Starting phenix.real_space_refine on Sat Jul 4 01:11:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kwc_62607/07_2026/9kwc_62607_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kwc_62607/07_2026/9kwc_62607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kwc_62607/07_2026/9kwc_62607_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kwc_62607/07_2026/9kwc_62607_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kwc_62607/07_2026/9kwc_62607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kwc_62607/07_2026/9kwc_62607.map" } resolution = 2.9 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9014 atoms to isotropic. 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 25 5.49 5 S 24 5.16 5 C 6074 2.51 5 N 1579 2.21 5 O 1912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 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: 9614 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9079 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1121, 9067 Classifications: {'peptide': 1121} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 22, 'TRANS': 1098} Chain breaks: 3 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 160 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 55 Conformer: "B" Number of residues, atoms: 1121, 9067 Classifications: {'peptide': 1121} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 22, 'TRANS': 1098} Chain breaks: 3 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 160 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 55 bond proxies already assigned to first conformer: 9236 Chain: "G" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 535 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 7, 'rna3p_pyr': 7} Link IDs: {'rna2p': 10, 'rna3p': 14} Time building chain proxies: 4.18, per 1000 atoms: 0.43 Number of scatterers: 9614 At special positions: 0 Unit cell: (81.51, 108.87, 122.55, 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 24 16.00 P 25 15.00 O 1912 8.00 N 1579 7.00 C 6074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 790.5 milliseconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 8 sheets defined 45.5% alpha, 8.5% beta 6 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 removed outlier: 3.846A pdb=" N LYS A 6 " --> pdb=" O SER A 2 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE A 7 " --> pdb=" O LYS A 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2 through 7' Processing helix chain 'A' and resid 26 through 34 Processing helix chain 'A' and resid 37 through 69 removed outlier: 5.633A pdb=" N LYS A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLY A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 109 removed outlier: 4.364A pdb=" N LEU A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.728A pdb=" N GLU A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 134 through 144 Processing helix chain 'A' and resid 151 through 161 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 190 through 196 removed outlier: 3.550A pdb=" N ALA A 195 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE A 196 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 209 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 233 through 238 removed outlier: 4.095A pdb=" N TYR A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.547A pdb=" N ILE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 323 removed outlier: 3.773A pdb=" N SER A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.914A pdb=" N GLU A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 352 removed outlier: 4.096A pdb=" N SER A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR A 346 " --> pdb=" O PRO A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 371 Processing helix chain 'A' and resid 378 through 392 removed outlier: 3.559A pdb=" N GLU A 382 " --> pdb=" O THR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 409 through 430 removed outlier: 3.535A pdb=" N VAL A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 449 through 472 removed outlier: 4.388A pdb=" N ALA A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 497 removed outlier: 3.623A pdb=" N ILE A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 512 removed outlier: 4.308A pdb=" N HIS A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 503 " --> pdb=" O