Starting phenix.real_space_refine on Tue Aug 4 23:41:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zlk_74405/08_2026/9zlk_74405_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zlk_74405/08_2026/9zlk_74405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zlk_74405/08_2026/9zlk_74405_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zlk_74405/08_2026/9zlk_74405_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zlk_74405/08_2026/9zlk_74405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zlk_74405/08_2026/9zlk_74405.map" } resolution = 2.79 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= 0.013 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: 8 Type Number sf(0) Gaussians K 1 8.98 5 P 3 5.49 5 Mg 4 5.21 5 S 40 5.16 5 C 4482 2.51 5 N 1126 2.21 5 O 1350 1.98 5 H 223 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7229 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 897, 7167 Classifications: {'peptide': 897} Link IDs: {'PTRANS': 32, 'TRANS': 864} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 62 Unusual residues: {' K': 1, ' MG': 4, 'ACP': 1} Classifications: {'undetermined': 6, 'water': 26} Link IDs: {None: 31} Time building chain proxies: 1.63, per 1000 atoms: 0.23 Number of scatterers: 7229 At special positions: 0 Unit cell: (73.47, 79.98, 139.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) K 1 19.00 S 40 16.00 P 3 15.00 Mg 4 11.99 O 1350 8.00 N 1126 7.00 C 4482 6.00 H 223 1.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 294.8 milliseconds 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1682 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 56.0% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 22 through 25 Processing helix chain 'A' and resid 26 through 33 Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 50 through 62 removed outlier: 4.113A pdb=" N GLU A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 84 through 102 removed outlier: 3.603A pdb=" N ILE A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 135 removed outlier: 3.579A pdb=" N ARG A 135 " --> pdb=" O VAL A 131 " (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 221 through 225 removed outlier: 3.573A pdb=" N GLU A 224 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 250 removed outlier: 3.865A pdb=" N THR A 250 " --> pdb=" O THR A 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 250' Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 268 through 298 removed outlier: 3.875A pdb=" N VAL A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 301 through 316 Processing helix chain 'A' and resid 320 through 339 Processing helix chain 'A' and resid 347 through 354 removed outlier: 3.549A pdb=" N ASN A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 398 removed outlier: 4.067A pdb=" N LEU A 388 " --> pdb=" O ASN A 384 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN A 398 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 416 Processing helix chain 'A' and resid 468 through 473 removed outlier: 3.565A pdb=" N ASP A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 505 removed outlier: 3.538A pdb=" N TYR A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 505 " --> pdb=" O LYS 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 594 removed outlier: 3.851A pdb=" N ILE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP A 594 " --> pdb=" O GLY A 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 589 through 594' Processing helix chain 'A' and resid 599 through 607 removed outlier: 3.949A pdb=" N GLN A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 628 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 666 Processing helix chain 'A' and resid 674 through 713 removed outlier: 4.071A pdb=" N TYR A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 709 " --> pdb=" O GLY A 705 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 710 " --> pdb=" O ASN A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 738 Processing helix chain 'A' and resid 739 through 744 Proline residue: A 742 - end of helix No H-bonds generated for 'chain 'A' and resid 739 through 744' Processing helix chain 'A' and resid 761 through 787 Proline residue: A 771 - end of helix removed outlier: 3.624A pdb=" N SER A 774 " --> pdb=" O GLY A 770 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE A 776 " --> pdb=" O THR A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 794 removed outlier: 3.500A pdb=" N ALA A 791 " --> pdb=" O VAL A 787 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 792 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 803 through 828 