Starting phenix.real_space_refine on Sat Jul 4 00:07:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zqh_60385/07_2026/8zqh_60385.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zqh_60385/07_2026/8zqh_60385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zqh_60385/07_2026/8zqh_60385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zqh_60385/07_2026/8zqh_60385.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zqh_60385/07_2026/8zqh_60385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zqh_60385/07_2026/8zqh_60385.map" } resolution = 3.12 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= 0.008 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: 6 Type Number sf(0) Gaussians P 74 5.49 5 S 25 5.16 5 C 5379 2.51 5 N 1643 2.21 5 O 1861 1.98 5 H 8203 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s 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: 17185 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1510 Classifications: {'RNA': 47} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 21, 'rna3p_pyr': 21} Link IDs: {'rna2p': 5, 'rna3p': 41} Chain breaks: 1 Chain: "C" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 607 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain breaks: 1 Chain: "A" Number of atoms: 14812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 14812 Classifications: {'peptide': 908} Link IDs: {'PTRANS': 32, 'TRANS': 875} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 256 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Time building chain proxies: 3.24, per 1000 atoms: 0.19 Number of scatterers: 17185 At special positions: 0 Unit cell: (93.06, 102.3, 112.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 25 16.00 P 74 15.00 O 1861 8.00 N 1643 7.00 C 5379 6.00 H 8203 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=0, symmetry=0 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 644.0 milliseconds 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 7 sheets defined 50.6% alpha, 16.4% beta 28 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 15 through 40 removed outlier: 3.567A pdb=" N LEU A 37 " --> pdb=" O MET A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.590A pdb=" N THR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.535A pdb=" N LEU A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 137 through 147 Processing helix chain 'A' and resid 152 through 158 removed outlier: 3.968A pdb=" N LYS A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 169 removed outlier: 4.282A pdb=" N ARG A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 187 through 200 Processing helix chain 'A' and resid 211 through 253 removed outlier: 3.798A pdb=" N GLY A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 272 Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 293 through 301 removed outlier: 4.715A pdb=" N ARG A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLY A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 314 through 329 Processing helix chain 'A' and resid 447 through 459 removed outlier: 3.567A pdb=" N ALA A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 553 removed outlier: 4.197A pdb=" N ARG A 541 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 548 " --> pdb=" O ARG A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.513A pdb=" N LEU A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 571 Processing helix chain 'A' and resid 578 through 606 removed outlier: 3.667A pdb=" N ARG A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 610 through 616 removed outlier: 4.371A pdb=" N ASP A 614 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 642 removed outlier: 4.257A pdb=" N PHE A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 690 Processing helix chain 'A' and resid 711 through 719 removed outlier: 3.504A pdb=" N ASN A 714 " --> pdb=" O ARG A 711 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 715 " --> pdb=" O LYS A 712 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU A 716 " --> pdb=" O GLU A 713 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 717 " --> pdb=" O ASN A 714 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 718 " --> pdb=" O SER A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 removed outlier: 3.759A pdb=" N VAL A 725 " --> pdb=" O ALA A 721 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 726 " --> pdb=" O PRO A 722 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A 728 " --> pdb=" O MET A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 796 removed outlier: 3.646A pdb=" N ALA A 786 " --> pdb=" O ALA A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 832 Processing helix chain 'A' and resid 854 through 864 removed outlier: 4.446A pdb=" N LEU A 858 " --> pdb=" O GLU A 854 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS A 864 " --> pdb=" O GLN A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 899 removed outlier: 3.862A pdb=" N GLU A 886 " --> pdb=" O GLU A 882 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 349 through 352 removed outlier: 4.406A pdb=" N LYS A 422 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N ASP A 438 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE A 424 " --> pdb=" O PHE A 436 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE A 436 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU A 426 " --> pdb=" O