Starting phenix.real_space_refine on Wed Aug 5 12:16:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8seb_40409/08_2026/8seb_40409.cif Found real_map, /net/cci-nas-00/data/ceres_data/8seb_40409/08_2026/8seb_40409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8seb_40409/08_2026/8seb_40409.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8seb_40409/08_2026/8seb_40409.cif" model { file = "/net/cci-nas-00/data/ceres_data/8seb_40409/08_2026/8seb_40409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8seb_40409/08_2026/8seb_40409.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8seb_40409/08_2026/8seb_40409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8seb_40409/08_2026/8seb_40409.map" } resolution = 3.24 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 36 5.16 5 C 6106 2.51 5 N 1687 2.21 5 O 1779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9609 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7693 Classifications: {'peptide': 989} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 65, 'TRANS': 923} Chain: "B" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 650 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "C" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1243 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 133} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 2.06, per 1000 atoms: 0.21 Number of scatterers: 9609 At special positions: 0 Unit cell: (103.317, 96.6512, 112.482, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 1 15.00 O 1779 8.00 N 1687 7.00 C 6106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS C 86 " distance=2.03 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: 0.82 Conformation dependent library (CDL) restraints added in 354.7 milliseconds 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2292 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 9 sheets defined 44.8% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 24 through 33 removed outlier: 3.731A pdb=" N ARG A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 55 Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.696A pdb=" N ASP A 71 " --> pdb=" O CYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 86 through 99 removed outlier: 3.874A pdb=" N GLU A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 119 Processing helix chain 'A' and resid 128 through 143 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 266 through 273 removed outlier: 3.885A pdb=" N LEU A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 305 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 342 through 353 Processing helix chain 'A' and resid 357 through 378 Processing helix chain 'A' and resid 392 through 395 removed outlier: 3.726A pdb=" N LEU A 395 " --> pdb=" O LEU A 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 392 through 395' Processing helix chain 'A' and resid 415 through 423 Processing helix chain 'A' and resid 423 through 432 Processing helix chain 'A' and resid 441 through 455 Processing helix chain 'A' and resid 491 through 504 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.725A pdb=" N GLU A 521 " --> pdb=" O PRO A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 541 through 556 Processing helix chain 'A' and resid 585 through 593 removed outlier: 4.354A pdb=" N ASP A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 604 removed outlier: 4.219A pdb=" N VAL A 601 " --> pdb=" O PRO A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 623 Processing helix chain 'A' and resid 624 through 630 removed outlier: 4.354A pdb=" N GLU A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 637 removed outlier: 4.318A pdb=" N ALA A 636 " --> pdb=" O HIS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 653 removed outlier: 4.042A pdb=" N THR A 650 " --> pdb=" O PRO A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 656 No H-bonds generated for 'chain 'A' and resid 654 through 656' Processing helix chain 'A' and resid 669 through 682 removed outlier: 3.915A pdb=" N HIS A 676 " --> pdb=" O TRP A 672 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 721 through 740 removed outlier: 3.649A pdb=" N LEU A 725 " --> pdb=" O GLN A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 757 removed outlier: 3.634A pdb=" N LEU A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 removed outlier: 3.832A pdb=" N MET A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 799 removed outlier: 3.981A pdb=" N GLN A 787 " --> pdb=" O GLY A 783 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 815 removed outlier: 3.503A pdb=" N ASN A 815 " --> pdb=" O ASP A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 812 through 815' Processing helix chain 'A' and resid 816 through 832 removed outlier: 3.684A pdb=" N GLN A 830 " --> pdb=" O SER A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 843 Processing helix chain 'A' and resid 853 through 872 removed outlier: 3.721A pdb=" N LYS A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 