Starting phenix.real_space_refine on Wed Mar 4 00:29:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xf5_33169/03_2026/7xf5_33169.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xf5_33169/03_2026/7xf5_33169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xf5_33169/03_2026/7xf5_33169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xf5_33169/03_2026/7xf5_33169.map" model { file = "/net/cci-nas-00/data/ceres_data/7xf5_33169/03_2026/7xf5_33169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xf5_33169/03_2026/7xf5_33169.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 57 5.16 5 C 6294 2.51 5 N 1615 2.21 5 O 1674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9640 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 4837 Classifications: {'peptide': 622} Link IDs: {'PTRANS': 29, 'TRANS': 592} Chain breaks: 3 Chain: "B" Number of atoms: 4803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4803 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 28, 'TRANS': 588} Chain breaks: 3 Time building chain proxies: 2.29, per 1000 atoms: 0.24 Number of scatterers: 9640 At special positions: 0 Unit cell: (111.915, 113.573, 116.06, 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 57 16.00 O 1674 8.00 N 1615 7.00 C 6294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 462.8 milliseconds 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2312 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 3 sheets defined 74.6% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 89 through 126 Processing helix chain 'A' and resid 129 through 156 Proline residue: A 141 - end of helix Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 181 through 198 Processing helix chain 'A' and resid 204 through 225 Processing helix chain 'A' and resid 226 through 231 removed outlier: 6.910A pdb=" N ILE A 229 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 253 removed outlier: 3.609A pdb=" N PHE A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.614A pdb=" N SER A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 296 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 320 through 352 removed outlier: 3.514A pdb=" N GLN A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 362 Processing helix chain 'A' and resid 364 through 378 removed outlier: 3.556A pdb=" N ALA A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.726A pdb=" N GLN A 385 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 419 through 425 Processing helix chain 'A' and resid 430 through 450 removed outlier: 4.142A pdb=" N TRP A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 481 Processing helix chain 'A' and resid 495 through 513 removed outlier: 3.872A pdb=" N TYR A 499 " --> pdb=" O VAL A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 removed outlier: 4.425A pdb=" N VAL A 519 " --> pdb=" O VAL A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 549 Processing helix chain 'A' and resid 551 through 560 Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.828A pdb=" N TYR A 576 " --> pdb=" O HIS A 573 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 578 " --> pdb=" O GLN A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 584 Processing helix chain 'A' and resid 596 through 607 removed outlier: 4.203A pdb=" N LEU A 600 " --> pdb=" O THR A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 640 removed outlier: 3.643A pdb=" N LEU A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 648 removed outlier: 3.706A pdb=" N ARG A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 778 removed outlier: 4.057A pdb=" N ILE A 771 " --> pdb=" O SER A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 814 removed outlier: 3.709A pdb=" N LEU A 813 " --> pdb=" O ILE A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 844 removed outlier: 4.120A pdb=" N LEU A 835 " --> pdb=" O THR A 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 126 removed outlier: 3.514A pdb=" N LEU B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 156 Proline residue: B 141 - end of helix Processing helix chain 'B' and resid 157 through 160 Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 181 through 198 Processing helix chain 'B' and resid 204 through 225 removed outlier: 3.854A pdb=" N LEU B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 removed outlier: 7.085A pdb=" N ILE B 229 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR B 230 " --> pdb=" O GLY B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 253 removed outlier: 3.647A pdb=" N PHE B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 removed