TYR A 434 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR A 434 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG A 428 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N TYR A 433 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 7 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU A 10 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE A 369 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 349 through 352 removed outlier: 5.052A pdb=" N THR A 408 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASN A 392 " --> pdb=" O THR A 408 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 47 removed outlier: 3.537A pdb=" N TYR A 44 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 513 through 517 removed outlier: 3.939A pdb=" N SER A 513 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 488 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N MET A 475 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N GLU A 697 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE A 477 " --> pdb=" O GLU A 697 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL A 694 " --> pdb=" O TRP A 741 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL A 743 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N MET A 696 " --> pdb=" O VAL A 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 499 through 503 removed outlier: 4.524A pdb=" N ILE A 499 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL A 503 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLU A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 760 through 761 Processing sheet with id=AA7, first strand: chain 'A' and resid 803 through 809 removed outlier: 3.723A pdb=" N ARG A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 845 " --> pdb=" O THR A 841 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1107 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 134 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 4.56 Time building geometry restraints manager: 2.27 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: 8192 1.03 - 1.23: 49 1.23 - 1.42: 4138 1.42 - 1.62: 5096 1.62 - 1.81: 39 Bond restraints: 17514 Sorted by residual: bond pdb=" C1' DT C -5 " pdb=" N1 DT C -5 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.21e+01 bond pdb=" C1' DT C 8 " pdb=" N1 DT C 8 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.40e+00 bond pdb=" C3' DT C -12 " pdb=" C2' DT C -12 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.57e+00 bond pdb=" C3' DC C -11 " pdb=" C2' DC C -11 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.71e+00 bond pdb=" N3 DA C -2 " pdb=" C4 DA C -2 " ideal model delta sigma weight residual 1.344 1.329 0.015 6.00e-03 2.78e+04 6.15e+00 ... (remaining 17509 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 31454 2.96 - 5.92: 91 5.92 - 8.88: 0 8.88 - 11.84: 0 11.84 - 14.80: 1 Bond angle restraints: 31546 Sorted by residual: angle pdb=" N3 DT D 5 " pdb=" C4 DT D 5 " pdb=" O4 DT D 5 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT C -10 " pdb=" C4 DT C -10 " pdb=" O4 DT C -10 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT C 8 " pdb=" C4 DT C 8 " pdb=" O4 DT C 8 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT C -13 " pdb=" C4 DT C -13 " pdb=" O4 DT C -13 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT D 7 " pdb=" C4 DT D 7 " pdb=" O4 DT D 7 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 ... (remaining 31541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 7658 35.67 - 71.33: 427 71.33 - 107.00: 33 107.00 - 142.66: 1 142.66 - 178.33: 2 Dihedral angle restraints: 8121 sinusoidal: 4999 harmonic: 3122 Sorted by residual: dihedral pdb=" CA PHE A 202 " pdb=" C PHE A 202 " pdb=" N PRO A 203 " pdb=" CA PRO A 203 " ideal model delta harmonic sigma weight residual 180.00 -138.25 -41.75 0 5.00e+00 4.00e-02 6.97e+01 dihedral pdb=" O4' U B -32 " pdb=" C1' U B -32 " pdb=" N1 U B -32 " pdb=" C2 U B -32 " ideal model delta sinusoidal sigma weight residual -128.00 50.33 -178.33 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA ARG A 122 " pdb=" C ARG A 122 " pdb=" N PRO A 123 " pdb=" CA PRO A 123 " ideal model delta harmonic sigma weight residual 180.00 154.22 25.78 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 8118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1083 0.041 - 0.082: 246 0.082 - 0.123: 66 0.123 - 0.165: 23 0.165 - 0.206: 7 Chirality restraints: 1425 Sorted by residual: chirality pdb=" C3' DT D 5 " pdb=" C4' DT D 5 " pdb=" O3' DT D 5 " pdb=" C2' DT D 5 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C3' DA C 4 " pdb=" C4' DA C 4 " pdb=" O3' DA C 4 " pdb=" C2' DA C 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" C3' DA C -1 " pdb=" C4' DA C -1 " pdb=" O3' DA C -1 " pdb=" C2' DA C -1 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.03e-01 ... (remaining 1422 not shown) Planarity restraints: 2342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 202 " 0.110 5.00e-02 4.00e+02 1.66e-01 4.42e+01 pdb=" N PRO A 203 " -0.287 5.00e-02 4.00e+02 pdb=" CA PRO A 203 " 0.096 5.00e-02 4.00e+02 pdb=" CD PRO A 203 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 72 " -0.046 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO A 73 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 568 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO A 569 