940 Processing helix chain 'A' and resid 959 through 967 Processing helix chain 'A' and resid 970 through 980 Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 118 through 120 No H-bonds generated for 'chain 'B' and resid 118 through 120' Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.594A pdb=" N LYS C 49 " --> pdb=" O TYR C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 114 Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 132 through 148 removed outlier: 3.619A pdb=" N PHE C 136 " --> pdb=" O ASN C 132 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.667A pdb=" N VAL A 121 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 155 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.667A pdb=" N VAL A 121 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.168A pdb=" N LEU A 208 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER A 212 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ALA A 252 " --> pdb=" O SER A 212 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 214 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLY A 250 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY A 216 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU A 248 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N ARG A 249 " --> pdb=" O HIS A 183 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS A 183 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 251 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 236 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 509 through 512 removed outlier: 7.052A pdb=" N LEU A 464 " --> pdb=" O ILE A 510 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LEU A 512 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 466 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU A 436 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ALA A 538 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL A 438 " --> pdb=" O ALA A 538 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 904 through 906 Processing sheet with id=AA7, first strand: chain 'A' and resid 917 through 920 removed outlier: 6.154A pdb=" N LEU A 917 " --> pdb=" O HIS A1009 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU A1011 " --> pdb=" O LEU A 917 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A 919 " --> pdb=" O GLU A1011 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 945 " --> pdb=" O SER A 995 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ARG A 944 " --> pdb=" O ALA A 955 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA A 955 " --> pdb=" O ARG A 944 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU A 946 " --> pdb=" O LEU A 953 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 98 Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 27 removed outlier: 5.718A pdb=" N ASN C 24 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU C 38 " --> pdb=" O ASN C 24 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2854 1.33 - 1.45: 1466 1.45 - 1.57: 5473 1.57 - 1.69: 4 1.69 - 1.81: 54 Bond restraints: 9851 Sorted by residual: bond pdb=" C1' AMP B 201 " pdb=" O4' AMP B 201 " ideal model delta sigma weight residual 1.415 1.621 -0.206 1.50e-02 4.44e+03 1.88e+02 bond pdb=" C1' AMP B 201 " pdb=" C2' AMP B 201 " ideal model delta sigma weight residual 1.526 1.363 0.163 1.50e-02 4.44e+03 1.18e+02 bond pdb=" C4' AMP B 201 " pdb=" O4' AMP B 201 " ideal model delta sigma weight residual 1.454 1.292 0.162 1.50e-02 4.44e+03 1.17e+02 bond pdb=" C6 AMP B 201 " pdb=" N6 AMP B 201 " ideal model delta sigma weight residual 1.355 1.496 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" C4 AMP B 201 " pdb=" C5 AMP B 201 " ideal model delta sigma weight residual 1.490 1.373 0.117 2.00e-02 2.50e+03 3.42e+01 ... (remaining 9846 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 13359 2.96 - 5.93: 51 5.93 - 8.89: 5 8.89 - 11.85: 1 11.85 - 14.81: 3 Bond angle restraints: 13419 Sorted by residual: angle pdb=" C2' AMP B 201 " pdb=" C1' AMP B 201 " pdb=" N9 AMP B 201 " ideal model delta sigma weight residual 114.00 127.40 -13.40 1.50e+00 4.44e-01 7.99e+01 angle pdb=" N9 AMP B 201 " pdb=" C1' AMP B 201 " pdb=" O4' AMP B 201 " ideal model delta sigma weight residual 108.20 96.21 11.99 1.50e+00 4.44e-01 6.39e+01 angle pdb=" C1' AMP B 201 " pdb=" O4' AMP B 201 " pdb=" C4' AMP B 201 " ideal model delta sigma weight residual 109.70 101.81 7.89 1.00e+00 1.00e+00 6.22e+01 angle pdb=" O2P AMP B 201 " pdb=" P AMP B 201 " pdb=" O3P AMP B 201 " ideal model delta sigma weight residual 119.90 105.09 14.81 3.00e+00 1.11e-01 2.44e+01 angle pdb=" C3' AMP B 201 " pdb=" C4' AMP B 201 " pdb=" C5' AMP B 201 " ideal model delta sigma weight residual 115.20 109.40 5.80 1.50e+00 4.44e-01 1.50e+01 ... (remaining 13414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.88: 5800 29.88 - 59.77: 128 59.77 - 89.65: 10 89.65 - 119.54: 0 119.54 - 149.42: 1 Dihedral angle restraints: 5939 sinusoidal: 2399 harmonic: 3540 Sorted by residual: