Starting phenix.real_space_refine on Tue Feb 3 21:22:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9me9_48191/02_2026/9me9_48191.cif Found real_map, /net/cci-nas-00/data/ceres_data/9me9_48191/02_2026/9me9_48191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9me9_48191/02_2026/9me9_48191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9me9_48191/02_2026/9me9_48191.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9me9_48191/02_2026/9me9_48191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9me9_48191/02_2026/9me9_48191.map" } resolution = 3.2 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= 0.024 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: 5 Type Number sf(0) Gaussians Mg 3 5.21 5 S 42 5.16 5 C 4397 2.51 5 N 1105 2.21 5 O 1285 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6832 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 888, 6829 Classifications: {'peptide': 888} Link IDs: {'CIS': 1, 'PTRANS': 32, 'TRANS': 854} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.71, per 1000 atoms: 0.25 Number of scatterers: 6832 At special positions: 0 Unit cell: (79.6671, 76.5429, 137.465, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 Mg 3 11.99 O 1285 8.00 N 1105 7.00 C 4397 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: 0.71 Conformation dependent library (CDL) restraints added in 265.0 milliseconds 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 58.3% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 22 through 33 removed outlier: 3.653A pdb=" N ARG A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 84 through 102 Processing helix chain 'A' and resid 111 through 136 removed outlier: 4.601A pdb=" N LEU A 115 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 268 through 299 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 301 through 317 removed outlier: 3.545A pdb=" N THR A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 339 Processing helix chain 'A' and resid 346 through 354 removed outlier: 4.259A pdb=" N GLN A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 Processing helix chain 'A' and resid 403 through 416 Processing helix chain 'A' and resid 454 through 458 removed outlier: 3.770A pdb=" N THR A 457 " --> pdb=" O ASN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 488 through 505 removed outlier: 4.019A pdb=" N GLU A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 529 Processing helix chain 'A' and resid 547 through 558 Processing helix chain 'A' and resid 569 through 581 Processing helix chain 'A' and resid 589 through 596 removed outlier: 3.540A pdb=" N ILE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 607 removed outlier: 3.909A pdb=" N ALA A 603 " --> pdb=" O ASN A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 629 removed outlier: 3.680A pdb=" N SER A 629 " --> pdb=" O THR A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 641 No H-bonds generated for 'chain 'A' and resid 639 through 641' Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 659 through 665 Processing helix chain 'A' and resid 674 through 713 removed outlier: 4.021A pdb=" N LEU A 678 " --> pdb=" O ASP A 674 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 739 Processing helix chain 'A' and resid 740 through 744 Processing helix chain 'A' and resid 747 through 753 removed outlier: 4.532A pdb=" N VAL A 753 " --> pdb=" O GLU A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 787 removed outlier: 3.539A pdb=" N SER A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) Proline residue: A 771 - end of helix removed outlier: 3.896A pdb=" N PHE A 776 " --> pdb=" O THR A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 794 Processing helix chain 'A' and resid 803 through 834 removed outlier: 3.939A pdb=" N ILE A 829 " --> pdb=" O GLN A 825 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N HIS A 830 " --> pdb=" O THR A 826 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET A 831 " --> pdb=" O LEU A 827 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR A 834 " --> pdb=" O HIS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 862 Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'A' and resid 879 through 907 removed outlier: 4.228A pdb=" N TRP A 883 " --> pdb=" O ASN A 879 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 164 removed outlier: 4.404A pdb=" N ASN A 152 