LYS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 563 removed outlier: 3.719A pdb=" N ALA A 563 " --> pdb=" O LYS A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 569 removed outlier: 3.630A pdb=" N LYS A 568 " --> pdb=" O LYS A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 697 Processing helix chain 'A' and resid 706 through 710 removed outlier: 3.520A pdb=" N SER A 710 " --> pdb=" O LYS A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 728 removed outlier: 3.608A pdb=" N PHE A 728 " --> pdb=" O PHE A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 756 Processing helix chain 'A' and resid 787 through 791 removed outlier: 3.639A pdb=" N GLU A 791 " --> pdb=" O ARG A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 823 removed outlier: 3.509A pdb=" N GLU A 815 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A 821 " --> pdb=" O ARG A 817 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 885 removed outlier: 3.509A pdb=" N GLU A 885 " --> pdb=" O LYS A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 888 No H-bonds generated for 'chain 'A' and resid 886 through 888' Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 939 through 954 Processing helix chain 'A' and resid 1020 through 1030 Processing helix chain 'A' and resid 1091 through 1103 Processing helix chain 'A' and resid 1111 through 1118 Processing helix chain 'A' and resid 1120 through 1136 removed outlier: 4.031A pdb=" N TYR A1124 " --> pdb=" O ASP A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1170 removed outlier: 3.757A pdb=" N TYR A1167 " --> pdb=" O ASP A1163 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A1169 " --> pdb=" O ARG A1165 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN A1170 " --> pdb=" O ASN A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1201 removed outlier: 3.673A pdb=" N LEU A1192 " --> pdb=" O ALA A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1206 Processing sheet with id=AA1, first strand: chain 'A' and resid 545 through 549 removed outlier: 3.583A pdb=" N LYS A 552 " --> pdb=" O TYR A 549 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TYR A 553 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 20 " --> pdb=" O TYR A 705 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 545 through 549 removed outlier: 3.583A pdb=" N LYS A 552 " --> pdb=" O TYR A 549 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TYR A 553 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 20 " --> pdb=" O TYR A 705 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 582 through 583 Processing sheet with id=AA4, first strand: chain 'A' and resid 841 through 844 removed outlier: 6.287A pdb=" N ILE A 841 " --> pdb=" O GLN A 853 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN A 853 " --> pdb=" O ILE A 841 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A 843 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 858 through 862 Processing sheet with id=AA6, first strand: chain 'A' and resid 1031 through 1037 removed outlier: 6.294A pdb=" N PHE A1031 " --> pdb=" O ASP A1048 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ASP A1048 " --> pdb=" O PHE A1031 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1070 through 1073 Processing sheet with id=AA8, first strand: chain 'A' and resid 1138 through 1139 362 hydrogen bonds defined for protein. 1017 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1614 1.32 - 1.44: 2806 1.44 - 1.56: 5350 1.56 - 1.69: 54 1.69 - 1.81: 40 Bond restraints: 9864 Sorted by residual: bond pdb=" C ASN A1070 " pdb=" O ASN A1070 " ideal model delta sigma weight residual 1.236 1.380 -0.145 1.21e-02 6.83e+03 1.43e+02 bond pdb=" C HIS A 714 " pdb=" O HIS A 714 " ideal model delta sigma weight residual 1.236 1.381 -0.145 1.32e-02 5.74e+03 1.21e+02 bond pdb=" C ASN A1070 " pdb=" CA BASN A1070 " ideal model delta sigma weight residual 1.522 1.619 -0.097 1.20e-02 6.94e+03 6.52e+01 bond pdb=" C ASN A1070 " pdb=" CA AASN A1070 " ideal model delta sigma weight residual 1.522 1.618 -0.096 1.20e-02 6.94e+03 6.44e+01 bond pdb=" C HIS A 714 " pdb=" CA BHIS A 714 " ideal model delta sigma weight residual 1.522 1.621 -0.099 1.39e-02 5.18e+03 5.05e+01 ... (remaining 9859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.87: 13299 5.87 - 11.73: 