dihedral pdb=" C5' AMP B 201 " pdb=" O5' AMP B 201 " pdb=" P AMP B 201 " pdb=" O3P AMP B 201 " ideal model delta sinusoidal sigma weight residual 300.00 150.58 149.42 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" C1' AMP B 201 " pdb=" C4' AMP B 201 " pdb=" O4' AMP B 201 " pdb=" C5' AMP B 201 " ideal model delta sinusoidal sigma weight residual -123.00 -156.55 33.55 1 8.00e+00 1.56e-02 2.50e+01 dihedral pdb=" CA GLN A 923 " pdb=" C GLN A 923 " pdb=" N PRO A 924 " pdb=" CA PRO A 924 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 5936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 855 0.025 - 0.050: 407 0.050 - 0.074: 123 0.074 - 0.099: 77 0.099 - 0.124: 34 Chirality restraints: 1496 Sorted by residual: chirality pdb=" CA ILE C 85 " pdb=" N ILE C 85 " pdb=" C ILE C 85 " pdb=" CB ILE C 85 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" C2' AMP B 201 " pdb=" C1' AMP B 201 " pdb=" C3' AMP B 201 " pdb=" O2' AMP B 201 " both_signs ideal model delta sigma weight residual False -2.52 -2.40 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE A 214 " pdb=" N ILE A 214 " pdb=" C ILE A 214 " pdb=" CB ILE A 214 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 1493 not shown) Planarity restraints: 1762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 645 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO A 646 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 646 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 646 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 517 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO A 518 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 518 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 518 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 692 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO A 693 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 693 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 693 " -0.017 5.00e-02 4.00e+02 ... (remaining 1759 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1095 2.75 - 3.29: 9826 3.29 - 3.83: 16019 3.83 - 4.36: 18622 4.36 - 4.90: 32187 Nonbonded interactions: 77749 Sorted by model distance: nonbonded pdb=" OG1 THR A 927 " pdb=" O LEU A 967 " model vdw 2.213 3.040 nonbonded pdb=" OD1 ASP A 517 " pdb=" OG1 THR A 519 " model vdw 2.231 3.040 nonbonded pdb=" O THR A 553 " pdb=" NH2 ARG A 916 " model vdw 2.264 3.120 nonbonded pdb=" O GLU A 621 " pdb=" OG SER A 626 " model vdw 2.268 3.040 nonbonded pdb=" OG1 THR C 99 " pdb=" OE1 GLN C 103 " model vdw 2.277 3.040 ... (remaining 77744 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: 0.000 Normalize map: mean=0, sd=1: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.960 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 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 : 0.005 0.206 9853 Z= 0.285 Angle : 0.583 14.813 13421 Z= 0.305 Chirality : 0.037 0.124 1496 Planarity : 0.004 0.053 1762 Dihedral : 12.083 149.425 3644 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.48 % Rotamer: Outliers : 1.74 % Allowed : 8.02 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.67 (0.25), residues: 1217 helix: 1.62 (0.25), residues: 448 sheet: 0.19 (0.39), residues: 182 loop : -0.34 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 204 TYR 0.007 0.001 TYR A 388 PHE 0.008 0.001 PHE A 146 TRP 0.013 0.001 TRP A 666 HIS 0.002 0.000 HIS A 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.27 ( 9851) covalent geometry : angle 0.58329 / 0.31 (13419) SS BOND : bond 0.00143 / 0.08 ( 1) SS BOND : angle 0.76750 / 0.44 ( 2) hydrogen bonds : bond 0.18190 / 11.72 ( 432) hydrogen bonds : angle 6.68135 / 4.76 ( 1251) Misc. bond : bond 0.08281 / 4.36 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7079 (mm-30) REVERT: A 177 LEU cc_start: 0.6400 (mm) cc_final: 0.5709 (mt) REVERT: A 224 ASP cc_start: 0.8906 (m-30) cc_final: 0.8695 (p0) REVERT: A 229 HIS cc_start: 0.6930 (t-90) cc_final: 0.6423 (t-90) REVERT: A 256 VAL cc_start: 0.8355 (t) cc_final: 0.7773 (m) REVERT: A 258 ARG cc_start: 0.7278 (ptp-110) cc_final: 0.6752 (mtt-85) REVERT: A 410 LEU cc_start: 0.8792 (mp) cc_final: 0.8499 (mt) REVERT: A 473 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7589 (mm-30) REVERT: A 476 ASN cc_start: 0.7845 (m110) cc_final: 0.7611 (m-40) REVERT: A 490 ARG cc_start: 0.8582 (mtp180) cc_final: 0.8209 (mtm110) REVERT: A 565 SER cc_start: 0.8111 (t) cc_final: 0.7471 (p) REVERT: A 738 MET cc_start: -0.0859 (mtp) cc_final: -0.1281 (mpp) REVERT: A 867 GLU cc_start: 0.7224 (mm-30) cc_final: 0.7018 (mm-30) REVERT: A 988 ARG cc_start: 0.7076 (mmp-170) cc_final: 0.6728 (mmp80) REVERT: B 87 ARG cc_start: 0.7951 (tpp80) cc_final: 0.7732 (tpp80) REVERT: C 26 SER cc_start: 0.7760 (p) cc_final: 0.7399 (t) REVERT: C 67 MET cc_start: 0.7287 (mpp) cc_final: 0.7021 (mpp) REVERT: C 136 PHE cc_start: 0.6273 (OUTLIER) cc_final: 0.5768 (m-80) outliers start: 18 outliers final: 6 residues processed: 177 average time/residue: 0.1058 