Processing helix chain 'A' and resid 828 through 833 Processing helix chain 'A' and resid 845 through 862 removed outlier: 3.713A pdb=" N ILE A 862 " --> pdb=" O GLY A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 871 Processing helix chain 'A' and resid 879 through 907 removed outlier: 4.400A pdb=" N TRP A 883 " --> pdb=" O THR A 879 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 164 removed outlier: 4.424A pdb=" N ASN A 152 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE A 173 " --> pdb=" O HIS A 154 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE A 195 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 238 " --> pdb=" O ASP A 193 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP A 193 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA A 240 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA A 191 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY A 242 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE A 189 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N VAL A 244 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ARG A 187 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 341 through 343 removed outlier: 6.285A pdb=" N GLY A 652 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU A 670 " --> pdb=" O GLY A 652 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER A 654 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A 633 " --> pdb=" O VAL A 651 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE A 653 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR A 635 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N VAL A 655 " --> pdb=" O TYR A 635 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N PHE A 611 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE A 564 " --> pdb=" O PHE A 611 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 373 through 377 removed outlier: 3.926A pdb=" N LEU A 373 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 536 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER A 446 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU A 435 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 448 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 377 removed outlier: 3.926A pdb=" N LEU A 373 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY A 536 " --> pdb=" O GLU A 479 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1107 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: 1.24 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 223 1.03 - 1.23: 59 1.23 - 1.42: 2755 1.42 - 1.62: 4207 1.62 - 1.82: 77 Bond restraints: 7321 Sorted by residual: bond pdb=" CA GLN A 461 " pdb=" C GLN A 461 " ideal model delta sigma weight residual 1.520 1.410 0.110 1.20e-02 6.94e+03 8.40e+01 bond pdb=" CA LYS A 515 " pdb=" C LYS A 515 " ideal model delta sigma weight residual 1.524 1.419 0.105 1.31e-02 5.83e+03 6.45e+01 bond pdb=" CA ARG A 26 " pdb=" C ARG A 26 " ideal model delta sigma weight residual 1.521 1.414 0.106 1.36e-02 5.41e+03 6.11e+01 bond pdb=" C GLN A 461 " pdb=" O GLN A 461 " ideal model delta sigma weight residual 1.234 1.151 0.083 1.15e-02 7.56e+03 5.23e+01 bond pdb=" C GLN A 461 " pdb=" N MET A 462 " ideal model delta sigma weight residual 1.330 1.230 0.100 1.39e-02 5.18e+03 5.19e+01 ... (remaining 7316 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 9975 2.75 - 5.50: 123 5.50 - 8.25: 23 8.25 - 11.00: 1 11.00 - 13.75: 8 Bond angle restraints: 10130 Sorted by residual: angle pdb=" N ARG A 26 " pdb=" CA ARG A 26 " pdb=" C ARG A 26 " ideal model delta sigma weight residual 113.41 100.89 12.52 1.22e+00 6.72e-01 1.05e+02 angle pdb=" CA PRO A 421 " pdb=" N PRO A 421 " pdb=" CD PRO A 421 " ideal model delta sigma weight residual 112.00 98.77 13.23 1.40e+00 5.10e-01 8.93e+01 angle pdb=" N THR A 516 " pdb=" CA THR A 516 " pdb=" C THR A 516 " ideal model delta sigma weight residual 112.88 124.32 -11.44 1.29e+00 6.01e-01 7.86e+01 angle pdb=" C GLN A 514 " pdb=" CA GLN A 514 " pdb=" CB GLN A 514 " ideal model delta sigma weight residual 111.42 100.02 11.40 1.31e+00 5.83e-01 7.57e+01 angle pdb=" C THR A 516 " pdb=" CA THR A 516 " pdb=" CB THR A 516 " ideal model delta sigma weight residual 110.72 96.97 13.75 1.69e+00 3.50e-01 6.62e+01 ... (remaining 10125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 3735 17.92 - 35.84: 435 35.84 - 53.76: 161 53.76 - 71.69: 34 71.69 - 89.61: 11 Dihedral angle restraints: 4376 sinusoidal: 1769 harmonic: 2607 Sorted by residual: dihedral pdb=" C ARG A 26 " pdb=" N ARG A 26 " pdb=" CA ARG A 26 " pdb=" CB ARG A 26 " ideal model delta harmonic sigma weight residual -122.60 -109.05 -13.55 0 2.50e+00 1.60e-01 2.94e+01 dihedral pdb=" C GLN A 514 " pdb=" N GLN A 514 " pdb=" CA GLN A 514 " pdb=" CB GLN A 514 " ideal model delta harmonic sigma weight residual -122.60 -111.04 -11.56 0 2.50e+00 1.60e-01 2.14e+01 dihedral pdb=" N GLN A 514 " pdb=" C GLN A 514 " pdb=" CA GLN A 514 " pdb=" CB GLN A 514 " ideal model delta harmonic sigma weight residual 122.80 113.50 9.30 0 2.50e+00 1.60e-01 1.38e+01 ... (remaining 4373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1077 0.082 - 0.163: 72 0.163 - 0.245: 3 0.245 - 0.327: 1 0.327 - 0.408: 1 Chirality restraints: 1154 Sorted by residual: chirality pdb=" CA THR A 516 " pdb=" N THR A 516 " pdb=" C THR A 516 " pdb=" CB THR A 516 " both_signs ideal model delta sigma weight residual False 2.53 2.12 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" C2' ACP A1001 " pdb=" C1' ACP A1001 " pdb=" C3' ACP A1001 " pdb=" O2' ACP A1001 " both_signs ideal model delta sigma weight residual False -2.75 -2.50 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA PRO A 421 " pdb=" N PRO A 421 " pdb=" C PRO A 421 " pdb=" CB PRO A 421 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.23e-01 ... (remaining 1151 not shown) Planarity restraints: 1215 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 79 " 0.017 2.00e-02 2.50e+03 2.17e-02 9.44e+00 pdb=" CG TYR A 79 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A 79 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 79 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR A 79 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 79 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 79 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 79 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 420 " 0.052 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO A 421 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 421 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 421 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 513 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.18e+00 pdb=" C ALA A 513 " -0.049 2.00e-02 2.50e+03 pdb=" O ALA A 513 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN A 514 " 0.017 2.00e-02 2.50e+03 ... (remaining 1212 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.46: 317 2.46 - 3.13: 6273 3.13 - 3.80: 13795 3.80 - 4.47: 21635 4.47 - 5.14: 35026 Nonbonded interactions: 77046 Sorted by model distance: nonbonded pdb=" OD1 ASP A 361 " pdb=" O3G ACP A1001 " model vdw 1.795 2.800 nonbonded pdb="HD21 ASN A 403 " pdb=" C2 ACP A1001 " model vdw 1.796 2.240 nonbonded pdb=" HZ3 LYS A 362 " pdb=" O2G ACP A1001 " model vdw 1.817 2.450 nonbonded pdb=" HB3 LYS A 465 " pdb=" HE3 LYS A 465 " model vdw 1.900 2.440 nonbonded pdb=" H LEU A 404 " pdb="HD23 LEU A 404 " model vdw 1.965 2.270 ... (remaining 77041 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: 3.830 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: 0.080 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.360 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:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.012 0.836 7099 Z= 1.082 Angle : 0.731 13.748 9620 Z= 0.417 Chirality : 0.044 0.408 1154 Planarity : 0.004 0.072 1198 Dihedral : 18.483 89.607 2635 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.24 % Allowed : 28.24 % Favored : 67.52 % Cbeta Deviations : 0.24 % 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: -0.29 (0.28), residues: 895 helix: 0.14 (0.25), residues: 443 sheet: 0.65 (0.57), residues: 82 loop : -0.65 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 135 TYR 0.053 0.002 TYR A 79 PHE 0.013 0.001 PHE A 818 TRP 0.006 0.001 TRP A 817 HIS 0.002 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00688 / 0.43 ( 7098) covalent geometry : angle 0.73106 / 0.42 ( 9620) hydrogen bonds : bond 0.22950 / 15.15 ( 375) hydrogen bonds : angle 7.64534 / 5.45 ( 1107) Misc. bond : bond 0.83632 / 44.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 58 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7880 (mtt90) REVERT: A 459 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8146 (ptmt) REVERT: A 460 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8709 (p) outliers start: 33 outliers final: 24 residues processed: 87 average time/residue: 0.4625 time to fit residues: 43.0162 Evaluate side-chains 84 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ARG Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 663 LYS Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 852 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.0370 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 