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE A 173 " --> pdb=" O HIS A 154 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE A 195 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY A 238 " --> pdb=" O ASP A 193 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP A 193 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA A 240 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA A 191 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLY A 242 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE A 189 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL A 244 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG A 187 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA A 246 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU A 194 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 164 removed outlier: 4.404A pdb=" N ASN A 152 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE A 173 " --> pdb=" O HIS A 154 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE A 195 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY A 238 " --> pdb=" O ASP A 193 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP A 193 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA A 240 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA A 191 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLY A 242 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE A 189 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL A 244 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG A 187 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA A 246 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 341 through 343 removed outlier: 6.042A pdb=" N GLY A 652 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU A 670 " --> pdb=" O GLY A 652 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER A 654 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL A 633 " --> pdb=" O VAL A 651 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ILE A 653 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR A 635 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N VAL A 655 " --> pdb=" O TYR A 635 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N PHE A 611 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE A 564 " --> pdb=" O PHE A 611 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 377 removed outlier: 4.312A pdb=" N LEU A 373 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL A 512 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR A 537 " --> pdb=" O ILE A 510 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE A 510 " --> pdb=" O TYR A 537 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA A 539 " --> pdb=" O ARG A 508 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG A 508 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N SER A 446 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU A 435 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A 448 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 373 through 377 removed outlier: 4.312A pdb=" N LEU A 373 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N MET A 532 " --> pdb=" O CYS A 475 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY A 536 " --> pdb=" O GLU A 479 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1242 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: 1.26 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2170 1.35 - 1.46: 1492 1.46 - 1.58: 3208 1.58 - 1.70: 0 1.70 - 1.81: 78 Bond restraints: 6948 Sorted by residual: bond pdb=" CB GLN A 80 " pdb=" CG GLN A 80 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.05e+00 bond pdb=" C PHE A 881 " pdb=" N PRO A 882 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.36e-02 5.41e+03 1.04e+00 bond pdb=" CB ASP A 638 " pdb=" CG ASP A 638 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.49e-01 bond pdb=" CA ASP A 638 " pdb=" CB ASP A 638 " ideal model delta sigma weight residual 1.533 1.553 -0.019 2.15e-02 2.16e+03 8.00e-01 bond pdb=" CB MET A 535 " pdb=" CG MET A 535 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.61e-01 ... (remaining 6943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 9280 1.79 - 3.58: 114 3.58 - 5.38: 18 5.38 - 7.17: 2 7.17 - 8.96: 1 Bond angle restraints: 9415 Sorted by residual: angle pdb=" CB MET A 535 " pdb=" CG MET A 535 " pdb=" SD MET A 535 " ideal model delta sigma weight