time to fit residues: 25.8397 Evaluate side-chains 104 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 0.0020 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 HIS A 132 GLN A 288 HIS A 433 GLN A 508 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN C 109 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.212372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.140984 restraints weight = 12680.225| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 3.78 r_work: 0.3388 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9853 Z= 0.150 Angle : 0.608 7.470 13421 Z= 0.297 Chirality : 0.041 0.189 1496 Planarity : 0.004 0.058 1762 Dihedral : 6.410 125.727 1337 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.19 % Favored : 95.65 % Rotamer: Outliers : 2.90 % Allowed : 11.30 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.59 (0.25), residues: 1217 helix: 1.56 (0.25), residues: 457 sheet: 0.08 (0.38), residues: 184 loop : -0.40 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 204 TYR 0.014 0.001 TYR C 21 PHE 0.011 0.001 PHE A 146 TRP 0.012 0.001 TRP A 666 HIS 0.011 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 9851) covalent geometry : angle 0.60839 / 0.30 (13419) SS BOND : bond 0.00226 / 0.12 ( 1) SS BOND : angle 0.40030 / 0.21 ( 2) hydrogen bonds : bond 0.04072 / 2.65 ( 432) hydrogen bonds : angle 5.39736 / 3.78 ( 1251) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8374 (mmm) cc_final: 0.7855 (mmm) REVERT: A 84 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7775 (mm-30) REVERT: A 229 HIS cc_start: 0.6874 (t-90) cc_final: 0.6506 (t-90) REVERT: A 256 VAL cc_start: 0.8844 (t) cc_final: 0.8434 (m) REVERT: A 258 ARG cc_start: 0.7573 (ptp-110) cc_final: 0.7178 (mtt-85) REVERT: A 468 ASP cc_start: 0.8012 (t0) cc_final: 0.7756 (t0) REVERT: A 470 ASP cc_start: 0.8152 (t0) cc_final: 0.7764 (t0) REVERT: A 477 LEU cc_start: 0.7747 (pt) cc_final: 0.7479 (pt) REVERT: A 565 SER cc_start: 0.8326 (t) cc_final: 0.7932 (p) REVERT: A 738 MET cc_start: -0.1326 (mtp) cc_final: -0.1832 (mpp) REVERT: A 807 MET cc_start: 0.2611 (tpt) cc_final: 0.2357 (tpt) REVERT: A 988 ARG cc_start: 0.7576 (mmp-170) cc_final: 0.7256 (mmp80) REVERT: B 87 ARG cc_start: 0.8234 (tpp80) cc_final: 0.7916 (tpp80) REVERT: C 26 SER cc_start: 0.7946 (p) cc_final: 0.7555 (t) REVERT: C 54 ARG cc_start: 0.6462 (ttm170) cc_final: 0.5966 (ptm160) REVERT: C 105 LEU cc_start: 0.9032 (mt) cc_final: 0.8716 (pp) REVERT: C 106 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8216 (mt-10) REVERT: C 136 PHE cc_start: 0.6462 (OUTLIER) cc_final: 0.5761 (m-80) outliers start: 30 outliers final: 18 residues processed: 132 average time/residue: 0.1023 time to fit residues: 18.5756 Evaluate side-chains 111 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 28 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 64 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 102 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 = 0.4539 r_free = 0.4539 target = 0.209863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.128472 restraints weight = 12729.882| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.91 r_work: 0.3470 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 0.040 9853 Z= 0.137 Angle : 0.575 6.701 13421 Z= 0.278 Chirality : 0.040 0.144 1496 Planarity : 0.004 0.058 1762 Dihedral : 6.204 102.473 1337 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.03 % Favored : 95.81 % Rotamer: Outliers : 3.29 % Allowed : 12.17 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.60 (0.25), residues: 1217 helix: 1.55 (0.24), residues: 461 sheet: 0.00 (0.36), residues: 189 loop : -0.37 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 195 TYR 0.017 0.001 TYR C 21 PHE 0.010 0.001 PHE C 63 TRP 0.012 0.001 TRP A 666 HIS 0.005 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 9851) covalent geometry : angle 0.57524 / 0.28 (13419) SS BOND : bond 0.00256 / 0.13 ( 1) SS BOND : angle 0.43517 / 0.23 ( 2) hydrogen bonds : bond 0.03611 / 2.37 ( 432) hydrogen bonds : angle 5.17031 / 3.62 ( 1251) Misc. bond : bond 0.00046 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8334 (mmm) cc_final: 0.7832 (mmm) REVERT: A 84 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7825 (mm-30) REVERT: A 229 HIS cc_start: 0.6836 (t-90) cc_final: 0.6449 (t-90) REVERT: A 256 VAL cc_start: 0.8922 (t) cc_final: 0.8590 (m) REVERT: A 258 ARG cc_start: 0.7555 (ptp-110) cc_final: 0.7148 (mtt-85) REVERT: A 263 ARG cc_start: 0.8336 (mtp85) cc_final: 0.8124 (ttp80) REVERT: A 468 ASP cc_start: 0.8123 (t0) cc_final: 0.7864 (t0) REVERT: A 470 ASP cc_start: 0.8286 (t0) cc_final: 0.7893 (t0) REVERT: A 565 SER cc_start: 0.8369 (t) cc_final: 0.8003 (p) REVERT: A 738 MET cc_start: -0.1354 (mtp) cc_final: -0.1827 (mpp) REVERT: A 807 MET cc_start: 0.2712 (tpt) cc_final: 0.2456 (tpt) REVERT: A 988 ARG cc_start: 0.7614 (mmp-170) cc_final: 0.7311 (mmp80) REVERT: B 87 ARG cc_start: 0.8291 (tpp80) cc_final: 0.7946 (tpp80) REVERT: C 26 