ASN ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.096430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.074178 restraints weight = 11229.362| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.46 r_work: 0.2737 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 7099 Z= 0.156 Angle : 0.476 4.785 9620 Z= 0.261 Chirality : 0.040 0.162 1154 Planarity : 0.003 0.031 1198 Dihedral : 9.566 87.951 1016 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.26 % Allowed : 25.03 % Favored : 69.70 % 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: 0.73 (0.29), residues: 895 helix: 1.26 (0.25), residues: 450 sheet: 0.87 (0.60), residues: 81 loop : -0.54 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 58 TYR 0.026 0.001 TYR A 79 PHE 0.013 0.001 PHE A 776 TRP 0.010 0.001 TRP A 278 HIS 0.002 0.000 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 7098) covalent geometry : angle 0.47562 / 0.26 ( 9620) hydrogen bonds : bond 0.05035 / 3.31 ( 375) hydrogen bonds : angle 4.76018 / 3.38 ( 1107) Misc. bond : bond 0.00372 / 0.20 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 62 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8724 (mtm-85) cc_final: 0.7990 (mtt180) REVERT: A 135 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7045 (mtm-85) REVERT: A 459 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8266 (ptmt) REVERT: A 460 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8903 (p) REVERT: A 479 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7425 (tm-30) REVERT: A 607 GLU cc_start: 0.8033 (pt0) cc_final: 0.7543 (pp20) REVERT: A 674 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7722 (t70) REVERT: A 722 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8479 (ttm) outliers start: 41 outliers final: 21 residues processed: 90 average time/residue: 0.5439 time to fit residues: 51.9654 Evaluate side-chains 87 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 910 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 54 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.094361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.072004 restraints weight = 11470.688| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.49 r_work: 0.2647 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7099 Z= 0.192 Angle : 0.475 4.632 9620 Z= 0.256 Chirality : 0.040 0.133 1154 Planarity : 0.003 0.034 1198 Dihedral : 8.591 86.870 991 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.72 % Allowed : 26.06 % Favored : 70.22 % 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: 0.91 (0.29), residues: 895 helix: 1.56 (0.25), residues: 451 sheet: 0.23 (0.63), residues: 76 loop : -0.46 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.027 0.002 TYR A 79 PHE 0.016 0.001 PHE A 776 TRP 0.009 0.001 TRP A 278 HIS 0.003 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 ( 7098) covalent geometry : angle 0.47518 / 0.26 ( 9620) hydrogen bonds : bond 0.04591 / 3.01 ( 375) hydrogen bonds : angle 4.37401 / 3.09 ( 1107) Misc. bond : bond 0.00337 / 0.18 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 0.292 Fit side-chains REVERT: A 25 ARG cc_start: 0.8731 (mtm-85) cc_final: 0.7978 (mtt180) REVERT: A 135 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7080 (mtm-85) REVERT: A 206 GLU cc_start: 0.8287 (pm20) cc_final: 0.8064 (pm20) REVERT: A 459 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8200 (pttp) REVERT: A 722 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8478 (ttm) REVERT: A 831 MET cc_start: 0.9054 (mmm) cc_final: 0.8610 (mmm) REVERT: A 874 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7981 (ttp) outliers start: 29 outliers final: 16 residues processed: 82 average time/residue: 0.5866 time to fit residues: 50.9814 Evaluate side-chains 79 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 910 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 77 optimal weight: 0.0040 chunk 53 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 83 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 9 optimal weight: 0.0020 overall best weight: 0.