0) cc_final: 0.8046 (mm-30) REVERT: A 322 ARG cc_start: 0.7464 (tmm-80) cc_final: 0.7112 (ttp80) REVERT: A 492 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7980 (tt) outliers start: 18 outliers final: 10 residues processed: 122 average time/residue: 1.2514 time to fit residues: 166.3558 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 : 1.150 ------------------------------------------------------------------------------- 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 69 LEU 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 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 283 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 1 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 57 optimal weight: 20.0000 chunk 7 optimal weight: 0.6980 chunk 16 optimal weight: 0.0980 chunk 91 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.230690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.169246 restraints weight = 15171.632| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.87 r_work: 0.3766 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11680 Z= 0.115 Angle : 0.601 15.648 15870 Z= 0.284 Chirality : 0.043 0.171 1782 Planarity : 0.004 0.038 2098 Dihedral : 5.284 56.616 1662 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.45 % Allowed : 16.67 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.72 (0.22), residues: 1452 helix: 2.57 (0.20), residues: 586 sheet: 0.64 (0.32), residues: 274 loop : -0.04 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 271 HIS 0.005 0.001 HIS B 26 PHE 0.018 0.002 PHE A 123 TYR 0.019 0.001 TYR A 250 ARG 0.009 0.000 ARG A 362 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 669) hydrogen bonds : angle 4.63175 ( 1893) covalent geometry : bond 0.00262 (11680) covalent geometry : angle 0.60062 (15870) *********************** 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 127 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2789 (mmm) cc_final: 0.2155 (mmm) REVERT: A 74 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: A 249 GLU cc_start: 0.8288 (tt0) cc_final: 0.8039 (mm-30) REVERT: A 322 ARG cc_start: 0.7413 (tmm-80) cc_final: 0.7107 (ttp80) REVERT: A 492 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7914 (tt) outliers start: 18 outliers final: 10 residues processed: 121 average time/residue: 1.3186 time to fit residues: 173.5435 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 : 1.387 ------------------------------------------------------------------------------- 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 69 LEU 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 637 LEU Chi-restraints excluded: chain A residue 715 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 77 optimal weight: 0.0170 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 66 optimal weight: 0.0060 chunk 46 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 overall best weight: 0.4834 ------------------------------------------------------------------------------- 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 470 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.230676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3975 r_free = 0.3975 target = 0.169607 restraints weight = 15103.155| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.85 r_work: 0.3758 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11680 Z= 0.116 Angle : 0.610 15.528 15870 Z= 0.289 Chirality : 0.043 0.169 1782 Planarity : 0.004 0.073 2098 Dihedral : 5.273 56.936 1662 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.21 % Allowed : 17.15 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.73 (0.22), residues: 1452 helix: 2.57 (0.20), residues: 587 sheet: 0.65 (0.32), residues: 274 loop : -0.02 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 423 HIS 0.005 0.001 HIS B 26 PHE 0.025 0.002 PHE A 123 TYR 0.019 0.001 TYR A 250 ARG 0.013 0.000 ARG A 506 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 669) hydrogen bonds : angle 4.61336 ( 1893) covalent geometry : bond 0.00264 (11680) covalent geometry : angle 0.60967 (15870) ********************** 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 127 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2739 (mmm) cc_final: 0.2061 (mmm) REVERT: A 74 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: A 104 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7322 (pp20) REVERT: A 249 GLU cc_start: 0.8299 (tt0) cc_final: 0.8042 (mm-30) REVERT: A 321 ARG cc_start: 0.6892 (mtp-110) cc_final: 0.6324 (ttt180) REVERT: A 492 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7879 (tt) outliers start: 15 outliers final: 9 residues processed: 122 average time/residue: 2.0466 time to fit residues: 274.2553 Evaluate side-chains 120 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 1.780 ------------------------------------------------------------------------------- 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 69 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 715 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 109 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 143 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 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 = 0.4616 r_free = 0.4616 target = 0.229582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.169180 restraints weight = 14999.210| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.41 r_work: 0.3743 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11680 Z= 0.142 Angle : 0.625 14.983 15870 Z= 0.298 Chirality : 0.044 0.179 1782 Planarity : 0.004 0.045 2098 Dihedral : 5.333 54.352 1662 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.97 % Allowed : 17.63 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.65 (0.22), residues: 1452 helix: 2.54 (0.21), residues: 588 sheet: 0.53 (0.31), residues: 279 loop : -0.08 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 423 HIS 0.006 0.001 HIS B 26 PHE 0.027 0.002 PHE A 123 TYR 0.021 0.002 TYR B 163 ARG 0.011 0.000 ARG A 506 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 669) hydrogen bonds : angle 4.67369 ( 1893) covalent geometry : bond 0.00333 (11680) covalent geometry : angle 0.62489 (15870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10970.10 seconds wall clock time: 192 minutes 31.29 seconds (11551.29 seconds total)