Starting phenix.real_space_refine on Wed Sep 25 22:58:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eut_19981/09_2024/9eut_19981_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eut_19981/09_2024/9eut_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eut_19981/09_2024/9eut_19981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eut_19981/09_2024/9eut_19981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eut_19981/09_2024/9eut_19981_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eut_19981/09_2024/9eut_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.10, per 1000 atoms: 0.71 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: 3.15 Conformation dependent library (CDL) restraints added in 1.7 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: 1.47 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: 4.56 Time building geometry restraints manager: 3.70 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: 0.00 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: 10.390 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.470 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 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:14.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.290 ------------------------------------------------------------------------------- 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= 0.344 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 *********************** 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 fitting. rotamer outliers: 7 poor density : 205 time to evaluate : 1.205 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: 1.5553 time to fit residues: 348.0852 Evaluate side-chains 128 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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= 0.248 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 *********************** 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 fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3412 (mmm) cc_final: 0.2542 (mmm) REVERT: A 74 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: A 380 ARG cc_start: 0.6280 (ttt180) cc_final: 0.5794 (tmm160) REVERT: A 481 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8633 (mt) REVERT: A 484 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7496 (tttp) REVERT: B 1 MET cc_start: -0.1140 (mmm) cc_final: -0.1441 (mmm) REVERT: B 501 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7155 (t70) outliers start: 28 outliers final: 7 residues processed: 143 average time/residue: 1.4772 time to fit residues: 227.8340 Evaluate side-chains 116 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 1.660 ------------------------------------------------------------------------------- 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 481 ILE 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 501 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 30.0000 chunk 40 optimal weight: 6.9990 chunk 108 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 129 optimal weight: 30.0000 chunk 44 optimal weight: 7.9990 chunk 105 optimal weight: 0.0770 overall best weight: 2.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 135 GLN A 137 HIS A 146 ASN ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN B 61 GLN B 126 ASN ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 11680 Z= 0.481 Angle : 0.730 9.127 15870 Z= 0.365 Chirality : 0.049 0.175 1782 Planarity : 0.005 0.047 2098 Dihedral : 6.095 61.342 1662 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.58 % Allowed : 14.01 % Favored : 83.41 % 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: 1.05 (0.22), residues: 1452 helix: 1.87 (0.20), residues: 581 sheet: 0.55 (0.31), residues: 272 loop : -0.36 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 423 HIS 0.012 0.001 HIS B 26 PHE 0.032 0.003 PHE B 222 TYR 0.028 0.003 TYR B 163 ARG 0.007 0.001 ARG A 701 *********************** 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 fitting. rotamer outliers: 32 poor density : 111 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3473 (mmm) cc_final: 0.2591 (mmm) REVERT: A 74 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: A 380 ARG cc_start: 0.6394 (ttt180) cc_final: 0.5939 (tmm160) REVERT: A 436 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7669 (ttp-170) REVERT: A 481 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8651 (mp) REVERT: A 484 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7651 (tttp) REVERT: A 492 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7892 (tt) REVERT: B 1 MET cc_start: -0.1241 (mmm) cc_final: -0.1576 (mmm) REVERT: B 501 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7098 (t70) outliers start: 32 outliers final: 9 residues processed: 132 average time/residue: 1.3744 time to fit residues: 196.4946 Evaluate side-chains 119 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 436 ARG Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 484 LYS 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 501 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.3980 chunk 98 optimal weight: 0.4980 chunk 67 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 87 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 B 93 HIS B 556 GLN B 580 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2874 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= 0.177 Angle : 0.580 10.574 15870 Z= 0.286 Chirality : 0.043 0.161 1782 Planarity : 0.004 0.037 2098 Dihedral : 5.621 57.449 1662 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.33 % Allowed : 14.57 % 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 (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: 1.38 (0.22), residues: 1452 helix: 2.25 (0.20), residues: 583 sheet: 0.64 (0.32), residues: 272 loop : -0.25 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 426 HIS 0.004 0.001 HIS A 26 PHE 0.023 0.002 PHE B 222 TYR 0.020 0.002 TYR A 250 ARG 0.014 0.000 ARG A 614 *********************** 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 149 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 1.187 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: 0.3428 (mmm) cc_final: 0.2560 (mmm) REVERT: A 74 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: A 380 ARG cc_start: 0.6366 (ttt180) cc_final: 0.5907 (tmm160) REVERT: A 490 MET cc_start: 0.7480 (ttp) cc_final: 0.7196 (ttp) REVERT: A 492 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7790 (tt) REVERT: B 1 MET cc_start: -0.1238 (mmm) cc_final: -0.1554 (mmm) REVERT: B 113 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.5912 (mtm180) outliers start: 29 outliers final: 9 residues processed: 137 average time/residue: 1.1946 time to fit residues: 177.6917 Evaluate side-chains 117 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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 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 113 ARG Chi-restraints excluded: chain B residue 184 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 118 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 71 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11680 Z= 0.237 Angle : 0.610 12.830 15870 Z= 0.294 Chirality : 0.044 0.176 1782 Planarity : 0.004 0.049 2098 Dihedral : 5.518 54.367 1662 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.66 % Allowed : 14.98 % Favored : 82.37 % 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: 1.49 (0.22), residues: 1452 helix: 2.39 (0.20), residues: 584 sheet: 0.67 (0.32), residues: 272 loop : -0.25 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 271 HIS 0.006 0.001 HIS B 26 PHE 0.021 0.002 PHE B 222 TYR 0.021 0.002 TYR B 163 ARG 0.011 0.000 ARG B 380 *********************** 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 145 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 112 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3432 (mmm) cc_final: 0.2562 (mmm) REVERT: A 74 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: A 380 ARG cc_start: 0.6406 (ttt180) cc_final: 0.5937 (tmm160) REVERT: A 492 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7798 (tt) REVERT: A 511 LEU cc_start: 0.5768 (mt) cc_final: 0.5408 (tt) REVERT: B 1 MET cc_start: -0.1317 (mmm) cc_final: -0.1661 (mmm) REVERT: B 113 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.5978 (mtm180) outliers start: 33 outliers final: 12 residues processed: 133 average time/residue: 1.1386 time to fit residues: 165.4095 Evaluate side-chains 124 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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 124 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 455 THR 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 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 113 ARG 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 46 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 0.0010 chunk 139 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3250 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= 0.238 Angle : 0.606 12.547 15870 Z= 0.294 Chirality : 0.044 0.155 1782 Planarity : 0.004 0.058 2098 Dihedral : 5.500 54.461 1662 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.17 % Allowed : 15.78 % 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: 1.50 (0.22), residues: 1452 helix: 2.43 (0.20), residues: 585 sheet: 0.64 (0.32), residues: 274 loop : -0.28 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 426 HIS 0.006 0.001 HIS B 26 PHE 0.020 0.002 PHE B 222 TYR 0.023 0.002 TYR A 250 ARG 0.012 0.000 ARG A 506 *********************** 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 142 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3434 (mmm) cc_final: 0.2557 (mmm) REVERT: A 74 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: A 380 ARG cc_start: 0.6409 (ttt180) cc_final: 0.5957 (tmm160) REVERT: A 484 LYS cc_start: 0.7871 (tttp) cc_final: 0.7595 (ttmm) REVERT: A 492 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7821 (tt) REVERT: B 1 MET cc_start: -0.1309 (mmm) cc_final: -0.1638 (mmm) REVERT: B 113 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6037 (mtm180) outliers start: 27 outliers final: 13 residues processed: 131 average time/residue: 1.1347 time to fit residues: 162.7727 Evaluate side-chains 122 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 455 THR 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 B residue 64 VAL 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 276 CYS Chi-restraints excluded: chain B residue 493 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 138 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3397 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= 0.231 Angle : 0.620 18.777 15870 Z= 0.297 Chirality : 0.044 0.154 1782 Planarity : 0.004 0.047 2098 Dihedral : 5.464 54.393 1662 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.69 % Allowed : 16.75 % 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 (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: 1.52 (0.22), residues: 1452 helix: 2.43 (0.20), residues: 585 sheet: 0.64 (0.32), residues: 275 loop : -0.24 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 426 HIS 0.005 0.001 HIS B 26 PHE 0.019 0.002 PHE B 222 TYR 0.021 0.002 TYR A 250 ARG 0.010 0.000 ARG A 614 *********************** 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 fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3428 (mmm) cc_final: 0.2553 (mmm) REVERT: A 74 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: A 380 ARG cc_start: 0.6363 (ttt180) cc_final: 0.5933 (tmm160) REVERT: A 492 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7786 (tt) REVERT: A 614 ARG cc_start: 0.8526 (mmp80) cc_final: 0.8277 (mmp80) REVERT: B 1 MET cc_start: -0.1317 (mmm) cc_final: -0.1653 (mmm) REVERT: B 113 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6090 (mtm180) outliers start: 21 outliers final: 11 residues processed: 127 average time/residue: 1.2194 time to fit residues: 169.7460 Evaluate side-chains 122 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 1.652 ------------------------------------------------------------------------------- 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 455 THR 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 113 ARG Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 493 