SER cc_start: 0.7987 (p) cc_final: 0.7576 (t) REVERT: C 54 ARG cc_start: 0.6371 (ttm170) cc_final: 0.5999 (ptm160) REVERT: C 105 LEU cc_start: 0.9077 (mt) cc_final: 0.8726 (pp) REVERT: C 106 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8154 (mt-10) REVERT: C 136 PHE cc_start: 0.6320 (OUTLIER) cc_final: 0.5617 (m-80) outliers start: 34 outliers final: 18 residues processed: 120 average time/residue: 0.0971 time to fit residues: 15.9459 Evaluate side-chains 108 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 82 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 85 optimal weight: 0.0030 chunk 44 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 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 = 0.4542 r_free = 0.4542 target = 0.210334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.135377 restraints weight = 12867.617| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 3.36 r_work: 0.3407 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9853 Z= 0.124 Angle : 0.564 9.142 13421 Z= 0.271 Chirality : 0.040 0.231 1496 Planarity : 0.004 0.058 1762 Dihedral : 5.754 78.561 1335 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.11 % Favored : 95.73 % Rotamer: Outliers : 3.48 % Allowed : 12.46 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.62 (0.25), residues: 1217 helix: 1.59 (0.24), residues: 461 sheet: -0.09 (0.37), residues: 184 loop : -0.32 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 204 TYR 0.018 0.001 TYR C 21 PHE 0.010 0.001 PHE C 63 TRP 0.012 0.001 TRP A 666 HIS 0.005 0.001 HIS C 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 9851) covalent geometry : angle 0.56380 / 0.27 (13419) SS BOND : bond 0.00249 / 0.13 ( 1) SS BOND : angle 0.36389 / 0.20 ( 2) hydrogen bonds : bond 0.03332 / 2.18 ( 432) hydrogen bonds : angle 5.01655 / 3.50 ( 1251) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8256 (mmm) cc_final: 0.7834 (mmm) REVERT: A 256 VAL cc_start: 0.8947 (t) cc_final: 0.8636 (m) REVERT: A 258 ARG cc_start: 0.7537 (ptp-110) cc_final: 0.7146 (mtt-85) REVERT: A 468 ASP cc_start: 0.7909 (t0) cc_final: 0.7689 (t0) REVERT: A 470 ASP cc_start: 0.8175 (t0) cc_final: 0.7856 (t0) REVERT: A 565 SER cc_start: 0.8322 (t) cc_final: 0.7946 (p) REVERT: A 738 MET cc_start: -0.1392 (mtp) cc_final: -0.1842 (mpp) REVERT: A 807 MET cc_start: 0.2664 (tpt) cc_final: 0.2443 (tpt) REVERT: A 988 ARG cc_start: 0.7551 (mmp-170) cc_final: 0.7268 (mmp80) REVERT: B 87 ARG cc_start: 0.8178 (tpp80) cc_final: 0.7866 (tpp80) REVERT: C 54 ARG cc_start: 0.6362 (ttm170) cc_final: 0.6032 (ptm160) REVERT: C 105 LEU cc_start: 0.9090 (mt) cc_final: 0.8780 (pp) REVERT: C 106 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8092 (mt-10) REVERT: C 136 PHE cc_start: 0.6276 (OUTLIER) cc_final: 0.5558 (m-80) outliers start: 36 outliers final: 23 residues processed: 123 average time/residue: 0.0836 time to fit residues: 14.4419 Evaluate side-chains 110 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 107 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 13 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 chunk 93 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.208971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.131743 restraints weight = 12888.325| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 3.78 r_work: 0.3409 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9853 Z= 0.141 Angle : 0.574 8.612 13421 Z= 0.277 Chirality : 0.040 0.200 1496 Planarity : 0.004 0.058 1762 Dihedral : 5.220 49.917 1335 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.94 % Favored : 95.89 % Rotamer: Outliers : 3.38 % Allowed : 13.72 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.59 (0.25), residues: 1217 helix: 1.54 (0.24), residues: 461 sheet: -0.09 (0.36), residues: 191 loop : -0.34 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 204 TYR 0.011 0.001 TYR A1010 PHE 0.012 0.001 PHE C 63 TRP 0.013 0.001 TRP A 666 HIS 0.005 0.001 HIS C 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 9851) covalent geometry : angle 0.57365 / 0.28 (13419) SS BOND : bond 0.00206 / 0.11 ( 1) SS BOND : angle 0.32565 / 0.17 ( 2) hydrogen bonds : bond 0.03280 / 2.15 ( 432) hydrogen bonds : angle 4.93944 / 3.44 ( 1251) Misc. bond : bond 0.00113 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8254 (mmm) cc_final: 0.7799 (mmm) REVERT: A 256 VAL cc_start: 0.8997 (t) cc_final: 0.8714 (m) REVERT: A 258 ARG cc_start: 0.7515 (ptp-110) cc_final: 0.7129 (mtt-85) REVERT: A 470 ASP cc_start: 0.8162 (t0) cc_final: 0.7848 (t0) REVERT: A 503 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7854 (tt) REVERT: A 565 SER cc_start: 0.8327 (t) cc_final: 0.7940 (p) REVERT: A 643 MET cc_start: -0.1022 (tpt) cc_final: -0.1354 (ttm) REVERT: A 738 MET cc_start: -0.1367 (mtp) cc_final: -0.1823 (mpp) REVERT: A 807 MET cc_start: 0.2690 (tpt) cc_final: 0.2396 (tpt) REVERT: A 988 ARG cc_start: 0.7553 (mmp-170) cc_final: 0.7272 (mmp80) REVERT: B 87 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7840 (tpp80) REVERT: C 54 ARG cc_start: 0.6364 (ttm170) cc_final: 0.6099 (ptt90) REVERT: C 105 LEU cc_start: 0.9071 (mt) cc_final: 0.8812 (pp) REVERT: C 106 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8180 (mt-10) REVERT: C 136 PHE cc_start: 0.6316 (OUTLIER) cc_final: 0.5590 (m-80) outliers start: 35 outliers final: 21 residues processed: 118 average time/residue: 0.0852 time to fit residues: 14.3719 Evaluate side-chains 111 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 83 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 GLN A 554 HIS A 610 HIS ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 HIS ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.205636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.142990 restraints weight = 12918.962| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 3.75 r_work: 0.3311 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 9853 Z= 0.351 Angle : 0.736 8.800 13421 Z= 0.366 Chirality : 0.045 0.170 1496 Planarity : 0.005 0.054 1762 Dihedral : 5.699 49.485 1335 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.18 % Favored : 94.66 % Rotamer: Outliers : 2.80 % Allowed : 15.17 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.19 (0.24), residues: 1217 helix: 0.83 (0.24), residues: 469 sheet: -0.58 (0.35), residues: 190 loop : -0.70 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 916 TYR 0.015 0.002 TYR A 388 PHE 0.018 0.002 PHE B 122 TRP 0.016 0.002 TRP A 666 HIS 0.006 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00847 / 0.35 ( 9851) covalent geometry : angle 0.73620 / 0.37 (13419) SS BOND : bond 0.00435 / 0.23 ( 1) SS BOND : angle 0.76001 / 0.40 ( 2) hydrogen bonds : bond 0.04331 / 2.94 ( 432) hydrogen bonds : angle 5.37592 / 3.75 ( 1251) Misc. bond : bond 0.00143 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 VAL cc_start: 0.8922 (t) cc_final: 0.8645 (m) REVERT: A 258 ARG cc_start: 0.7705 (ptp-110) cc_final: 0.7338 (mtt-85) REVERT: A 503 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8131 (tt) REVERT: A 738 MET cc_start: -0.1188 (mtp) cc_final: -0.1643 (mpp) REVERT: A 807 MET cc_start: 0.2740 (tpt) cc_final: 0.2449 (tpt) REVERT: A 867 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7602 (mm-30) REVERT: A 988 ARG cc_start: 0.7663 (mmp-170) cc_final: 0.7351 (mmp80) REVERT: B 134 GLN cc_start: 0.8250 (tp40) cc_final: 0.8012 (tp-100) REVERT: B 139 GLU cc_start: 0.8638 (tt0) cc_final: 0.8327 (tt0) REVERT: C 54 ARG cc_start: 0.6434 (ttm170) cc_final: 0.6063 (ptt90) REVERT: C 105 LEU cc_start: 0.9083 (mt) cc_final: 0.8813 (pp) REVERT: C 106 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8085 (mt-10) REVERT: C 136 PHE cc_start: 0.6214 (OUTLIER) cc_final: 0.5500 (m-80) outliers start: 29 outliers final: 20 residues processed: 117 average time/residue: 0.0981 time to fit residues: 16.5823 Evaluate side-chains 107 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 110 optimal weight: 0.0060 chunk 5 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 83 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 104 optimal weight: 0.0060 chunk 42 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.5214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 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 = 0.4515 r_free = 0.4515 target = 0.208554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.128813 restraints weight = 12699.022| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.32 r_work: 0.3423 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9853 Z= 0.122 Angle : 0.590 8.942 13421 Z= 0.285 Chirality : 0.040 0.261 1496 Planarity : 0.004 0.057 1762 Dihedral : 5.076 47.775 1334 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.11 % Favored : 95.73 % Rotamer: Outliers : 2.32 % Allowed : 15.65 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.24 (0.24), residues: 1217 helix: 1.27 (0.24), residues: 469 sheet: -0.44 (0.36), residues: 189 loop : -0.51 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 942 TYR 0.015 0.001 TYR C 21 PHE 0.010 0.001 PHE C 63 TRP 0.015 0.001 TRP A 666 HIS 0.006 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 9851) covalent geometry : angle 0.59017 / 0.29 (13419) SS BOND : bond 0.00298 / 0.16 ( 1) SS BOND : angle 0.59091 / 0.31 ( 2) hydrogen bonds : bond 0.03198 / 2.10 ( 432) hydrogen bonds : angle 4.92090 / 3.42 ( 1251) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8429 (mmm) cc_final: 0.7777 (mmm) REVERT: A 256 VAL cc_start: 0.8911 (t) cc_final: 0.8647 (m) REVERT: A 258 ARG cc_start: 0.7578 (ptp-110) cc_final: 0.7173 (mtt-85) REVERT: A 363 MET cc_start: 0.7146 (tpt) cc_final: 0.6837 (tpt) REVERT: A 468 ASP cc_start: 0.8005 (t70) cc_final: 0.7743 (t0) REVERT: A 470 ASP cc_start: 0.8049 (t0) cc_final: 0.7678 (t0) REVERT: A 503 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8055 (tt) REVERT: A 565 SER cc_start: 0.8250 (t) cc_final: 0.7850 (p) REVERT: A 738 MET cc_start: -0.1145 (mtp) cc_final: -0.1600 (mpp) REVERT: A 