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.097047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.074714 restraints weight = 11489.935| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.52 r_work: 0.2708 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 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 : 0.002 0.046 7099 Z= 0.101 Angle : 0.399 5.226 9620 Z= 0.218 Chirality : 0.038 0.128 1154 Planarity : 0.002 0.029 1198 Dihedral : 7.263 73.092 984 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.95 % Allowed : 27.98 % Favored : 69.06 % 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: 1.45 (0.30), residues: 895 helix: 1.98 (0.26), residues: 459 sheet: 1.06 (0.61), residues: 81 loop : -0.40 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 443 TYR 0.031 0.001 TYR A 79 PHE 0.011 0.001 PHE A 290 TRP 0.009 0.001 TRP A 278 HIS 0.001 0.000 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 7098) covalent geometry : angle 0.39946 / 0.22 ( 9620) hydrogen bonds : bond 0.03596 / 2.37 ( 375) hydrogen bonds : angle 4.02799 / 2.85 ( 1107) Misc. bond : bond 0.00303 / 0.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.289 Fit side-chains REVERT: A 25 ARG cc_start: 0.8760 (mtm-85) cc_final: 0.7962 (mtt180) REVERT: A 79 TYR cc_start: 0.6913 (p90) cc_final: 0.6624 (OUTLIER) REVERT: A 206 GLU cc_start: 0.8264 (pm20) cc_final: 0.8052 (pm20) REVERT: A 459 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8104 (pttp) REVERT: A 479 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7462 (tm-30) REVERT: A 908 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7510 (pt0) outliers start: 23 outliers final: 14 residues processed: 79 average time/residue: 0.5559 time to fit residues: 46.8752 Evaluate side-chains 74 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 910 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 0.0570 chunk 78 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.095073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.072700 restraints weight = 11424.039| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.51 r_work: 0.2665 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7099 Z= 0.169 Angle : 0.444 4.353 9620 Z= 0.238 Chirality : 0.040 0.130 1154 Planarity : 0.003 0.031 1198 Dihedral : 6.971 57.979 983 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.88 % Allowed : 25.29 % Favored : 69.83 % 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: 1.39 (0.29), residues: 895 helix: 1.98 (0.26), residues: 457 sheet: 0.35 (0.63), residues: 76 loop : -0.28 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 621 TYR 0.022 0.001 TYR A 79 PHE 0.016 0.001 PHE A 776 TRP 0.009 0.001 TRP A 278 HIS 0.002 0.000 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 7098) covalent geometry : angle 0.44382 / 0.24 ( 9620) hydrogen bonds : bond 0.04062 / 2.67 ( 375) hydrogen bonds : angle 4.08641 / 2.89 ( 1107) Misc. bond : bond 0.00266 / 0.14 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 58 time to evaluate : 0.295 Fit side-chains REVERT: A 25 ARG cc_start: 0.8744 (mtm-85) cc_final: 0.7992 (mtt180) REVERT: A 135 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7222 (mtm-85) REVERT: A 206 GLU cc_start: 0.8290 (pm20) cc_final: 0.8047 (pm20) REVERT: A 459 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8200 (pttp) REVERT: A 722 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8451 (ttm) REVERT: A 874 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.7995 (ttp) REVERT: A 908 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7518 (pt0) outliers start: 38 outliers final: 21 residues processed: 85 average time/residue: 0.5984 time to fit residues: 53.9970 Evaluate side-chains 85 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 79 TYR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 910 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 48 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 81 optimal weight: 0.0980 chunk 77 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 61 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.096898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.074519 restraints weight = 11443.596| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.51 r_work: 0.2695 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7099 Z= 0.106 Angle : 0.396 4.694 9620 Z= 0.216 Chirality : 0.038 0.127 1154 Planarity : 0.002 0.029 1198 Dihedral : 6.499 59.628 983 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.47 % Allowed : 26.57 % Favored : 69.96 % 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 (0.30), residues: 895 helix: 2.21 (0.26), residues: 460 sheet: 1.07 (0.60), residues: 81 loop : -0.31 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 686 TYR 0.024 0.001 TYR A 79 PHE 0.010 0.001 PHE A 776 TRP 0.009 0.001 TRP A 278 HIS 0.001 0.000 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 7098) covalent geometry : angle 0.39560 / 0.22 ( 9620) hydrogen bonds : bond 0.03523 / 2.32 ( 375) hydrogen bonds : angle 3.91159 / 2.77 ( 1107) Misc. bond : bond 0.00290 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8733 (mtm-85) cc_final: 