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 569 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 569 " -0.036 5.00e-02 4.00e+02 ... (remaining 2339 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 346 2.08 - 2.71: 26883 2.71 - 3.34: 48258 3.34 - 3.97: 61439 3.97 - 4.60: 95814 Nonbonded interactions: 232740 Sorted by model distance: nonbonded pdb=" OE1 GLU A 17 " pdb=" H GLU A 17 " model vdw 1.446 2.450 nonbonded pdb=" OP2 U B -32 " pdb=" HH TYR A 666 " model vdw 1.582 2.450 nonbonded pdb=" OE2 GLU A 463 " pdb="HH11 ARG A 465 " model vdw 1.588 2.450 nonbonded pdb="HH11 ARG A 27 " pdb=" OE2 GLU A 208 " model vdw 1.594 2.450 nonbonded pdb=" OE2 GLU A 133 " pdb=" H ASP A 173 " model vdw 1.600 2.450 ... (remaining 232735 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 5.410 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: 0.110 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.840 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 : 0.004 0.077 9311 Z= 0.303 Angle : 0.654 14.796 12887 Z= 0.460 Chirality : 0.042 0.206 1425 Planarity : 0.007 0.166 1410 Dihedral : 20.127 178.331 3935 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.64 % Favored : 95.14 % Rotamer: Outliers : 0.13 % Allowed : 16.45 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -0.51 (0.28), residues: 906 helix: 1.07 (0.26), residues: 395 sheet: -0.67 (0.45), residues: 142 loop : -1.78 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 582 TYR 0.014 0.002 TYR A 872 PHE 0.018 0.002 PHE A 436 TRP 0.009 0.001 TRP A 328 HIS 0.004 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.30 ( 9311) covalent geometry : angle 0.65448 / 0.46 (12887) hydrogen bonds : bond 0.15657 / 14.39 ( 452) hydrogen bonds : angle 6.04308 / 7.84 ( 1241) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.3687 time to fit residues: 52.5394 Evaluate side-chains 64 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 632 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.094668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.061849 restraints weight = 65944.912| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.30 r_work: 0.2828 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9311 Z= 0.205 Angle : 0.615 15.022 12887 Z= 0.346 Chirality : 0.038 0.149 1425 Planarity : 0.007 0.169 1410 Dihedral : 20.028 178.510 2058 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.19 % Favored : 95.58 % Rotamer: Outliers : 1.15 % Allowed : 15.43 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -0.16 (0.28), residues: 906 helix: 1.53 (0.26), residues: 403 sheet: -0.58 (0.41), residues: 154 loop : -1.88 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 49 TYR 0.010 0.001 TYR A 623 PHE 0.012 0.001 PHE A 64 TRP 0.008 0.001 TRP A 720 HIS 0.012 0.002 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 ( 9311) covalent geometry : angle 0.61499 / 0.35 (12887) hydrogen bonds : bond 0.06062 / 5.90 ( 452) hydrogen bonds : angle 4.85358 / 6.21 ( 1241) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8786 (t0) cc_final: 0.8526 (t0) outliers start: 9 outliers final: 8 residues processed: 70 average time/residue: 0.2463 time to fit residues: 22.7475 Evaluate side-chains 64 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 724 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.092717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.059626 restraints weight = 66485.730| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.38 r_work: 0.2783 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9311 Z= 0.241 Angle : 0.588 15.624 12887 Z= 0.330 Chirality : 0.038 0.138 1425 Planarity : 0.006 0.170 1410 Dihedral : 19.962 179.264 2058 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.86 % Favored : 95.92 % Rotamer: Outliers : 1.66 % Allowed : 15.18 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -0.16 (0.28), residues: 906 helix: 1.59 (0.25), residues: 405 sheet: -0.63 (0.41), residues: 152 loop : -1.95 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 625 TYR 0.020 0.002 TYR A 125 PHE 0.014 0.001 PHE A 571 TRP 0.009 0.001 TRP A 229 HIS 0.004 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.24 ( 9311) covalent geometry : angle 0.58772 / 0.33 (12887) hydrogen bonds : bond 0.05322 / 5.20 ( 452) hydrogen bonds : angle 4.61899 / 5.92 ( 1241) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 696 MET cc_start: 0.9417 (ttp) cc_final: 0.9147 (ttp) outliers start: 13 outliers final: 5 residues processed: 71 average time/residue: 0.2812 time to fit residues: 26.1169 Evaluate side-chains 61 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 725 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 632 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.092819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.059707 restraints weight = 66265.388| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.34 r_work: 0.2780 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9311 Z= 0.173 Angle : 0.555 15.008 12887 Z= 0.308 Chirality : 0.037 0.144 1425 Planarity : 0.006 0.169 1410 Dihedral : 19.952 179.193 2058 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.75 % Favored : 95.03 % Rotamer: Outliers : 1.28 % Allowed : 15.05 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 0.00 (0.28), residues: 906 helix: 1.79 (0.25), residues: 408 sheet: -0.77 (0.39), residues: 166 loop : -1.91 