outlier: 3.716A pdb=" N VAL B 259 " --> pdb=" O PRO B 255 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 267 " --> pdb=" O ILE B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 296 Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 320 through 352 Processing helix chain 'B' and resid 352 through 363 Processing helix chain 'B' and resid 364 through 378 removed outlier: 3.574A pdb=" N ALA B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 386 removed outlier: 3.674A pdb=" N GLN B 385 " --> pdb=" O GLY B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 430 through 450 removed outlier: 4.073A pdb=" N TRP B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 481 Processing helix chain 'B' and resid 495 through 513 removed outlier: 3.866A pdb=" N TYR B 499 " --> pdb=" O VAL B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 526 Processing helix chain 'B' and resid 530 through 549 Processing helix chain 'B' and resid 551 through 560 Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.847A pdb=" N TYR B 576 " --> pdb=" O HIS B 573 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 578 " --> pdb=" O GLN B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 584 removed outlier: 3.576A pdb=" N MET B 584 " --> pdb=" O GLU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 607 removed outlier: 3.867A pdb=" N LEU B 600 " --> pdb=" O THR B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 640 removed outlier: 3.751A pdb=" N LEU B 640 " --> pdb=" O LEU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 648 removed outlier: 4.552A pdb=" N ARG B 645 " --> pdb=" O SER B 641 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS B 648 " --> pdb=" O ARG B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 778 Processing helix chain 'B' and resid 802 through 810 Processing helix chain 'B' and resid 832 through 841 Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA2, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA3, first strand: chain 'B' and resid 485 through 487 649 hydrogen bonds defined for protein. 1860 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.43 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3038 1.34 - 1.46: 2194 1.46 - 1.58: 4533 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 9861 Sorted by residual: bond pdb=" CA LEU B 812 " pdb=" C LEU B 812 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.34e-02 5.57e+03 4.52e+00 bond pdb=" CA LEU B 813 " pdb=" C LEU B 813 " ideal model delta sigma weight residual 1.521 1.503 0.018 1.36e-02 5.41e+03 1.71e+00 bond pdb=" N ILE B 170 " pdb=" CA ILE B 170 " ideal model delta sigma weight residual 1.461 1.447 0.014 1.19e-02 7.06e+03 1.34e+00 bond pdb=" C LYS B 168 " pdb=" O LYS B 168 " ideal model delta sigma weight residual 1.237 1.223 0.014 1.19e-02 7.06e+03 1.30e+00 bond pdb=" C THR B 169 " pdb=" O THR B 169 " ideal model delta sigma weight residual 1.237 1.223 0.014 1.19e-02 7.06e+03 1.30e+00 ... (remaining 9856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 13301 2.71 - 5.43: 86 5.43 - 8.14: 8 8.14 - 10.86: 3 10.86 - 13.57: 1 Bond angle restraints: 13399 Sorted by residual: angle pdb=" N LEU B 813 " pdb=" CA LEU B 813 " pdb=" C LEU B 813 " ideal model delta sigma weight residual 113.41 99.84 13.57 1.22e+00 6.72e-01 1.24e+02 angle pdb=" N SER B 811 " pdb=" CA SER B 811 " pdb=" C SER B 811 " ideal model delta sigma weight residual 114.64 109.05 5.59 1.52e+00 4.33e-01 1.35e+01 angle pdb=" N PHE B 810 " pdb=" CA PHE B 810 " pdb=" C PHE B 810 " ideal model delta sigma weight residual 113.37 108.50 4.87 1.38e+00 5.25e-01 1.25e+01 angle pdb=" CB MET A 167 " pdb=" CG MET A 167 " pdb=" SD MET A 167 " ideal model delta sigma weight residual 112.70 104.08 8.62 3.00e+00 1.11e-01 8.26e+00 angle pdb=" C TYR B 230 " pdb=" N GLU B 231 " pdb=" CA GLU B 231 " ideal model delta sigma weight residual 121.94 116.23 5.71 2.00e+00 2.50e-01 8.16e+00 ... (remaining 13394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 5322 17.22 - 34.43: 377 34.43 - 51.65: 81 51.65 - 68.87: 27 68.87 - 86.08: 22 Dihedral angle restraints: 5829 sinusoidal: 2262 harmonic: 3567 Sorted by residual: dihedral pdb=" CB GLU B 166 " pdb=" CG GLU B 166 " pdb=" CD GLU B 166 " pdb=" OE1 GLU B 166 " ideal model delta sinusoidal sigma weight residual 0.00 -85.33 85.33 1 3.00e+01 1.11e-03 9.80e+00 dihedral pdb=" CA LEU B 813 " pdb=" CB LEU B 813 " pdb=" CG LEU B 813 " pdb=" CD1 LEU B 813 " ideal model delta sinusoidal sigma weight residual 60.00 116.27 -56.27 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" CG ARG A 558 " pdb=" CD ARG A 558 " pdb=" NE ARG A 558 " pdb=" CZ ARG A 558 " ideal model delta sinusoidal sigma weight residual -180.00 -138.50 -41.50 2 1.50e+01 4.44e-03 9.37e+00 ... (remaining 5826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1194 0.043 - 0.085: 298 0.085 - 0.127: 79 0.127 - 0.170: 5 0.170 - 0.212: 2 Chirality restraints: 1578 Sorted by residual: chirality pdb=" CA LEU B 813 " pdb=" N LEU B 813 " pdb=" C LEU B 813 " pdb=" CB LEU B 813 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA LEU B 812 " pdb=" N LEU B 812 " pdb=" C LEU B 812 " pdb=" CB LEU B 812 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CA GLU B 231 " pdb=" N GLU B 231 " pdb=" C GLU B 231 " pdb=" CB GLU B 231 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 1575 not shown) Planarity restraints: 1671 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 444 " -0.019 2.00e-02 2.50e+03 1.45e-02 5.28e+00 pdb=" CG TRP A 444 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 444 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 444 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 444 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 444 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 444 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 444 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 444 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 444 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 444 " 0.012 2.00e-02 2.50e+03 1.25e-02 3.89e+00 pdb=" CG TRP B 444 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 444 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 444 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 444 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 444 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 444 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 444 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 444 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 444 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 379 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO B 380 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 380 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 380 " -0.022 5.00e-02 4.00e+02 ... (remaining 1668 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1459 2.76 - 3.29: 9581 3.29 - 3.83: 16013 3.83 - 4.36: 17154 4.36 - 4.90: 30157 Nonbonded interactions: 74364 Sorted by model distance: nonbonded pdb=" OE2 GLU A 320 " pdb=" OH TYR A 499 " model vdw 2.222 3.040 nonbonded pdb=" OE2 GLU B 320 " pdb=" OH TYR B 499 " model vdw 2.226 3.040 nonbonded pdb=" O GLU A 166 " pdb=" OG1 THR A 169 " model vdw 2.233 3.040 nonbonded pdb=" O ASP A 402 " pdb=" NH1 ARG A 471 " model vdw 2.284 3.120 nonbonded pdb=" O ARG B 601 " pdb=" ND1 HIS B 605 " model vdw 2.308 3.120 ... (remaining 74359 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' and (resid 89 through 649 or resid 769 through 845)) 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.660 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9861 Z= 0.142 Angle : 0.607 13.571 13399 Z= 0.348 Chirality : 0.040 0.212 1578 Planarity : 0.004 0.040 1671 Dihedral : 14.141 86.085 3517 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.63 % Rotamer: Outliers : 0.58 % Allowed : 0.29 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.24), residues: 1223 helix: 1.51 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -0.93 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 277 TYR 0.016 0.001 TYR A 140 PHE 0.021 0.001 PHE B 147 TRP 0.040 0.001 TRP A 444 HIS 0.012 0.001 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9861) covalent geometry : angle 0.60673 (13399) hydrogen bonds : bond 0.14173 ( 649) hydrogen bonds : angle 5.60635 ( 1860) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 344 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 HIS cc_start: 0.7891 (t-170) cc_final: 0.7565 (t70) REVERT: A 239 MET cc_start: 0.7214 (mmt) cc_final: 0.6759 (ptm) REVERT: A 309 ARG cc_start: 0.6994 (ttp-170) cc_final: 0.6200 (mtm110) REVERT: A 340 TYR cc_start: 0.6818 (t80) cc_final: 0.6472 (t80) REVERT: A 374 ILE cc_start: 0.8639 (tt) cc_final: 0.8155 (mt) REVERT: A 439 ILE cc_start: 0.8192 (mm) cc_final: 0.7980 (mt) REVERT: A 531 ILE cc_start: 0.9316 (tt) cc_final: 0.9045 (tt) REVERT: A 549 GLN cc_start: 0.7704 (tp-100) cc_final: 0.7359 (tt0) REVERT: A 558 ARG cc_start: 0.6490 (mmt180) cc_final: 0.5991 (mtt-85) REVERT: A 801 THR cc_start: 0.5389 (m) cc_final: 0.5177 (m) REVERT: B 219 LEU cc_start: 0.8581 (tp) cc_final: 0.8373 (tp) REVERT: B 374 ILE cc_start: 0.8657 (tt) cc_final: 0.8180 (mt) REVERT: B 558 ARG cc_start: 0.6348 (mmt180) cc_final: 0.5626 (mtt180) REVERT: B 815 VAL cc_start: 0.5453 (OUTLIER) cc_final: 0.5240 (m) outliers start: 6 outliers final: 1 residues processed: 347 average time/residue: 0.1005 time to fit residues: 47.9802 Evaluate side-chains 217 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 215 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 815 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.0470 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.0010 chunk 117 optimal weight: 1.9990 overall best weight: 0.7286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 HIS A 546 GLN ** B 549 GLN ** 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 = 0.4396 r_free = 0.4396 target = 0.209287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.164117 restraints weight = 15871.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.167998 restraints weight = 8785.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.170708 restraints weight = 5998.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.172243 restraints weight = 4675.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.173487 restraints weight = 4031.270| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9861 Z= 0.142 Angle : 0.581 9.254 13399 Z= 0.294 Chirality : 0.043 0.218 1578 Planarity : 0.004 0.035 1671 Dihedral : 4.112 50.889 1324 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.84 % Allowed : 9.22 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.25), residues: 1223 helix: 1.76 (0.18), residues: 839 sheet: None (None), residues: 0 loop : -0.70 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 361 TYR 0.018 0.001 TYR B 134 PHE 0.017 0.002 PHE A 306 TRP 0.018 0.001 TRP A 444 HIS 0.003 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9861) covalent geometry : angle 0.58112 (13399) hydrogen bonds : bond 0.04342 ( 649) hydrogen bonds : angle 4.10930 ( 1860) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 234 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.7039 (mmm) cc_final: 0.6800 (mmm) REVERT: A 283 THR cc_start: 0.8229 (m) cc_final: 0.7866 (p) REVERT: A 344 LYS cc_start: 0.8173 (mmmm) cc_final: 0.7933 (mmmt) REVERT: A 374 ILE cc_start: 0.8658 (tt) cc_final: 0.8192 (mt) REVERT: A 385 GLN cc_start: 0.8151 (pt0) cc_final: 0.7902 (pt0) REVERT: A 477 MET cc_start: 0.7643 (mmm) cc_final: 0.7441 (mmm) REVERT: A 558 ARG cc_start: 0.6541 (mmt180) cc_final: 0.5940 (mtt-85) REVERT: B 215 CYS cc_start: 0.6718 (p) cc_final: 0.6437 (p) REVERT: B 274 ASN cc_start: 0.7922 (m-40) cc_final: 0.7637 (m-40) REVERT: B 374 ILE cc_start: 0.8607 (tt) cc_final: 0.8283 (mt) REVERT: B 385 GLN cc_start: 0.8203 (pt0) cc_final: 0.8000 (pt0) REVERT: B 395 GLU cc_start: 0.7615 (pm20) cc_final: 0.7390 (mp0) REVERT: B 515 VAL cc_start: 0.8870 (t) cc_final: 0.8444 (m) REVERT: B 558 ARG cc_start: 0.6378 (mmt180) cc_final: 0.5874 (mtt-85) REVERT: B 815 VAL cc_start: 0.5510 (OUTLIER) cc_final: 0.5309 (m) outliers start: 19 outliers final: 14 residues processed: 246 average time/residue: 0.0996 time to fit residues: 33.9521 Evaluate side-chains 222 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 207 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 815 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 108 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 GLN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** 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 = 0.4376 r_free = 0.4376 target = 0.207554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.163089 restraints weight = 15750.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.167002 restraints weight = 8653.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.169642 restraints weight = 5812.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.171212 restraints weight = 4508.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.172331 restraints weight = 3849.543| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9861 Z= 0.122 Angle : 0.545 15.179 13399 Z= 0.274 Chirality : 0.042 0.169 1578 Planarity : 0.004 0.034 1671 Dihedral : 3.626 37.421 1322 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.43 % Allowed : 11.26 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.24), residues: 1223 helix: 1.80 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -0.55 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 277 TYR 0.018 0.001 TYR A 140 PHE 0.018 0.002 PHE A 289 TRP 0.011 0.001 TRP A 444 HIS 0.006 0.001 HIS B 807 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9861) covalent