residual 112.70 121.66 -8.96 3.00e+00 1.11e-01 8.92e+00 angle pdb=" CA MET A 535 " pdb=" CB MET A 535 " pdb=" CG MET A 535 " ideal model delta sigma weight residual 114.10 119.44 -5.34 2.00e+00 2.50e-01 7.13e+00 angle pdb=" N ILE A 385 " pdb=" CA ILE A 385 " pdb=" C ILE A 385 " ideal model delta sigma weight residual 112.96 110.43 2.53 1.00e+00 1.00e+00 6.41e+00 angle pdb=" CB GLN A 80 " pdb=" CG GLN A 80 " pdb=" CD GLN A 80 " ideal model delta sigma weight residual 112.60 116.82 -4.22 1.70e+00 3.46e-01 6.15e+00 angle pdb=" N ILE A 222 " pdb=" CA ILE A 222 " pdb=" C ILE A 222 " ideal model delta sigma weight residual 109.34 113.88 -4.54 2.08e+00 2.31e-01 4.77e+00 ... (remaining 9410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 3690 17.16 - 34.33: 402 34.33 - 51.49: 96 51.49 - 68.65: 17 68.65 - 85.82: 6 Dihedral angle restraints: 4211 sinusoidal: 1642 harmonic: 2569 Sorted by residual: dihedral pdb=" CA PRO A 318 " pdb=" C PRO A 318 " pdb=" N GLU A 319 " pdb=" CA GLU A 319 " ideal model delta harmonic sigma weight residual -180.00 -159.83 -20.17 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CG ARG A 389 " pdb=" CD ARG A 389 " pdb=" NE ARG A 389 " pdb=" CZ ARG A 389 " ideal model delta sinusoidal sigma weight residual 180.00 137.01 42.99 2 1.50e+01 4.44e-03 9.92e+00 dihedral pdb=" CB GLU A 141 " pdb=" CG GLU A 141 " pdb=" CD GLU A 141 " pdb=" OE1 GLU A 141 " ideal model delta sinusoidal sigma weight residual 0.00 85.82 -85.82 1 3.00e+01 1.11e-03 9.89e+00 ... (remaining 4208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 744 0.032 - 0.063: 267 0.063 - 0.094: 80 0.094 - 0.126: 46 0.126 - 0.157: 2 Chirality restraints: 1139 Sorted by residual: chirality pdb=" CB THR A 826 " pdb=" CA THR A 826 " pdb=" OG1 THR A 826 " pdb=" CG2 THR A 826 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CA ILE A 837 " pdb=" N ILE A 837 " pdb=" C ILE A 837 " pdb=" CB ILE A 837 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA PRO A 838 " pdb=" N PRO A 838 " pdb=" C PRO A 838 " pdb=" CB PRO A 838 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 1136 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 770 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A 771 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 771 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 771 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 84 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO A 85 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 881 " 0.017 5.00e-02 4.00e+02 2.58e-02 1.06e+00 pdb=" N PRO A 882 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 882 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 882 " 0.015 5.00e-02 4.00e+02 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 37 2.58 - 3.16: 5548 3.16 - 3.74: 10697 3.74 - 4.32: 13948 4.32 - 4.90: 24216 Nonbonded interactions: 54446 Sorted by model distance: nonbonded pdb=" OD1 ASN A 706 " pdb="MG MG A1003 " model vdw 2.002 2.170 nonbonded pdb=" OD1 ASP A 180 " pdb="MG MG A1002 " model vdw 2.052 2.170 nonbonded pdb=" O ILE A 379 " pdb=" OH TYR A 537 " model vdw 2.168 3.040 nonbonded pdb=" O PHE A 230 " pdb=" OG SER A 233 " model vdw 2.254 3.040 nonbonded pdb=" O SER A 221 " pdb=" N THR A 223 " model vdw 2.255 3.120 ... (remaining 54441 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.120 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.240 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 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 0.031 6948 Z= 0.119 Angle : 0.509 8.958 9415 Z= 0.273 Chirality : 0.040 0.157 1139 Planarity : 0.003 0.039 1175 Dihedral : 15.230 85.815 2547 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.35 % Favored : 98.42 % Rotamer: Outliers : 1.44 % Allowed : 17.30 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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 (0.28), residues: 886 helix: 2.38 (0.24), residues: 459 sheet: -0.06 (0.61), residues: 72 loop : -0.49 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 26 TYR 0.015 0.001 TYR A 79 PHE 0.014 0.001 PHE A 818 TRP 0.012 0.001 TRP A 817 HIS 0.002 0.000 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6948) covalent geometry : angle 0.50950 ( 9415) hydrogen bonds : bond 0.14319 ( 407) hydrogen bonds : angle 5.82910 ( 1242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.8509 (tmtt) cc_final: 0.8258 (tppp) REVERT: A 231 MET cc_start: 0.8258 (ttp) cc_final: 0.7903 (ttp) REVERT: A 566 THR cc_start: 0.7971 (p) cc_final: 0.7662 (t) REVERT: A 722 MET cc_start: 0.8175 (ttp) cc_final: 0.7925 (mtp) REVERT: A 781 TYR cc_start: 0.7620 (m-10) cc_final: 0.7380 (m-10) REVERT: A 784 MET cc_start: 0.8749 (tpp) cc_final: 0.8326 (mmp) outliers start: 11 outliers final: 10 residues processed: 70 average time/residue: 0.0725 time to fit residues: 7.4329 Evaluate side-chains 69 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 832 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 132 GLN A 825 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.106668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.084668 restraints weight = 11595.151| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.33 r_work: 0.3035 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6948 Z= 0.188 Angle : 0.538 6.029 9415 Z= 0.285 Chirality : 0.042 0.140 1139 Planarity : 0.004 0.046 1175 Dihedral : 5.533 60.435 949 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.47 % Favored : 98.31 % Rotamer: Outliers : 5.24 % Allowed : 13.89 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: 1.33 (0.28), residues: 886 helix: 2.14 (0.24), residues: 469 sheet: -0.16 (0.58), residues: 72 loop : -0.65 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 444 TYR 0.014 0.002 TYR A 537 PHE 0.016 0.002 PHE A 818 TRP 0.009 0.001 TRP A 817 HIS 0.004 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 6948) covalent geometry : angle 0.53784 ( 9415) hydrogen bonds : bond 0.04428 ( 407) hydrogen bonds : angle 4.61933 ( 1242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 59 time to evaluate : 0.333 Fit side-chains REVERT: A 71 LYS cc_start: 0.8512 (tmtt) cc_final: 0.8238 (tppp) REVERT: A 209 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7390 (tp30) REVERT: A 231 MET cc_start: 0.8445 (ttp) cc_final: 0.8088 (ttp) REVERT: A 320 MET cc_start: 0.7578 (mtp) cc_final: 0.6985 (mtp) REVERT: A 510 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8409 (mt) REVERT: A 566 THR cc_start: 0.8102 (p) cc_final: 0.7720 (t) REVERT: A 650 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.7981 (m-30) REVERT: A 722 MET cc_start: 0.8568 (ttp) cc_final: 0.8244 (mtp) REVERT: A 781 TYR cc_start: 0.7731 (m-10) cc_final: 0.7156 (m-80) REVERT: A 784 MET cc_start: 0.8694 (tpp) cc_final: 0.8210 (mmp) REVERT: A 851 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.6897 (tp) outliers start: 40 outliers final: 20 residues processed: 90 average time/residue: 0.0668 time to fit residues: 8.9014 Evaluate side-chains 79 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 892 MET Chi-restraints excluded: chain A residue 903 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 85 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 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 46 ASN A 154 HIS ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.106134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.083915 restraints weight = 11476.818| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.32 r_work: 0.3035 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6948 Z= 0.162 Angle : 0.514 6.229 9415 Z= 0.271 Chirality : 0.041 0.136 1139 Planarity : 0.004 0.047 1175 Dihedral : 5.002 60.926 937 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.13 % Favored : 98.65 % Rotamer: Outliers : 3.80 % Allowed : 15.20 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: 1.39 (0.28), residues: 886 helix: 2.17 (0.24), residues: 469 sheet: 0.04 (0.55), residues: 77 loop : -0.65 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 444 TYR 0.013 0.002 TYR A 397 PHE 0.013 0.001 PHE A 818 TRP 0.009 0.001 TRP A 817 HIS 0.004 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 6948) covalent geometry : angle 0.51422 ( 9415) hydrogen bonds : bond 0.04107 ( 407) hydrogen bonds : angle 4.45515 ( 1242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.273 Fit side-chains REVERT: A 71 LYS cc_start: 0.8566 (tmtt) cc_final: 0.8281 (tppp) REVERT: A 231 MET cc_start: 0.8443 (ttp) cc_final: 0.8233 (ttp) REVERT: A 510 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8330 (mt) REVERT: A 522 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8449 (p0) REVERT: A 566 THR cc_start: 0.7989 (p) cc_final: 0.7627 (t) REVERT: A 784 MET cc_start: 0.8652 (tpp) cc_final: 0.7687 (mmp) REVERT: A 851 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.6824 (tp) outliers start: 29 outliers final: 17 residues processed: 83 average time/residue: 0.0661 time to fit residues: 8.1634 Evaluate side-chains 77 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 862 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 86 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.105387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.083138 restraints weight = 11623.546| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.34 r_work: 0.3009 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6948 Z= 0.166 Angle : 0.519 7.368 9415 Z= 0.271 Chirality : 0.041 0.136 1139 Planarity : 0.004 0.048 1175 Dihedral : 4.997 62.617 937 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.69 % Favored : 98.08 % Rotamer: Outliers : 5.24 % Allowed : 14.55 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: 1.43 (0.28), residues: 886 helix: 2.19 (0.24), residues: 469 sheet: 0.07 (0.56), residues: 77 loop : -0.61 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 444 TYR 0.012 0.002 TYR A 397 PHE 0.013 0.001 PHE A 283 TRP 0.007 0.001 TRP A 278 HIS 0.004 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 6948) covalent geometry : angle 0.51924 ( 9415) hydrogen bonds : bond 0.04016 ( 407) hydrogen bonds : angle 4.36237 ( 1242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 59 time to evaluate : 0.282 Fit side-chains REVERT: A 71 LYS cc_start: 0.8556 (tmtt) cc_final: 0.8267 (tppp) REVERT: A 209 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7357 (tp30) REVERT: A 224 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8375 (pm20) REVERT: A 231 MET cc_start: 0.8468 (ttp) cc_final: 0.8133 (ttp) REVERT: A 303 MET cc_start: 0.7414 (tpp) cc_final: 0.7127 (tpp) REVERT: A 510 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8394 (mt) REVERT: A 566 THR cc_start: 0.8054 (p) cc_final: 0.7673 (t) REVERT: A 650 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.7803 (m-30) REVERT: A 722 MET cc_start: 0.8635 (ttp) cc_final: 0.8431 (mtp) REVERT: A 784 MET cc_start: 0.8658 (tpp) cc_final: 0.7727 (mmp) REVERT: A 851 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.6847 (tp) outliers start: 40 outliers final: 25 residues processed: 90 average time/residue: 0.0614 time to fit residues: 8.2743 Evaluate side-chains 86 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 56 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 892 MET Chi-restraints excluded: chain A residue 903 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 46 optimal weight: 0.0470 chunk 87 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.106198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.084115 restraints weight = 11577.754| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.33 r_work: 0.3036 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6948 Z= 0.131 Angle : 0.483 5.879 9415 Z= 0.253 Chirality : 0.040 0.140 1139 Planarity : 0.004 0.048 1175 Dihedral : 4.747 63.795 935 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.24 % Favored : 98.53 % Rotamer: Outliers : 5.11 % Allowed : 14.02 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: 1.58 (0.28), residues: 886 helix: 2.33 (0.24), residues: 469 sheet: 0.06 (0.57), residues: 77 loop : -0.55 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 444 TYR 0.012 0.001 TYR A 537 PHE 0.014 0.001 PHE A 776 TRP 0.008 0.001 TRP A 817 HIS 0.002 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6948) covalent geometry : angle 0.48275 ( 9415) hydrogen bonds : bond 0.03748 ( 407) hydrogen bonds : angle 4.24289 ( 1242) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 62 time to evaluate : 0.301 Fit side-chains REVERT: A 209 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7351 (tp30) REVERT: A 224 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8399 (pm20) REVERT: A 231 MET cc_start: 0.8210 (ttp) cc_final: 0.7838 (ttp) REVERT: A 303 MET cc_start: 0.7469 (tpp) cc_final: 0.7159 (tpp) REVERT: A 510 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8403 (mt) REVERT: A 522 ASP cc_start: 0.8966 (OUTLIER) cc_final: 0.8512 (p0) REVERT: A 566 THR cc_start: 0.7960 (p) cc_final: 0.7676 (t) REVERT: A 650 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.7788 (m-30) REVERT: A 722 MET cc_start: 0.8616 (ttp) cc_final: 0.8371 (mtp) REVERT: A 724 SER cc_start: 