Starting phenix.real_space_refine on Thu Jul 2 07:24:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zlk_74405/07_2026/9zlk_74405_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zlk_74405/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9zlk_74405/07_2026/9zlk_74405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zlk_74405/07_2026/9zlk_74405.map" model { file = "/net/cci-nas-00/data/ceres_data/9zlk_74405/07_2026/9zlk_74405_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zlk_74405/07_2026/9zlk_74405_neut_trim.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 61 Ad-hoc single atom residues: {' K': 1} Unusual residues: {' MG': 4, 'ACP': 1} Classifications: {'undetermined': 5, 'water': 26} Link IDs: {None: 29} Chain breaks: 1 Time building chain proxies: 1.32, per 1000 atoms: 0.18 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: 0.36 Conformation dependent library (CDL) restraints added in 361.1 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: 0.79 Time building geometry restraints manager: 0.56 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: 0.000 Normalize map: mean=0, sd=1: 4.210 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: 0.060 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.110 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:5.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.400 ------------------------------------------------------------------------------- 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 : 0.276 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: 0.3728 time to fit residues: 34.7720 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 : 0.298 ------------------------------------------------------------------------------- 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: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 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 = 0.096438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.074198 restraints weight = 11227.016| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.45 r_work: 0.2735 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 7099 Z= 0.155 Angle : 0.476 4.829 9620 Z= 0.261 Chirality : 0.040 0.168 1154 Planarity : 0.003 0.030 1198 Dihedral : 9.584 87.820 1016 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.39 % Allowed : 24.65 % 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: 0.72 (0.29), residues: 895 helix: 1.26 (0.26), residues: 450 sheet: 0.86 (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 0.025 0.001 TYR A 79 PHE 0.012 0.001 PHE A 818 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 0.00357 / 0.16 ( 7098) covalent geometry : angle 0.47557 / 0.26 ( 9620) hydrogen bonds : bond 0.05080 / 3.34 ( 375) hydrogen bonds : angle 4.77405 / 3.39 ( 1107) Misc. bond : bond 0.00534 / 0.28 ( 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 105 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 63 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8733 (mtm-85) cc_final: 0.7993 (mtt180) REVERT: A 135 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7047 (mtm-85) REVERT: A 459 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8265 (ptmt) REVERT: A 460 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8903 (p) REVERT: A 479 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7426 (tm-30) REVERT: A 607 GLU cc_start: 0.8037 (pt0) cc_final: 0.7544 (pp20) REVERT: A 674 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7726 (t70) REVERT: A 722 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8478 (ttm) outliers start: 42 outliers final: 21 residues processed: 92 average time/residue: 0.4118 time to fit residues: 40.2234 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 : 0.231 ------------------------------------------------------------------------------- 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: 0.9990 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN A 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.095224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.072814 restraints weight = 11481.756| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.50 r_work: 0.2665 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7099 Z= 0.169 Angle : 0.457 4.351 9620 Z= 0.247 Chirality : 0.040 0.132 1154 Planarity : 0.003 0.033 1198 Dihedral : 8.499 86.100 991 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.72 % Allowed : 26.44 % 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: 0.97 (0.29), residues: 895 helix: 1.61 (0.26), residues: 451 sheet: 0.25 (0.63), residues: 76 loop : -0.44 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.028 0.002 TYR A 79 PHE 0.015 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 0.00397 / 0.17 ( 7098) covalent geometry : angle 0.45659 / 0.25 ( 9620) hydrogen bonds : bond 0.04423 / 2.90 ( 375) hydrogen bonds : angle 4.32996 / 3.06 ( 1107) Misc. bond : bond 0.00263 / 0.14 ( 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 : 0.213 Fit side-chains REVERT: A 25 ARG cc_start: 0.8723 (mtm-85) cc_final: 0.7952 (mtt180) REVERT: A 135 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7069 (mtm-85) REVERT: A 206 GLU cc_start: 0.8263 (pm20) cc_final: 0.8059 (pm20) REVERT: A 459 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8151 (ptmt) REVERT: A 722 