807 MET cc_start: 0.2617 (tpt) cc_final: 0.2352 (tpt) REVERT: A 988 ARG cc_start: 0.7553 (mmp-170) cc_final: 0.7277 (mmp80) REVERT: A 1011 GLU cc_start: 0.7417 (mp0) cc_final: 0.7049 (mp0) REVERT: B 87 ARG cc_start: 0.8225 (tpp80) cc_final: 0.7938 (tpp80) REVERT: C 105 LEU cc_start: 0.9049 (mt) cc_final: 0.8823 (pp) REVERT: C 106 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8101 (mt-10) outliers start: 24 outliers final: 18 residues processed: 122 average time/residue: 0.1009 time to fit residues: 17.5047 Evaluate side-chains 113 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 76 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 99 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 72 optimal weight: 20.0000 chunk 100 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 554 HIS ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.207981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.131133 restraints weight = 12809.154| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.72 r_work: 0.3349 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9853 Z= 0.141 Angle : 0.602 9.228 13421 Z= 0.290 Chirality : 0.041 0.236 1496 Planarity : 0.004 0.056 1762 Dihedral : 4.833 45.376 1332 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.19 % Favored : 95.65 % Rotamer: Outliers : 2.80 % Allowed : 15.27 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.32 (0.25), residues: 1217 helix: 1.37 (0.24), residues: 469 sheet: -0.43 (0.36), residues: 189 loop : -0.49 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 204 TYR 0.011 0.001 TYR A1010 PHE 0.010 0.001 PHE C 63 TRP 0.015 0.001 TRP A 666 HIS 0.004 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 9851) covalent geometry : angle 0.60231 / 0.29 (13419) SS BOND : bond 0.00289 / 0.15 ( 1) SS BOND : angle 0.41676 / 0.22 ( 2) hydrogen bonds : bond 0.03188 / 2.11 ( 432) hydrogen bonds : angle 4.83877 / 3.36 ( 1251) Misc. bond : bond 0.00059 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8417 (mmm) cc_final: 0.7810 (mmm) REVERT: A 256 VAL cc_start: 0.8943 (t) cc_final: 0.8683 (m) REVERT: A 258 ARG cc_start: 0.7600 (ptp-110) cc_final: 0.7188 (mtt-85) REVERT: A 468 ASP cc_start: 0.8201 (t70) cc_final: 0.7922 (t0) REVERT: A 470 ASP cc_start: 0.8110 (t0) cc_final: 0.7727 (t0) REVERT: A 503 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8040 (tt) REVERT: A 565 SER cc_start: 0.8379 (t) cc_final: 0.7997 (p) REVERT: A 738 MET cc_start: -0.1077 (mtp) cc_final: -0.1546 (mpp) REVERT: A 807 MET cc_start: 0.2637 (tpt) cc_final: 0.2358 (tpt) REVERT: A 988 ARG cc_start: 0.7554 (mmp-170) cc_final: 0.7273 (mmp80) REVERT: A 1011 GLU cc_start: 0.7484 (mp0) cc_final: 0.7104 (mp0) REVERT: B 87 ARG cc_start: 0.8271 (tpp80) cc_final: 0.7942 (tpp80) REVERT: C 105 LEU cc_start: 0.9058 (mt) cc_final: 0.8816 (pp) REVERT: C 106 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8081 (mt-10) outliers start: 29 outliers final: 21 residues processed: 117 average time/residue: 0.0911 time to fit residues: 15.2524 Evaluate side-chains 118 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain C residue 76 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 63 optimal weight: 0.3980 chunk 68 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 65 optimal weight: 30.0000 chunk 84 optimal weight: 0.0980 chunk 61 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 110 optimal weight: 0.0370 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 554 HIS ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.211032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.137106 restraints weight = 12578.579| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 3.90 r_work: 0.3387 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9853 Z= 0.110 Angle : 0.591 9.633 13421 Z= 0.280 Chirality : 0.040 0.225 1496 Planarity : 0.004 0.056 1762 Dihedral : 4.681 44.335 1332 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.19 % Favored : 95.65 % Rotamer: Outliers : 2.32 % Allowed : 16.14 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.46 (0.25), residues: 1217 helix: 1.52 (0.24), residues: 469 sheet: -0.36 (0.36), residues: 189 loop : -0.43 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 490 TYR 0.011 0.001 TYR A1010 PHE 0.010 0.001 PHE B 122 TRP 0.015 0.001 TRP A 666 HIS 0.004 0.000 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 9851) covalent geometry : angle 0.59140 / 0.28 (13419) SS BOND : bond 0.00227 / 0.12 ( 1) SS BOND : angle 0.29269 / 0.15 ( 2) hydrogen bonds : bond 0.03020 / 1.99 ( 432) hydrogen bonds : angle 4.74267 / 3.30 ( 1251) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8376 (mmm) cc_final: 0.7776 (mmm) REVERT: A 217 MET cc_start: 0.4546 (mpp) cc_final: 0.3839 (mmt) REVERT: A 256 VAL cc_start: 0.8927 (t) cc_final: 0.8656 (m) REVERT: A 258 ARG cc_start: 0.7509 (ptp-110) cc_final: 0.7089 (mtt-85) REVERT: A 363 MET cc_start: 0.7238 (tpt) cc_final: 0.6792 (tpt) REVERT: A 468 ASP cc_start: 0.8147 (t70) cc_final: 0.7863 (t0) REVERT: A 470 ASP cc_start: 0.8078 (t0) cc_final: 0.7687 (t0) REVERT: A 503 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7924 (tt) REVERT: A 565 SER cc_start: 0.8326 (t) cc_final: 0.7918 (p) REVERT: A 738 MET cc_start: -0.1044 (mtp) cc_final: -0.1525 (mpp) REVERT: A 807 MET cc_start: 0.2601 (tpt) cc_final: 0.2366 (tpt) REVERT: A 988 ARG cc_start: 0.7520 (mmp-170) cc_final: 0.7260 (mmp80) REVERT: A 1011 GLU cc_start: 0.7392 (mp0) cc_final: 0.7054 (mp0) REVERT: B 87 ARG cc_start: 0.8248 (tpp80) cc_final: 0.7914 (tpp80) REVERT: C 89 ILE cc_start: 0.8196 (mm) cc_final: 0.7946 (mp) REVERT: C 105 LEU cc_start: 0.9065 (mt) cc_final: 0.8811 (pp) REVERT: C 106 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8065 (mt-10) outliers start: 24 outliers final: 21 residues processed: 122 average time/residue: 0.0969 time to fit residues: 16.7529 Evaluate side-chains 121 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain C residue 76 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 45 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.209083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.136927 restraints weight = 12749.661| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 4.23 r_work: 0.3399 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9853 Z= 0.137 Angle : 0.604 10.072 13421 Z= 0.288 Chirality : 0.041 0.231 1496 Planarity : 0.004 0.054 1762 Dihedral : 4.702 44.934 1332 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.86 % Favored : 95.97 % Rotamer: Outliers : 2.42 % Allowed : 16.43 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.44 (0.25), residues: 1217 helix: 1.47 (0.24), residues: 469 sheet: -0.35 (0.36), residues: 189 loop : -0.43 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 490 TYR 0.011 0.001 TYR A1010 PHE 0.012 0.001 PHE B 122 TRP 0.015 0.001 TRP A 666 HIS 0.004 0.001 HIS C 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 9851) covalent geometry : angle 0.60396 / 0.29 (13419) SS BOND : bond 0.00254 / 0.13 ( 1) SS BOND : angle 0.30757 / 0.16 ( 2) hydrogen bonds : bond 0.03152 / 2.09 ( 432) hydrogen bonds : angle 4.73034 / 3.29 ( 1251) Misc. bond : bond 0.00045 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8375 (mmm) cc_final: 0.7795 (mmm) REVERT: A 217 MET cc_start: 0.4462 (mpp) cc_final: 0.3701 (mmt) REVERT: A 256 VAL cc_start: 0.8944 (t) cc_final: 0.8683 (m) REVERT: A 258 ARG cc_start: 0.7536 (ptp-110) cc_final: 0.7142 (mtt-85) REVERT: A 363 MET cc_start: 0.7287 (tpt) cc_final: 0.6840 (tpt) REVERT: A 468 ASP cc_start: 0.7993 (t70) cc_final: 0.7725 (t70) REVERT: A 470 ASP cc_start: 0.7953 (t0) cc_final: 0.7591 (t0) REVERT: A 503 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7958 (tt) REVERT: A 565 SER cc_start: 0.8327 (t) cc_final: 0.7955 (p) REVERT: A 738 MET cc_start: -0.1049 (mtp) cc_final: -0.1536 (mpp) REVERT: A 807 MET cc_start: 0.2594 (tpt) cc_final: 0.2350 (tpt) REVERT: A 988 ARG cc_start: 0.7539 (mmp-170) cc_final: 0.7290 (mmp80) REVERT: A 1011 GLU cc_start: 0.7423 (mp0) cc_final: 0.7106 (mp0) REVERT: C 89 ILE cc_start: 0.8294 (mm) cc_final: 0.8038 (mp) REVERT: C 105 LEU cc_start: 0.9065 (mt) cc_final: 0.8840 (pp) REVERT: C 106 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8042 (mt-10) outliers start: 25 outliers final: 23 residues processed: 113 average time/residue: 0.0879 time to fit residues: 13.9063 Evaluate side-chains 120 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain C residue 76 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 114 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 72 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 0.2980 chunk 115 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 554 HIS ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.211043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136290 restraints weight = 12707.804| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.77 r_work: 0.3364 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9853 Z= 0.193 Angle : 0.634 9.856 13421 Z= 0.305 Chirality : 0.042 0.234 1496 Planarity : 0.004 0.053 1762 Dihedral : 4.856 46.097 1332 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.44 % Favored : 95.40 % Rotamer: Outliers : 2.32 % Allowed : 16.62 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.28 (0.24), residues: 1217 helix: 1.34 (0.24), residues: 468 sheet: -0.47 (0.36), residues: 190 loop : -0.50 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 490 TYR 0.011 0.001 TYR A 388 PHE 0.017 0.001 PHE B 122 TRP 0.016 0.001 TRP A 666 HIS 0.004 0.001 HIS C 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 ( 9851) covalent geometry : angle 0.63443 / 0.30 (13419) SS BOND : bond 0.00320 / 0.17 ( 1) SS BOND : angle 0.38731 / 0.20 ( 2) hydrogen bonds : bond 0.03386 / 2.26 ( 432) hydrogen bonds : angle 4.84681 / 3.38 ( 1251) Misc. bond : bond 0.00064 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2760.45 seconds wall clock time: 47 minutes 49.96 seconds (2869.96 seconds total)