0.7458 (OUTLIER) cc_final: 0.7252 (t) REVERT: A 784 MET cc_start: 0.8517 (tpp) cc_final: 0.7486 (mmp) REVERT: A 822 MET cc_start: 0.8086 (tpt) cc_final: 0.7696 (tpp) REVERT: A 851 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.6807 (tp) outliers start: 39 outliers final: 22 residues processed: 93 average time/residue: 0.0587 time to fit residues: 8.0775 Evaluate side-chains 88 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 892 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.105516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.083093 restraints weight = 11553.159| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.36 r_work: 0.3012 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6948 Z= 0.148 Angle : 0.497 7.301 9415 Z= 0.259 Chirality : 0.041 0.150 1139 Planarity : 0.004 0.048 1175 Dihedral : 4.074 40.611 932 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.81 % Favored : 98.08 % Rotamer: Outliers : 4.98 % Allowed : 14.15 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: 1.56 (0.28), residues: 886 helix: 2.30 (0.24), residues: 469 sheet: -0.05 (0.56), residues: 77 loop : -0.50 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 444 TYR 0.011 0.001 TYR A 397 PHE 0.014 0.001 PHE A 776 TRP 0.008 0.001 TRP A 817 HIS 0.003 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6948) covalent geometry : angle 0.49721 ( 9415) hydrogen bonds : bond 0.03803 ( 407) hydrogen bonds : angle 4.24392 ( 1242) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 56 time to evaluate : 0.159 Fit side-chains REVERT: A 209 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7380 (tp30) REVERT: A 231 MET cc_start: 0.8242 (ttp) cc_final: 0.7777 (ttp) REVERT: A 303 MET cc_start: 0.7504 (tpp) cc_final: 0.7186 (tpp) REVERT: A 459 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7746 (mmmt) REVERT: A 510 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8436 (mt) REVERT: A 522 ASP cc_start: 0.8994 (OUTLIER) cc_final: 0.8541 (p0) REVERT: A 566 THR cc_start: 0.8019 (p) cc_final: 0.7720 (t) REVERT: A 650 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.7768 (m-30) REVERT: A 724 SER cc_start: 0.7504 (OUTLIER) cc_final: 0.7301 (t) REVERT: A 784 MET cc_start: 0.8596 (tpp) cc_final: 0.7575 (mmp) REVERT: A 822 MET cc_start: 0.8139 (tpt) cc_final: 0.7729 (tpp) REVERT: A 851 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.6830 (tp) outliers start: 38 outliers final: 26 residues processed: 85 average time/residue: 0.0521 time to fit residues: 6.5534 Evaluate side-chains 88 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 55 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 892 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.105647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.083429 restraints weight = 11484.104| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.33 r_work: 0.3017 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6948 Z= 0.144 Angle : 0.492 6.573 9415 Z= 0.257 Chirality : 0.041 0.158 1139 Planarity : 0.004 0.048 1175 Dihedral : 4.052 40.559 932 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.58 % Favored : 98.31 % Rotamer: Outliers : 5.37 % Allowed : 14.29 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: 1.60 (0.28), residues: 886 helix: 2.32 (0.24), residues: 469 sheet: -0.01 (0.57), residues: 77 loop : -0.47 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 444 TYR 0.011 0.001 TYR A 689 PHE 0.014 0.001 PHE A 776 TRP 0.007 0.001 TRP A 278 HIS 0.003 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6948) covalent geometry : angle 0.49227 ( 9415) hydrogen bonds : bond 0.03754 ( 407) hydrogen bonds : angle 4.22804 ( 1242) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 58 time to evaluate : 0.310 Fit side-chains REVERT: A 46 ASN cc_start: 0.8980 (OUTLIER) cc_final: 0.8553 (t0) REVERT: A 209 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7386 (tp30) REVERT: A 224 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8405 (pm20) REVERT: A 231 MET cc_start: 0.8249 (ttp) cc_final: 0.7779 (ttp) REVERT: A 303 MET cc_start: 0.7418 (tpp) cc_final: 0.7107 (tpp) REVERT: A 459 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7731 (mmmt) REVERT: A 510 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8455 (mt) REVERT: A 566 THR cc_start: 0.8070 (p) cc_final: 0.7777 (t) REVERT: A 650 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.7779 (m-30) REVERT: A 724 SER cc_start: 0.7512 (OUTLIER) cc_final: 0.7297 (t) REVERT: A 741 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.7206 (mm) REVERT: A 784 MET cc_start: 0.8587 (tpp) cc_final: 0.7582 (mmp) REVERT: A 822 MET cc_start: 0.8143 (tpt) cc_final: 0.7726 (tpp) REVERT: A 851 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.6836 (tp) outliers start: 41 outliers final: 27 residues processed: 89 average time/residue: 0.0711 time to fit residues: 9.2769 Evaluate side-chains 92 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 56 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 892 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 45 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.0470 chunk 6 optimal weight: 0.0980 chunk 62 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.106753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.084805 restraints weight = 11455.870| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.31 r_work: 0.3039 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6948 Z= 0.112 Angle : 0.486 8.097 9415 Z= 0.251 Chirality : 0.040 0.160 1139 Planarity : 0.003 0.048 1175 Dihedral : 3.986 39.001 932 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.47 % Favored : 98.42 % Rotamer: Outliers : 4.85 % Allowed : 15.60 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: 1.70 (0.28), residues: 886 helix: 2.42 (0.24), residues: 469 sheet: 0.12 (0.57), residues: 77 loop : -0.49 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 26 TYR 0.011 0.001 TYR A 537 PHE 0.014 0.001 PHE A 283 TRP 0.008 0.001 TRP A 278 HIS 0.003 0.001 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6948) covalent geometry : angle 0.48617 ( 9415) hydrogen bonds : bond 0.03530 ( 407) hydrogen bonds : angle 4.14263 ( 1242) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 59 time to evaluate : 0.282 Fit side-chains REVERT: A 209 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7262 (tp30) REVERT: A 224 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8387 (pm20) REVERT: A 231 MET cc_start: 0.8219 (ttp) cc_final: 0.7739 (ttp) REVERT: A 303 MET cc_start: 0.7475 (tpp) cc_final: 0.7162 (tpp) REVERT: A 459 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7795 (mmmt) REVERT: A 566 THR cc_start: 0.8051 (p) cc_final: 0.7752 (t) REVERT: A 650 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.7779 (m-30) REVERT: A 741 ILE cc_start: 0.7415 (OUTLIER) cc_final: 0.7154 (mm) REVERT: A 784 MET cc_start: 0.8504 (tpp) cc_final: 0.7522 (mmp) REVERT: A 822 MET cc_start: 0.8067 (tpt) cc_final: 0.7685 (tpp) REVERT: A 851 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.6823 (tp) outliers start: 37 outliers final: 24 residues processed: 85 average time/residue: 0.0639 time to fit residues: 8.0503 Evaluate side-chains 86 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 56 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 892 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.105396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.083302 restraints weight = 11601.787| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.33 r_work: 0.3010 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6948 Z= 0.152 Angle : 0.510 7.788 9415 Z= 0.263 Chirality : 0.041 0.155 1139 Planarity : 0.004 0.048 1175 Dihedral : 4.042 39.827 932 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.81 % Favored : 98.08 % Rotamer: Outliers : 5.11 % Allowed : 15.20 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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 (0.28), residues: 886 helix: 2.32 (0.24), residues: 469 sheet: 0.06 (0.57), residues: 77 loop : -0.46 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 444 TYR 0.011 0.001 TYR A 397 PHE 0.015 0.001 PHE A 283 TRP 0.007 0.001 TRP A 278 HIS 0.003 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 6948) covalent geometry : angle 0.51045 ( 9415) hydrogen bonds : bond 0.03777 ( 407) hydrogen bonds : angle 4.18608 ( 1242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 59 time to evaluate : 0.282 Fit side-chains REVERT: A 209 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7389 (tp30) REVERT: A 224 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8585 (pm20) REVERT: A 231 MET cc_start: 0.8260 (ttp) cc_final: 0.7788 (ttp) REVERT: A 303 MET cc_start: 0.7431 (tpp) cc_final: 