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8506 (ttm) REVERT: A 831 MET cc_start: 0.9002 (mmm) cc_final: 0.8596 (mmm) REVERT: A 874 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7974 (ttp) outliers start: 29 outliers final: 15 residues processed: 81 average time/residue: 0.4128 time to fit residues: 35.3884 Evaluate side-chains 78 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 20 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 77 optimal weight: 0.3980 chunk 53 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 9 optimal weight: 0.0370 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.3189 r_free = 0.3189 target = 0.096788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.074458 restraints weight = 11496.431| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.50 r_work: 0.2694 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7099 Z= 0.114 Angle : 0.407 5.174 9620 Z= 0.221 Chirality : 0.038 0.128 1154 Planarity : 0.002 0.029 1198 Dihedral : 7.190 70.778 984 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.95 % Allowed : 27.86 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.30), residues: 895 helix: 1.98 (0.26), residues: 459 sheet: 1.07 (0.61), residues: 81 loop : -0.37 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 686 TYR 0.032 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 0.00262 / 0.11 ( 7098) covalent geometry : angle 0.40651 / 0.22 ( 9620) hydrogen bonds : bond 0.03674 / 2.42 ( 375) hydrogen bonds : angle 4.03288 / 2.85 ( 1107) Misc. bond : bond 0.00291 / 0.15 ( 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 84 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.190 Fit side-chains REVERT: A 25 ARG cc_start: 0.8775 (mtm-85) cc_final: 0.7979 (mtt180) REVERT: A 79 TYR cc_start: 0.6949 (p90) cc_final: 0.6678 (OUTLIER) REVERT: A 206 GLU cc_start: 0.8270 (pm20) cc_final: 0.8062 (pm20) REVERT: A 459 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8117 (pttp) REVERT: A 479 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: A 722 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8493 (ttm) REVERT: A 908 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7512 (pt0) outliers start: 23 outliers final: 15 residues processed: 76 average time/residue: 0.4425 time to fit residues: 35.6975 Evaluate side-chains 78 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 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 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 674 ASP 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: 0.9980 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 0.0870 chunk 78 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.3171 r_free = 0.3171 target = 0.095578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.073204 restraints weight = 11425.864| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.51 r_work: 0.2664 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7099 Z= 0.149 Angle : 0.428 4.280 9620 Z= 0.231 Chirality : 0.039 0.129 1154 Planarity : 0.003 0.030 1198 Dihedral : 6.899 59.620 983 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.36 % Allowed : 26.32 % Favored : 69.32 % 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: 1.48 (0.30), residues: 895 helix: 2.04 (0.26), residues: 458 sheet: 0.38 (0.63), residues: 76 loop : -0.22 (0.33), residues: 361 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 0.015 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 0.00349 / 0.15 ( 7098) covalent geometry : angle 0.42801 / 0.23 ( 9620) hydrogen bonds : bond 0.03915 / 2.57 ( 375) hydrogen bonds : angle 4.03248 / 2.85 ( 1107) Misc. bond : bond 0.00248 / 0.13 ( 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 93 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 59 time to evaluate : 0.213 Fit side-chains REVERT: A 25 ARG cc_start: 0.8739 (mtm-85) cc_final: 0.7943 (mtm180) REVERT: A 135 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7208 (mtm-85) REVERT: A 206 GLU cc_start: 0.8285 (pm20) cc_final: 0.8045 (pm20) REVERT: A 459 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8214 (pttp) REVERT: A 722 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8510 (ttm) REVERT: A 874 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.7951 (ttp) REVERT: A 908 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7514 (pt0) outliers start: 34 outliers final: 17 residues processed: 82 average time/residue: 0.4506 time to fit residues: 39.1030 Evaluate side-chains 81 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 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 532 MET 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 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: 0.5980 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 81 optimal weight: 0.0470 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.3181 r_free = 0.3181 target = 0.096308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.073815 restraints weight = 11451.977| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.52 r_work: 0.2686 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7099 Z= 0.122 Angle : 0.407 5.595 9620 Z= 0.221 Chirality : 0.039 0.128 1154 Planarity : 0.002 0.029 1198 Dihedral : 6.440 57.471 981 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.59 % Allowed : 26.70 % 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: 