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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 26 HIS B 61 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3508 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= 0.204 Angle : 0.613 16.122 15870 Z= 0.292 Chirality : 0.043 0.154 1782 Planarity : 0.004 0.036 2098 Dihedral : 5.386 54.350 1662 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.61 % Allowed : 17.23 % 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 (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: 1.57 (0.22), residues: 1452 helix: 2.48 (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 TRP 0.012 0.001 TRP B 395 HIS 0.005 0.001 HIS B 26 PHE 0.018 0.002 PHE B 222 TYR 0.020 0.002 TYR A 250 ARG 0.010 0.000 ARG A 614 *********************** 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 131 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3441 (mmm) cc_final: 0.2544 (mmm) REVERT: A 74 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: A 150 GLU cc_start: 0.7987 (tp30) cc_final: 0.7779 (tp30) REVERT: A 492 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7791 (tt) REVERT: B 1 MET cc_start: -0.1276 (mmm) cc_final: -0.1615 (mmm) outliers start: 20 outliers final: 13 residues processed: 126 average time/residue: 1.1616 time to fit residues: 159.6490 Evaluate side-chains 121 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 48 LEU 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 455 THR 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 276 CYS Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 493 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 56 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3579 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= 0.242 Angle : 0.628 15.746 15870 Z= 0.300 Chirality : 0.044 0.162 1782 Planarity : 0.004 0.040 2098 Dihedral : 5.427 54.542 1662 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.53 % Allowed : 17.55 % Favored : 80.92 % 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: 1.53 (0.22), residues: 1452 helix: 2.46 (0.21), residues: 585 sheet: 0.64 (0.32), residues: 275 loop : -0.24 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 426 HIS 0.005 0.001 HIS A 100 PHE 0.025 0.002 PHE A 123 TYR 0.021 0.002 TYR A 250 ARG 0.009 0.000 ARG A 614 *********************** 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 132 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3399 (mmm) cc_final: 0.2463 (mmm) REVERT: A 74 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: A 104 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7143 (pp20) REVERT: A 492 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7785 (tt) REVERT: B 1 MET cc_start: -0.1270 (mmm) cc_final: -0.1683 (mmm) outliers start: 19 outliers final: 11 residues processed: 127 average time/residue: 1.2710 time to fit residues: 175.5358 Evaluate side-chains 120 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 455 THR 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 276 CYS Chi-restraints excluded: chain B residue 493 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.6980 chunk 83 optimal weight: 0.0570 chunk 64 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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** A 417 HIS B 61 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11680 Z= 0.214 Angle : 0.631 15.704 15870 Z= 0.300 Chirality : 0.044 0.194 1782 Planarity : 0.004 0.038 2098 Dihedral : 5.384 54.091 1662 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.45 % Allowed : 17.71 % 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 (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: 1.56 (0.22), residues: 1452 helix: 2.45 (0.21), residues: 585 sheet: 0.67 (0.32), residues: 275 loop : -0.20 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 426 HIS 0.004 0.001 HIS A 26 PHE 0.027 0.002 PHE A 123 TYR 0.020 0.002 TYR A 250 ARG 0.009 0.000 ARG A 362 ********************** 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 129 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3402 (mmm) cc_final: 0.2453 (mmm) REVERT: A 74 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6931 (mp0) REVERT: A 104 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7164 (pp20) REVERT: A 323 LEU cc_start: 0.8245 (mp) cc_final: 0.7995 (mm) REVERT: A 492 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7791 (tt) REVERT: B 1 MET cc_start: -0.1189 (mmm) cc_final: -0.1652 (mmm) outliers start: 18 outliers final: 13 residues processed: 124 average time/residue: 1.1401 time to fit residues: 154.2791 Evaluate side-chains 123 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.234 ------------------------------------------------------------------------------- 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 455 THR 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 269 LYS Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 493 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 117 optimal weight: 0.0020 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 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 = 0.4612 r_free = 0.4612 target = 0.229061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3951 r_free = 0.3951 target = 0.167303 restraints weight = 14941.309| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.87 r_work: 0.3726 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3727 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= 0.215 Angle : 0.624 15.481 15870 Z= 0.297 Chirality : 0.044 0.193 1782 Planarity : 0.004 0.072 2098 Dihedral : 5.367 54.113 1662 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.53 % Allowed : 17.63 % 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 (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: 1.59 (0.22), residues: 1452 helix: 2.48 (0.21), residues: 585 sheet: 0.67 (0.32), residues: 275 loop : -0.19 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 426 HIS 0.004 0.001 HIS A 26 PHE 0.026 0.002 PHE A 123 TYR 0.020 0.002 TYR A 250 ARG 0.009 0.000 ARG A 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4514.89 seconds wall clock time: 80 minutes 10.48 seconds (4810.48 seconds total)