0.7112 (tpp) REVERT: A 459 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7796 (mmmt) REVERT: A 566 THR cc_start: 0.8114 (p) cc_final: 0.7804 (t) REVERT: A 650 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.7787 (m-30) REVERT: A 741 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7219 (mm) REVERT: A 784 MET cc_start: 0.8577 (tpp) cc_final: 0.7580 (mmp) REVERT: A 822 MET cc_start: 0.8150 (tpt) cc_final: 0.7733 (tpp) REVERT: A 851 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.6873 (tp) outliers start: 39 outliers final: 26 residues processed: 89 average time/residue: 0.0689 time to fit residues: 9.0737 Evaluate side-chains 89 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 57 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 892 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 36 optimal weight: 0.0980 chunk 48 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.106323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.084369 restraints weight = 11502.196| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.31 r_work: 0.3033 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6948 Z= 0.126 Angle : 0.492 7.361 9415 Z= 0.255 Chirality : 0.041 0.157 1139 Planarity : 0.003 0.048 1175 Dihedral : 4.004 39.649 932 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.81 % Favored : 98.08 % Rotamer: Outliers : 4.19 % Allowed : 15.99 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: 1.64 (0.28), residues: 886 helix: 2.30 (0.24), residues: 476 sheet: -0.09 (0.55), residues: 83 loop : -0.39 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 26 TYR 0.010 0.001 TYR A 689 PHE 0.014 0.001 PHE A 776 TRP 0.008 0.001 TRP A 278 HIS 0.003 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6948) covalent geometry : angle 0.49177 ( 9415) hydrogen bonds : bond 0.03587 ( 407) hydrogen bonds : angle 4.13224 ( 1242) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 0.291 Fit side-chains REVERT: A 71 LYS cc_start: 0.8353 (tppt) cc_final: 0.8122 (tppt) REVERT: A 209 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7283 (tp30) REVERT: A 231 MET cc_start: 0.8239 (ttp) cc_final: 0.7764 (ttp) REVERT: A 303 MET cc_start: 0.7487 (tpp) cc_final: 0.7173 (tpp) REVERT: A 459 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7529 (mmmt) REVERT: A 471 MET cc_start: 0.7073 (tpp) cc_final: 0.6746 (ttm) REVERT: A 566 THR cc_start: 0.8309 (p) cc_final: 0.8014 (t) REVERT: A 650 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.7766 (m-30) REVERT: A 741 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.7182 (mm) REVERT: A 784 MET cc_start: 0.8504 (tpp) cc_final: 0.7526 (mmp) REVERT: A 822 MET cc_start: 0.8100 (tpt) cc_final: 0.7706 (tpp) REVERT: A 851 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.6851 (tp) outliers start: 32 outliers final: 25 residues processed: 85 average time/residue: 0.0708 time to fit residues: 8.8291 Evaluate side-chains 87 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 57 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 892 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 86 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 56 optimal weight: 0.0060 chunk 54 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.106609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.084710 restraints weight = 11508.029| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.32 r_work: 0.3037 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6948 Z= 0.123 Angle : 0.499 8.286 9415 Z= 0.259 Chirality : 0.041 0.148 1139 Planarity : 0.003 0.048 1175 Dihedral : 4.004 41.063 932 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.58 % Favored : 98.31 % Rotamer: Outliers : 4.46 % Allowed : 15.99 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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 (0.28), residues: 886 helix: 2.32 (0.24), residues: 476 sheet: -0.05 (0.55), residues: 83 loop : -0.38 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 26 TYR 0.010 0.001 TYR A 689 PHE 0.014 0.001 PHE A 283 TRP 0.009 0.001 TRP A 278 HIS 0.002 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6948) covalent geometry : angle 0.49915 ( 9415) hydrogen bonds : bond 0.03549 ( 407) hydrogen bonds : angle 4.10849 ( 1242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1488.68 seconds wall clock time: 26 minutes 21.49 seconds (1581.49 seconds total)