geometry : angle 0.54467 (13399) hydrogen bonds : bond 0.04024 ( 649) hydrogen bonds : angle 3.93268 ( 1860) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.7126 (mmm) cc_final: 0.6898 (mmm) REVERT: A 314 PHE cc_start: 0.5699 (m-80) cc_final: 0.5389 (m-80) REVERT: A 374 ILE cc_start: 0.8596 (tt) cc_final: 0.8165 (mt) REVERT: A 385 GLN cc_start: 0.8111 (pt0) cc_final: 0.7857 (pt0) REVERT: A 558 ARG cc_start: 0.6563 (mmt180) cc_final: 0.6177 (mmt180) REVERT: B 167 MET cc_start: 0.7130 (mmp) cc_final: 0.6872 (mmm) REVERT: B 385 GLN cc_start: 0.8211 (pt0) cc_final: 0.7984 (pt0) REVERT: B 395 GLU cc_start: 0.7560 (pm20) cc_final: 0.7341 (mp0) REVERT: B 558 ARG cc_start: 0.6432 (mmt180) cc_final: 0.6022 (mmt180) outliers start: 25 outliers final: 16 residues processed: 239 average time/residue: 0.0919 time to fit residues: 31.2584 Evaluate side-chains 215 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 806 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 54 optimal weight: 30.0000 chunk 73 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 49 optimal weight: 0.0670 chunk 70 optimal weight: 1.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN ** B 133 GLN ** 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 = 0.4355 r_free = 0.4355 target = 0.205394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.161138 restraints weight = 15852.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.164975 restraints weight = 8605.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.167518 restraints weight = 5838.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.169129 restraints weight = 4567.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.170258 restraints weight = 3907.007| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9861 Z= 0.122 Angle : 0.563 14.344 13399 Z= 0.278 Chirality : 0.042 0.295 1578 Planarity : 0.004 0.033 1671 Dihedral : 3.435 15.696 1321 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.62 % Allowed : 12.23 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.24), residues: 1223 helix: 1.74 (0.18), residues: 839 sheet: None (None), residues: 0 loop : -0.72 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 297 TYR 0.013 0.001 TYR B 134 PHE 0.021 0.001 PHE B 289 TRP 0.011 0.001 TRP B 276 HIS 0.004 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9861) covalent geometry : angle 0.56304 (13399) hydrogen bonds : bond 0.03979 ( 649) hydrogen bonds : angle 3.92776 ( 1860) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 HIS cc_start: 0.7870 (t-90) cc_final: 0.7552 (t-170) REVERT: A 314 PHE cc_start: 0.5743 (m-80) cc_final: 0.5459 (m-80) REVERT: A 385 GLN cc_start: 0.8105 (pt0) cc_final: 0.7870 (pt0) REVERT: A 477 MET cc_start: 0.7344 (mmm) cc_final: 0.7091 (mmm) REVERT: B 167 MET cc_start: 0.7332 (mmp) cc_final: 0.7036 (mmm) REVERT: B 218 LEU cc_start: 0.7096 (tt) cc_final: 0.6167 (mt) REVERT: B 558 ARG cc_start: 0.6563 (mmt180) cc_final: 0.6135 (mmt180) REVERT: B 807 HIS cc_start: 0.5549 (t-90) cc_final: 0.5309 (t-170) outliers start: 27 outliers final: 20 residues processed: 231 average time/residue: 0.0925 time to fit residues: 30.2240 Evaluate side-chains 227 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 555 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 5 optimal weight: 0.0270 chunk 113 optimal weight: 0.0980 chunk 57 optimal weight: 0.0570 chunk 44 optimal weight: 0.7980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN A 530 HIS B 133 GLN B 422 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.206862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.161638 restraints weight = 15710.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.165446 restraints weight = 8705.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.168070 restraints weight = 5957.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.169785 restraints weight = 4654.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.170704 restraints weight = 3966.144| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9861 Z= 0.108 Angle : 0.538 15.648 13399 Z= 0.265 Chirality : 0.041 0.185 1578 Planarity : 0.004 0.034 1671 Dihedral : 3.368 14.649 1321 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.94 % Allowed : 14.47 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.24), residues: 1223 helix: 1.84 (0.18), residues: 833 sheet: None (None), residues: 0 loop : -0.51 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 297 TYR 0.012 0.001 TYR B 134 PHE 0.025 0.001 PHE B 279 TRP 0.012 0.001 TRP B 276 HIS 0.004 0.000 