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 49 TYR 0.012 0.001 TYR A 22 PHE 0.013 0.001 PHE A 571 TRP 0.008 0.001 TRP A 229 HIS 0.004 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 9311) covalent geometry : angle 0.55513 / 0.31 (12887) hydrogen bonds : bond 0.04709 / 4.60 ( 452) hydrogen bonds : angle 4.30739 / 5.56 ( 1241) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.9058 (t0) cc_final: 0.8773 (t0) REVERT: A 622 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8913 (mp0) outliers start: 10 outliers final: 6 residues processed: 65 average time/residue: 0.2887 time to fit residues: 24.3275 Evaluate side-chains 61 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 774 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.091877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.058785 restraints weight = 66328.018| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.25 r_work: 0.2770 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9311 Z= 0.212 Angle : 0.556 15.170 12887 Z= 0.309 Chirality : 0.037 0.154 1425 Planarity : 0.006 0.169 1410 Dihedral : 19.911 179.494 2058 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.86 % Favored : 94.92 % Rotamer: Outliers : 1.02 % Allowed : 16.20 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 0.08 (0.29), residues: 906 helix: 1.92 (0.25), residues: 409 sheet: -0.83 (0.39), residues: 164 loop : -1.92 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 49 TYR 0.011 0.001 TYR A 22 PHE 0.013 0.001 PHE A 571 TRP 0.008 0.001 TRP A 229 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.21 ( 9311) covalent geometry : angle 0.55608 / 0.31 (12887) hydrogen bonds : bond 0.04632 / 4.52 ( 452) hydrogen bonds : angle 4.26056 / 5.49 ( 1241) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.2736 time to fit residues: 20.9586 Evaluate side-chains 58 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 441 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 2 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.091663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.058595 restraints weight = 65998.398| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.26 r_work: 0.2761 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9311 Z= 0.188 Angle : 0.550 14.988 12887 Z= 0.304 Chirality : 0.037 0.139 1425 Planarity : 0.006 0.169 1410 Dihedral : 19.948 179.253 2058 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.30 % Favored : 94.37 % Rotamer: Outliers : 1.40 % Allowed : 15.05 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 0.15 (0.29), residues: 906 helix: 2.03 (0.25), residues: 409 sheet: -0.86 (0.39), residues: 166 loop : -1.92 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 49 TYR 0.012 0.001 TYR A 22 PHE 0.013 0.001 PHE A 571 TRP 0.008 0.001 TRP A 229 HIS 0.004 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 ( 9311) covalent geometry : angle 0.54987 / 0.30 (12887) hydrogen bonds : bond 0.04427 / 4.30 ( 452) hydrogen bonds : angle 4.13446 / 5.33 ( 1241) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 ILE cc_start: 0.8932 (mm) cc_final: 0.8650 (mm) REVERT: A 622 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8949 (mp0) outliers start: 11 outliers final: 6 residues processed: 61 average time/residue: 0.2694 time to fit residues: 21.2203 Evaluate side-chains 58 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 798 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 18 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.091809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.058946 restraints weight = 66205.388| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.25 r_work: 0.2776 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9311 Z= 0.154 Angle : 0.533 14.690 12887 Z= 0.295 Chirality : 0.036 0.138 1425 Planarity : 0.006 0.168 1410 Dihedral : 19.979 179.120 2058 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.30 % Favored : 95.47 % Rotamer: Outliers : 1.02 % Allowed : 15.82 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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 (0.29), residues: 906 helix: 2.12 (0.25), residues: 413 sheet: -0.83 (0.39), residues: 166 loop : -1.84 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 49 TYR 0.011 0.001 TYR A 22 PHE 0.011 0.001 PHE A 571 TRP 0.009 0.001 TRP A 229 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 9311) covalent geometry : angle 0.53329 / 0.29 (12887) hydrogen bonds : bond 0.04238 / 4.10 ( 452) hydrogen bonds : angle 4.02906 / 5.18 ( 1241) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 ILE cc_start: 0.8923 (mm) cc_final: 0.8651 (mm) REVERT: A 732 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8763 (mm-30) outliers start: 8 outliers final: 8 residues processed: 57 average time/residue: 0.2768 time to fit residues: 20.4174 Evaluate side-chains 58 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 798 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 78 optimal weight: 0.2980 chunk 47 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.091742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.058984 restraints weight = 66023.856| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.30 r_work: 0.2774 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9311 Z= 0.149 Angle : 0.528 14.532 12887 Z= 0.291 Chirality : 0.036 0.139 1425 Planarity : 0.006 0.167 1410 Dihedral : 19.992 179.095 2058 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.42 % Favored : 95.25 % Rotamer: Outliers : 1.53 % Allowed : 15.31 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 0.37 (0.29), residues: 906 helix: 2.21 (0.25), residues: 413 sheet: -0.82 (0.39), residues: 166 loop : -1.82 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 TYR 0.011 0.001 TYR A 22 PHE 0.011 0.001 PHE A 571 TRP 0.009 0.001 TRP A 229 HIS 0.003 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 9311) covalent geometry : angle 0.52826 / 0.29 (12887) hydrogen bonds : bond 0.04164 / 4.03 ( 452) hydrogen bonds : angle 3.96486 / 5.11 ( 1241) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ARG cc_start: 0.8041 (tmm-80) cc_final: 0.7740 (ttp80) REVERT: A 444 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: A 520 ILE cc_start: 0.8935 (mm) cc_final: 0.8654 (mm) outliers start: 12 outliers final: 9 residues processed: 61 average time/residue: 0.2766 time to fit residues: 22.1236 Evaluate side-chains 61 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 879 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 46 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.091013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.058163 restraints weight = 67029.215| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.21 r_work: 0.2761 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9311 Z= 0.182 Angle : 0.541 14.705 12887 Z= 0.299 Chirality : 0.036 0.148 1425 Planarity : 0.006 0.168 1410 Dihedral : 20.016 179.180 2058 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.53 % Favored : 95.14 % Rotamer: Outliers : 1.53 % Allowed : 15.18 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 0.38 (0.29), residues: 906 helix: 2.19 (0.25), residues: 415 sheet: -0.87 (0.40), residues: 166 loop : -1.75 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 49 TYR 0.011 0.001 TYR A 22 PHE 0.012 0.001 PHE A 571 TRP 0.010 0.001 TRP A 229 HIS 0.004 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 ( 9311) covalent geometry : angle 0.54134 / 0.30 (12887) hydrogen bonds : bond 0.04263 / 4.16 ( 452) hydrogen bonds : angle 3.98143 / 5.14 ( 1241) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ARG cc_start: 0.8074 (tmm-80) cc_final: 0.7776 (ttp80) REVERT: A 444 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.7818 (mp0) REVERT: A 520 ILE cc_start: 0.8958 (mm) cc_final: 0.8706 (mm) outliers start: 12 outliers final: 9 residues processed: 59 average time/residue: 0.2644 time to fit residues: 20.6764 Evaluate side-chains 61 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 877 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 70 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.091242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.058551 restraints weight = 66540.993| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.19 r_work: 0.2769 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9311 Z= 0.156 Angle : 0.528 14.517 12887 Z= 0.291 Chirality : 0.036 0.150 1425 Planarity : 0.006 0.167 1410 Dihedral : 20.063 178.893 2058 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.64 % Favored : 95.03 % Rotamer: Outliers : 1.28 % Allowed : 15.43 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 0.47 (0.29), residues: 906 helix: 2.24 (0.25), residues: 416 sheet: -0.85 (0.40), residues: 166 loop : -1.68 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 179 TYR 0.011 0.001 TYR A 22 PHE 0.011 0.001 PHE A 571 TRP 0.009 0.001 TRP A 229 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 ( 9311) covalent geometry : angle 0.52751 / 0.29 (12887) hydrogen bonds : bond 0.04149 / 4.05 ( 452) hydrogen bonds : angle 3.91536 / 5.05 ( 1241) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ARG cc_start: 0.8097 (tmm-80) cc_final: 0.7795 (ttp80) REVERT: A 444 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: A 520 ILE cc_start: 0.8957 (mm) cc_final: 0.8708 (mm) outliers start: 10 outliers final: 8 residues processed: 58 average time/residue: 0.2840 time to fit residues: 21.7331 Evaluate side-chains 59 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 877 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 644 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.092078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.059420 restraints weight = 66567.689| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.21 r_work: 0.2796 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 9311 Z= 0.112 Angle : 0.511 14.034 12887 Z= 0.281 Chirality : 0.035 0.152 1425 Planarity : 0.006 0.166 1410 Dihedral : 20.088 178.649 2058 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.75 % Favored : 96.03 % Rotamer: Outliers : 1.53 % Allowed : 15.18 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 0.67 (0.30), residues: 906 helix: 2.40 (0.26), residues: 416 sheet: -0.74 (0.40), residues: 166 loop : -1.57 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 225 TYR 0.011 0.001 TYR A 22 PHE 0.010 0.001 PHE A 485 TRP 0.010 0.001 TRP A 229 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 9311) covalent geometry : angle 0.51114 / 0.28 (12887) hydrogen bonds : bond 0.03944 / 3.84 ( 452) hydrogen bonds : angle 3.78107 / 4.87 ( 1241) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4017.37 seconds wall clock time: 68 minutes 53.67 seconds (4133.67 seconds total)