0.7946 (mtm180) REVERT: A 135 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7209 (mtm-85) REVERT: A 206 GLU cc_start: 0.8287 (pm20) cc_final: 0.8052 (pm20) REVERT: A 459 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8262 (pttp) REVERT: A 722 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8532 (ttm) REVERT: A 874 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7852 (ttp) outliers start: 27 outliers final: 19 residues processed: 78 average time/residue: 0.5899 time to fit residues: 48.9335 Evaluate side-chains 83 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 910 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 74 optimal weight: 0.2980 chunk 86 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN A 398 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.096213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.073796 restraints weight = 11402.591| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.50 r_work: 0.2689 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7099 Z= 0.127 Angle : 0.408 5.715 9620 Z= 0.221 Chirality : 0.039 0.126 1154 Planarity : 0.002 0.029 1198 Dihedral : 6.307 55.708 980 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.72 % Allowed : 26.57 % Favored : 69.70 % 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: 1.75 (0.30), residues: 895 helix: 2.26 (0.26), residues: 460 sheet: 1.05 (0.60), residues: 81 loop : -0.29 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 492 TYR 0.041 0.002 TYR A 79 PHE 0.013 0.001 PHE A 776 TRP 0.008 0.001 TRP A 278 HIS 0.001 0.000 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 7098) covalent geometry : angle 0.40832 / 0.22 ( 9620) hydrogen bonds : bond 0.03640 / 2.40 ( 375) hydrogen bonds : angle 3.91005 / 2.77 ( 1107) Misc. bond : bond 0.00274 / 0.14 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 0.324 Fit side-chains REVERT: A 135 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7145 (mtm-85) REVERT: A 206 GLU cc_start: 0.8292 (pm20) cc_final: 0.8047 (pm20) REVERT: A 459 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8243 (pttp) REVERT: A 722 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8450 (ttm) REVERT: A 874 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.7892 (ttp) REVERT: A 908 GLU cc_start: 0.7712 (pt0) cc_final: 0.7479 (pt0) outliers start: 29 outliers final: 19 residues processed: 80 average time/residue: 0.5851 time to fit residues: 49.5986 Evaluate side-chains 81 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 910 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 14 optimal weight: 1.9990 chunk 84 optimal weight: 0.0270 chunk 75 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 chunk 88 optimal weight: 0.0670 chunk 30 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.097511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.075248 restraints weight = 11402.974| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.50 r_work: 0.2710 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7099 Z= 0.093 Angle : 0.385 6.145 9620 Z= 0.210 Chirality : 0.038 0.127 1154 Planarity : 0.002 0.028 1198 Dihedral : 6.102 53.758 980 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.72 % Allowed : 26.57 % Favored : 69.70 % 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: 1.97 (0.30), residues: 895 helix: 2.49 (0.26), residues: 460 sheet: 1.13 (0.59), residues: 81 loop : -0.24 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 492 TYR 0.011 0.001 TYR A 806 PHE 0.010 0.001 PHE A 290 TRP 0.008 0.001 TRP A 278 HIS 0.001 0.000 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 ( 7098) covalent geometry : angle 0.38453 / 0.21 ( 9620) hydrogen bonds : bond 0.03295 / 2.17 ( 375) hydrogen bonds : angle 3.78713 / 2.68 ( 1107) Misc. bond : bond 0.00290 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.234 Fit side-chains REVERT: A 135 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7161 (mtm-85) REVERT: A 206 GLU cc_start: 0.8287 (pm20) cc_final: 0.8054 (pm20) REVERT: A 459 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8210 (pttp) REVERT: A 908 GLU cc_start: 0.7741 (pt0) cc_final: 0.7518 (pt0) outliers start: 29 outliers final: 22 residues processed: 85 average time/residue: 0.5108 time to fit residues: 46.1662 Evaluate side-chains 87 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 910 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 52 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 HIS A 161 GLN A 398 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.094403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.072158 restraints