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9861) covalent geometry : angle 0.53753 (13399) hydrogen bonds : bond 0.03739 ( 649) hydrogen bonds : angle 3.87949 ( 1860) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 221 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 HIS cc_start: 0.7950 (t-90) cc_final: 0.7521 (t-90) REVERT: A 314 PHE cc_start: 0.5693 (m-80) cc_final: 0.5393 (m-80) REVERT: A 477 MET cc_start: 0.7453 (mmm) cc_final: 0.7216 (mmm) REVERT: A 558 ARG cc_start: 0.6473 (mmt180) cc_final: 0.5810 (mtt-85) REVERT: B 90 ASP cc_start: 0.6385 (p0) cc_final: 0.5805 (m-30) REVERT: B 277 ARG cc_start: 0.6838 (mtp85) cc_final: 0.6472 (mtm180) outliers start: 20 outliers final: 16 residues processed: 226 average time/residue: 0.0872 time to fit residues: 28.0362 Evaluate side-chains 218 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 515 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 46 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 chunk 103 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 95 optimal weight: 0.0370 chunk 55 optimal weight: 7.9990 chunk 30 optimal weight: 0.1980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.206267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.160658 restraints weight = 15709.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.164545 restraints weight = 8671.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.167302 restraints weight = 5906.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.168710 restraints weight = 4584.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.169903 restraints weight = 3990.600| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9861 Z= 0.113 Angle : 0.539 14.180 13399 Z= 0.266 Chirality : 0.040 0.174 1578 Planarity : 0.004 0.034 1671 Dihedral : 3.344 14.198 1321 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.14 % Allowed : 15.05 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.24), residues: 1223 helix: 1.82 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -0.47 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 277 TYR 0.014 0.001 TYR A 140 PHE 0.022 0.001 PHE A 287 TRP 0.011 0.001 TRP B 276 HIS 0.004 0.000 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9861) covalent geometry : angle 0.53929 (13399) hydrogen bonds : bond 0.03704 ( 649) hydrogen bonds : angle 3.85358 ( 1860) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 HIS cc_start: 0.7944 (t-90) cc_final: 0.7624 (t-170) REVERT: A 558 ARG cc_start: 0.6530 (mmt180) cc_final: 0.6325 (mmt180) REVERT: B 90 ASP cc_start: 0.6184 (p0) cc_final: 0.5761 (m-30) REVERT: B 218 LEU cc_start: 0.7187 (tt) cc_final: 0.6367 (mt) REVERT: B 558 ARG cc_start: 0.6254 (mmt180) cc_final: 0.5642 (mtt-85) outliers start: 22 outliers final: 17 residues processed: 221 average time/residue: 0.0907 time to fit residues: 28.3802 Evaluate side-chains 226 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 515 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 104 optimal weight: 0.1980 chunk 28 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.204171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.158186 restraints weight = 15739.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.161996 restraints weight = 8884.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.164579 restraints weight = 6123.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.166245 restraints weight = 4830.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.167114 restraints weight = 4160.565| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9861 Z= 0.113 Angle : 0.554 16.187 13399 Z= 0.271 Chirality : 0.041 0.166 1578 Planarity : 0.004 0.035 1671 Dihedral : 3.337 14.065 1321 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.04 % Allowed : 16.50 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.25), residues: 1223 helix: 1.82 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -0.42 (0.34), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 343 TYR 0.019 0.001 TYR A 140 PHE 0.023 0.001 PHE A 289 TRP 0.013 0.001 TRP B 276 HIS 0.006 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9861) covalent geometry : angle 0.55369 (13399) hydrogen bonds : bond 0.03718 ( 649) hydrogen bonds : angle 3.88935 ( 1860) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.7019 (mmm) cc_final: 0.6600 (mmm) REVERT: A 186 ILE cc_start: 0.8472 (mm) cc_final: 0.8265 (mm) REVERT: A 210 HIS cc_start: 0.8010 (t-90) cc_final: 0.7739 (t-170) REVERT: A 284 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6894 (m-80) REVERT: A 314 PHE cc_start: 0.5642 (m-80) cc_final: 