1.67 (0.30), residues: 895 helix: 2.18 (0.26), residues: 460 sheet: 1.05 (0.60), residues: 81 loop : -0.32 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 755 TYR 0.037 0.001 TYR A 79 PHE 0.012 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 0.00279 / 0.12 ( 7098) covalent geometry : angle 0.40693 / 0.22 ( 9620) hydrogen bonds : bond 0.03642 / 2.40 ( 375) hydrogen bonds : angle 3.93165 / 2.78 ( 1107) Misc. bond : bond 0.00264 / 0.14 ( 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 89 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.223 Fit side-chains REVERT: A 25 ARG cc_start: 0.8730 (mtm-85) cc_final: 0.7980 (mtm180) REVERT: A 135 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7202 (mtm-85) REVERT: A 206 GLU cc_start: 0.8290 (pm20) cc_final: 0.8054 (pm20) REVERT: A 459 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8262 (pttp) REVERT: A 722 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8522 (ttm) REVERT: A 874 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7857 (ttp) REVERT: A 908 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7547 (pt0) outliers start: 28 outliers final: 18 residues processed: 80 average time/residue: 0.4605 time to fit residues: 39.0259 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 : 0.181 ------------------------------------------------------------------------------- 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 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 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 908 GLU 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: 1.9990 chunk 31 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 chunk 86 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3175 r_free = 0.3175 target = 0.095849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.073542 restraints weight = 11417.854| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.50 r_work: 0.2680 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1757 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= 0.137 Angle : 0.414 4.434 9620 Z= 0.224 Chirality : 0.039 0.127 1154 Planarity : 0.003 0.029 1198 Dihedral : 6.360 54.889 980 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.85 % Allowed : 26.70 % Favored : 69.45 % 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: 1.04 (0.60), residues: 81 loop : -0.30 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 492 TYR 0.032 0.001 TYR A 79 PHE 0.013 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 0.00318 / 0.14 ( 7098) covalent geometry : angle 0.41370 / 0.22 ( 9620) hydrogen bonds : bond 0.03729 / 2.45 ( 375) hydrogen bonds : angle 3.93731 / 2.79 ( 1107) Misc. bond : bond 0.00252 / 0.13 ( 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 89 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 59 time to evaluate : 0.182 Fit side-chains REVERT: A 135 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7161 (mtm-85) REVERT: A 206 GLU cc_start: 0.8295 (pm20) cc_final: 0.8055 (pm20) REVERT: A 459 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8239 (pttp) REVERT: A 722 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8504 (ttm) REVERT: A 874 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.7960 (ttp) outliers start: 30 outliers final: 21 residues processed: 81 average time/residue: 0.4623 time to fit residues: 39.8223 Evaluate side-chains 83 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 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 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: 0.0030 chunk 75 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 88 optimal weight: 0.0870 chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 overall best weight: 0.4568 ------------------------------------------------------------------------------- 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 = 0.3185 r_free = 0.3185 target = 0.096531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.074229 restraints weight = 11445.909| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.51 r_work: 0.2684 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1805 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= 0.112 Angle : 0.398 5.350 9620 Z= 0.217 Chirality : 0.038 0.127 1154 Planarity : 0.002 0.028 1198 Dihedral : 6.248 54.304 980 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.85 % Allowed : 26.70 % Favored : 69.45 % 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: 1.79 (0.30), residues: 895 helix: 2.34 (0.26), residues: 460 sheet: 0.46 (0.62), residues: 76 loop : -0.14 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 492 TYR 0.035 0.001 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 0.00256 / 0.11 ( 7098) covalent geometry : angle 0.39790 / 0.22 ( 9620) hydrogen bonds : bond 0.03527 / 2.32 ( 375) hydrogen bonds : angle 3.86582 / 2.74 ( 1107) Misc. bond : bond 0.00259 / 0.14 ( 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 92 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 0.175 Fit side-chains REVERT: A 135 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7158 (mtm-85) REVERT: A 206 GLU cc_start: 0.8295 (pm20) cc_final: 0.8055 (pm20) REVERT: A 459 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8219 (pttp) REVERT: A 722 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8521 (ttm) REVERT: A 874 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.7890 (ttp) outliers start: 30 outliers final: 22 residues processed: 84 average time/residue: 0.4349 time to fit residues: 38.8713 Evaluate side-chains 87 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 52 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 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: 0.7980 chunk 59 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3177 r_free = 0.3177 target = 0.095980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.073712 restraints weight = 11376.641| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.50 r_work: 0.2691 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1849 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= 0.133 Angle : 0.412 6.030 9620 Z= 0.224 Chirality : 0.039 0.126 1154 Planarity : 0.002 0.029 1198 Dihedral : 6.264 54.899 980 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.59 % Allowed : 26.83 % 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: 1.80 (0.30), residues: 895 helix: 2.32 (0.26), residues: 460 sheet: 0.46 (0.59), residues: 82 loop : -0.10 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 258 TYR 0.044 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 0.00310 / 0.13 ( 7098) covalent geometry : angle 0.41224 / 0.22 ( 9620) hydrogen bonds : bond 0.03657 / 2.40 ( 375) hydrogen bonds : angle 3.89058 / 2.76 ( 1107) Misc. bond : bond 0.00244 / 0.13 ( 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 87 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 59 time to evaluate : 0.222 Fit side-chains REVERT: A 135 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7124 (mtm-85) REVERT: A 459 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8217 (pttp) REVERT: A 722 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8485 (ttm) REVERT: A 874 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7906 (ttp) outliers start: 28 outliers final: 20 residues processed: 81 average time/residue: 0.3932 time to fit residues: 34.0276 Evaluate side-chains 82 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN 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 200 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 20 optimal weight: 0.0670 chunk 60 optimal weight: 0.1980 chunk 4 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3183 r_free = 0.3183 target = 0.096396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.074154 restraints weight = 11373.856| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.45 r_work: 0.2691 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1841 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= 0.118 Angle : 0.403 6.756 9620 Z= 0.219 Chirality : 0.038 0.126 1154 Planarity : 0.002 0.029 1198 Dihedral : 6.207 54.775 980 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.34 % Allowed : 27.21 % Favored : 69.45 % 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: 1.87 (0.30), residues: 895 helix: 2.38 (0.26), residues: 460 sheet: 0.48 (0.59), residues: 82 loop : -0.09 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 492 TYR 0.012 0.001 TYR A 806 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 0.00272 / 0.12 ( 7098) covalent geometry : angle 0.40264 / 0.22 ( 9620) hydrogen bonds : bond 0.03534 / 2.32 ( 375) hydrogen bonds : angle 3.84188 / 2.73 ( 1107) Misc. bond : bond 0.00245 / 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 86 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.333 Fit side-chains REVERT: A 135 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7117 (mtm-85) REVERT: A 459 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8175 (pttp) REVERT: A 722 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8518 (ttm) REVERT: A 874 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7889 (ttp) outliers start: 26 outliers final: 21 residues processed: 79 average time/residue: 0.5404 time to fit residues: 45.5958 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 : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 47 optimal weight: 0.6980 chunk 74 optimal weight: 0.0020 chunk 31 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 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 = 0.3175 r_free = 0.3175 target = 0.095867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.073461 restraints weight = 11424.831| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.52 r_work: 0.2672 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7099 Z= 0.140 Angle : 0.414 5.707 9620 Z= 0.225 Chirality : 0.039 0.126 1154 Planarity : 0.003 0.029 1198 Dihedral : 6.242 55.422 980 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.47 % Allowed : 26.96 % 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: 1.83 (0.30), residues: 895 helix: 2.35 (0.26), residues: 460 sheet: 0.48 (0.59), residues: 82 loop : -0.10 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 135 TYR 0.039 0.002 TYR A 79 PHE 0.014 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 0.00326 / 0.14 ( 7098) covalent geometry : angle 0.41424 / 0.22 ( 9620) hydrogen bonds : bond 0.03681 / 2.42 ( 375) hydrogen bonds : angle 3.88184 / 2.75 ( 1107) Misc. bond : bond 0.00234 / 0.12 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1979.93 seconds wall clock time: 34 minutes 35.61 seconds (2075.61 seconds total)