weight = 11442.429| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.50 r_work: 0.2665 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7099 Z= 0.197 Angle : 0.463 5.397 9620 Z= 0.248 Chirality : 0.040 0.130 1154 Planarity : 0.003 0.029 1198 Dihedral : 6.338 53.882 980 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.21 % Allowed : 27.21 % Favored : 69.58 % 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 (0.29), residues: 895 helix: 2.21 (0.26), residues: 457 sheet: 0.97 (0.57), residues: 87 loop : -0.32 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 755 TYR 0.014 0.001 TYR A 806 PHE 0.019 0.001 PHE A 776 TRP 0.009 0.001 TRP A 278 HIS 0.002 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 ( 7098) covalent geometry : angle 0.46264 / 0.25 ( 9620) hydrogen bonds : bond 0.04132 / 2.70 ( 375) hydrogen bonds : angle 4.01965 / 2.85 ( 1107) Misc. bond : bond 0.00231 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.205 Fit side-chains REVERT: A 23 ILE cc_start: 0.8142 (mt) cc_final: 0.7911 (mp) REVERT: A 459 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8225 (pttp) REVERT: A 722 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8461 (ttm) REVERT: A 874 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8043 (ttp) REVERT: A 908 GLU cc_start: 0.7860 (pt0) cc_final: 0.7656 (pt0) outliers start: 25 outliers final: 17 residues processed: 77 average time/residue: 0.5105 time to fit residues: 41.7612 Evaluate side-chains 77 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 874 MET Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 910 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.095439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.073059 restraints weight = 11430.623| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.51 r_work: 0.2682 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7099 Z= 0.144 Angle : 0.424 5.667 9620 Z= 0.230 Chirality : 0.039 0.129 1154 Planarity : 0.002 0.028 1198 Dihedral : 6.263 54.639 980 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.95 % Allowed : 27.47 % Favored : 69.58 % 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: 1.74 (0.30), residues: 895 helix: 2.28 (0.26), residues: 457 sheet: 0.94 (0.56), residues: 87 loop : -0.31 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 621 TYR 0.013 0.001 TYR A 806 PHE 0.014 0.001 PHE A 776 TRP 0.009 0.001 TRP A 278 HIS 0.001 0.000 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 7098) covalent geometry : angle 0.42379 / 0.23 ( 9620) hydrogen bonds : bond 0.03792 / 2.49 ( 375) hydrogen bonds : angle 3.94075 / 2.79 ( 1107) Misc. bond : bond 0.00243 / 0.13 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.227 Fit side-chains REVERT: A 23 ILE cc_start: 0.8110 (mt) cc_final: 0.7907 (mp) REVERT: A 206 GLU cc_start: 0.8302 (pm20) cc_final: 0.8063 (pm20) REVERT: A 459 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8193 (pttp) REVERT: A 722 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8455 (ttm) outliers start: 23 outliers final: 18 residues processed: 77 average time/residue: 0.5326 time to fit residues: 43.6517 Evaluate side-chains 79 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 537 TYR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 910 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 47 optimal weight: 0.0770 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 9 optimal weight: 0.0970 chunk 4 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.096131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.073795 restraints weight = 11392.990| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.50 r_work: 0.2696 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7099 Z= 0.119 Angle : 0.405 5.768 9620 Z= 0.220 Chirality : 0.039 0.127 1154 Planarity : 0.002 0.029 1198 Dihedral : 6.172 55.337 980 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.82 % Allowed : 27.60 % Favored : 69.58 % 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: 1.84 (0.30), residues: 895 helix: 2.37 (0.26), residues: 460 sheet: 1.08 (0.58), residues: 81 loop : -0.29 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 492 TYR 0.043 0.002 TYR A 79 PHE 0.012 0.001 PHE A 776 TRP 0.008 0.001 TRP A 278 HIS 0.001 0.000 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 7098) covalent geometry : angle 0.40466 / 0.22 ( 9620) hydrogen bonds : bond 0.03576 / 2.35 ( 375) hydrogen bonds : angle 3.85982 / 2.73 ( 1107) Misc. bond : bond 0.00249 / 0.13 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2446.38 seconds wall clock time: 42 minutes 29.94 seconds (2549.94 seconds total)