0.5323 (m-80) REVERT: A 558 ARG cc_start: 0.6623 (mmt180) cc_final: 0.6406 (mmt180) REVERT: B 90 ASP cc_start: 0.6291 (p0) cc_final: 0.5624 (m-30) REVERT: B 277 ARG cc_start: 0.7020 (mtp85) cc_final: 0.6706 (mtm180) REVERT: B 453 PRO cc_start: 0.8393 (Cg_endo) cc_final: 0.8137 (Cg_exo) outliers start: 21 outliers final: 18 residues processed: 225 average time/residue: 0.0909 time to fit residues: 28.8708 Evaluate side-chains 227 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 515 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 97 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.202818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.155738 restraints weight = 15780.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.159465 restraints weight = 8834.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.162099 restraints weight = 6111.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.163734 restraints weight = 4823.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.164373 restraints weight = 4172.812| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9861 Z= 0.121 Angle : 0.561 15.360 13399 Z= 0.279 Chirality : 0.041 0.190 1578 Planarity : 0.004 0.034 1671 Dihedral : 3.391 14.536 1321 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.33 % Allowed : 16.41 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.25), residues: 1223 helix: 1.83 (0.18), residues: 836 sheet: None (None), residues: 0 loop : -0.41 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 235 TYR 0.021 0.001 TYR A 140 PHE 0.023 0.001 PHE A 287 TRP 0.012 0.001 TRP B 276 HIS 0.004 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9861) covalent geometry : angle 0.56112 (13399) hydrogen bonds : bond 0.03873 ( 649) hydrogen bonds : angle 3.95199 ( 1860) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.6933 (t-100) cc_final: 0.5970 (t60) REVERT: A 167 MET cc_start: 0.6991 (mmm) cc_final: 0.6565 (mmm) REVERT: A 210 HIS cc_start: 0.7988 (t-90) cc_final: 0.7777 (t-170) REVERT: A 289 PHE cc_start: 0.8253 (t80) cc_final: 0.7981 (t80) REVERT: A 314 PHE cc_start: 0.5682 (m-80) cc_final: 0.5379 (m-80) REVERT: A 558 ARG cc_start: 0.6676 (mmt180) cc_final: 0.6432 (mmt180) REVERT: B 90 ASP cc_start: 0.6244 (p0) cc_final: 0.5994 (m-30) REVERT: B 91 TRP cc_start: 0.6148 (m-10) cc_final: 0.5896 (m-10) REVERT: B 218 LEU cc_start: 0.7307 (tt) cc_final: 0.6425 (mt) REVERT: B 453 PRO cc_start: 0.8438 (Cg_endo) cc_final: 0.8181 (Cg_exo) outliers start: 24 outliers final: 21 residues processed: 225 average time/residue: 0.0897 time to fit residues: 28.5897 Evaluate side-chains 229 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 515 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 32 optimal weight: 0.0050 chunk 10 optimal weight: 0.8980 chunk 98 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 52 optimal weight: 0.0020 chunk 84 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 overall best weight: 0.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.203620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.157824 restraints weight = 15552.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.161604 restraints weight = 8807.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.164131 restraints weight = 6078.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.165712 restraints weight = 4822.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.166572 restraints weight = 4174.415| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9861 Z= 0.113 Angle : 0.571 17.101 13399 Z= 0.280 Chirality : 0.041 0.204 1578 Planarity : 0.004 0.037 1671 Dihedral : 3.370 13.577 1321 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.94 % Allowed : 16.99 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.25), residues: 1223 helix: 1.82 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -0.43 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 343 TYR 0.026 0.001 TYR A 140 PHE 0.025 0.001 PHE A 287 TRP 0.013 0.001 TRP B 276 HIS 0.005 0.000 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9861) covalent geometry : angle 0.57103 (13399) hydrogen bonds : bond 0.03712 ( 649) hydrogen bonds : angle 3.94763 ( 1860) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.6876 (t-100) cc_final: 0.5927 (t60) REVERT: A 167 MET cc_start: 0.7011 (mmm) cc_final: 0.6556 (mmm) REVERT: A 186 ILE cc_start: 0.8458 (mm) cc_final: 0.8202 (mm) REVERT: A 235 ARG cc_start: 0.3152 (mtt-85) cc_final: 0.2656 (ptt90) REVERT: A 289 PHE cc_start: 0.8205 (t80) cc_final: 0.7932 (t80) REVERT: A 314 PHE cc_start: 0.5635 (m-80) cc_final: 0.5310 (m-80) REVERT: A 558 ARG cc_start: 0.6667 (mmt180) cc_final: 0.6429 (mmt180) REVERT: B 90 ASP cc_start: 0.6240 (p0) cc_final: 0.5717 (m-30) REVERT: B 277 ARG cc_start: 0.7187 (mtp85) cc_final: 0.6934 (mtm180) REVERT: B 453 PRO cc_start: 0.8428 (Cg_endo) cc_final: 0.8191 (Cg_exo) REVERT: B 611 MET cc_start: 0.1179 (mmp) cc_final: 0.0940 (mtp) outliers start: 20 outliers final: 17 residues processed: 218 average time/residue: 0.0963 time to fit residues: 29.5765 Evaluate side-chains 219 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 621 MET Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 515 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 80 optimal weight: 0.4980 chunk 115 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.201928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.155984 restraints weight = 15676.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.159545 restraints weight = 8953.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.162020 restraints weight = 6308.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.163336 restraints weight = 5021.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.164557 restraints weight = 4413.982| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9861 Z= 0.122 Angle : 0.601 17.283 13399 Z= 0.293 Chirality : 0.042 0.233 1578 Planarity : 0.004 0.036 1671 Dihedral : 3.422 14.187 1321 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.65 % Allowed : 17.57 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.25), residues: 1223 helix: 1.81 (0.18), residues: 829 sheet: None (None), residues: 0 loop : -0.50 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 343 TYR 0.030 0.001 TYR A 140 PHE 0.028 0.001 PHE A 287 TRP 0.012 0.001 TRP B 276 HIS 0.006 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9861) covalent geometry : angle 0.60050 (13399) hydrogen bonds : bond 0.03839 ( 649) hydrogen bonds : angle 4.00724 ( 1860) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 213 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.6879 (t-100) cc_final: 0.5884 (t60) REVERT: A 167 MET cc_start: 0.6954 (mmm) cc_final: 0.6563 (mmm) REVERT: A 235 ARG cc_start: 0.3119 (mtt-85) cc_final: 0.2605 (ptt90) REVERT: A 289 PHE cc_start: 0.8259 (t80) cc_final: 0.8023 (t80) REVERT: A 314 PHE cc_start: 0.5716 (m-80) cc_final: 0.5391 (m-80) REVERT: A 558 ARG cc_start: 0.6726 (mmt180) cc_final: 0.6496 (mmt180) REVERT: B 90 ASP cc_start: 0.6320 (p0) cc_final: 0.5827 (m-30) REVERT: B 91 TRP cc_start: 0.6198 (m-10) cc_final: 0.5857 (m-10) REVERT: B 218 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6406 (mt) REVERT: B 277 ARG cc_start: 0.7233 (mtp85) cc_final: 0.6987 (mtm180) REVERT: B 453 PRO cc_start: 0.8448 (Cg_endo) cc_final: 0.8216 (Cg_exo) REVERT: B 611 MET cc_start: 0.1047 (mmp) cc_final: 0.0385 (ptp) outliers start: 17 outliers final: 15 residues processed: 218 average time/residue: 0.0925 time to fit residues: 28.7027 Evaluate side-chains 225 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 515 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 73 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 118 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 54 optimal weight: 50.0000 chunk 33 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.199787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.153005 restraints weight = 15759.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.156599 restraints weight = 9042.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.158908 restraints weight = 6355.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.159900 restraints weight = 5119.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.161329 restraints weight = 4596.250| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9861 Z= 0.132 Angle : 0.625 17.262 13399 Z= 0.306 Chirality : 0.043 0.252 1578 Planarity : 0.004 0.036 1671 Dihedral : 3.489 14.470 1321 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.84 % Allowed : 17.96 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.24), residues: 1223 helix: 1.78 (0.18), residues: 830 sheet: None (None), residues: 0 loop : -0.58 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 343 TYR 0.030 0.002 TYR A 140 PHE 0.027 0.002 PHE A 287 TRP 0.012 0.001 TRP B 276 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9861) covalent geometry : angle 0.62511 (13399) hydrogen bonds : bond 0.04061 ( 649) hydrogen bonds : angle 4.04232 ( 1860) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1754.43 seconds wall clock time: 30 minutes 50.66 seconds (1850.66 seconds total)