110 11.73 - 17.60: 17 17.60 - 23.46: 0 23.46 - 29.33: 1 Bond angle restraints: 13427 Sorted by residual: angle pdb=" O ASN A1070 " pdb=" C ASN A1070 " pdb=" CA AASN A1070 " ideal model delta sigma weight residual 120.38 136.11 -15.73 1.09e+00 8.42e-01 2.08e+02 angle pdb=" O ASN A1070 " pdb=" C ASN A1070 " pdb=" CA BASN A1070 " ideal model delta sigma weight residual 120.38 136.08 -15.70 1.09e+00 8.42e-01 2.08e+02 angle pdb=" N GLU A1220 " pdb=" CA GLU A1220 " pdb=" C GLU A1220 " ideal model delta sigma weight residual 110.80 81.47 29.33 2.13e+00 2.20e-01 1.90e+02 angle pdb=" O HIS A 714 " pdb=" C HIS A 714 " pdb=" CA AHIS A 714 " ideal model delta sigma weight residual 119.31 135.76 -16.45 1.24e+00 6.50e-01 1.76e+02 angle pdb=" O HIS A 714 " pdb=" C HIS A 714 " pdb=" CA BHIS A 714 " ideal model delta sigma weight residual 119.31 135.75 -16.44 1.24e+00 6.50e-01 1.76e+02 ... (remaining 13422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 5155 35.64 - 71.27: 776 71.27 - 106.90: 24 106.90 - 142.54: 0 142.54 - 178.17: 2 Dihedral angle restraints: 5957 sinusoidal: 2625 harmonic: 3332 Sorted by residual: dihedral pdb=" O4' U G 16 " pdb=" C1' U G 16 " pdb=" N1 U G 16 " pdb=" C2 U G 16 " ideal model delta sinusoidal sigma weight residual 232.00 55.01 176.99 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" C THR A 776 " pdb=" N THR A 776 " pdb=" CA THR A 776 " pdb=" CB THR A 776 " ideal model delta harmonic sigma weight residual -122.00 -137.94 15.94 0 2.50e+00 1.60e-01 4.07e+01 dihedral pdb=" C GLU A1220 " pdb=" N GLU A1220 " pdb=" CA GLU A1220 " pdb=" CB GLU A1220 " ideal model delta harmonic sigma weight residual -122.60 -107.94 -14.66 0 2.50e+00 1.60e-01 3.44e+01 ... (remaining 5954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1240 0.127 - 0.254: 202 0.254 - 0.381: 30 0.381 - 0.508: 4 0.508 - 0.635: 3 Chirality restraints: 1479 Sorted by residual: chirality pdb=" C3' A G 14 " pdb=" C4' A G 14 " pdb=" O3' A G 14 " pdb=" C2' A G 14 " both_signs ideal model delta sigma weight residual False -2.74 -2.11 -0.63 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CA THR A 776 " pdb=" N THR A 776 " pdb=" C THR A 776 " pdb=" CB THR A 776 " both_signs ideal model delta sigma weight residual False 2.53 1.94 0.58 2.00e-01 2.50e+01 8.55e+00 chirality pdb=" CA LYS A 267 " pdb=" N LYS A 267 " pdb=" C LYS A 267 " pdb=" CB LYS A 267 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.53e+00 ... (remaining 1476 not shown) Planarity restraints: 1632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " -0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO A 271 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 128 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.16e+00 pdb=" N PRO A 129 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 825 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO A 826 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 826 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 826 " -0.029 5.00e-02 4.00e+02 ... (remaining 1629 not shown) Histogram of nonbonded interaction distances: 1.06 - 1.83: 24 1.83 - 2.60: 283 2.60 - 3.36: 12606 3.36 - 4.13: 29808 4.13 - 4.90: 48917 Nonbonded interactions: 91638 Sorted by model distance: nonbonded pdb=" N GLU A1039 " pdb=" OE1 GLU A1039 " model vdw 1.061 3.120 nonbonded pdb=" CG1 VAL A 303 " pdb=" O THR A 307 " model vdw 1.112 3.460 nonbonded pdb=" O ASN A 145 " pdb=" N PHE A 147 " model vdw 1.126 3.120 nonbonded pdb=" CG2 ILE A 240 " pdb=" O GLY A 254 " model vdw 1.164 3.460 nonbonded pdb=" CE2 PHE A 220 " pdb=" CD1 LEU A 255 " model vdw 1.212 3.760 ... (remaining 91633 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=0.47 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: 13.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.860 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:9.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 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 : 0.009 0.189 9866 Z= 0.665 Angle : 1.512 29.325 13427 Z= 1.014 Chirality : 0.101 0.635 1479 Planarity : 0.005 0.088 1632 Dihedral : 26.635 178.173 3811 Min Nonbonded Distance : 1.061 Molprobity Statistics. All-atom Clashscore : 37.33 Ramachandran Plot: Outliers : 3.68 % Allowed : 16.35 % Favored : 79.96 % Rotamer: Outliers : 44.05 % Allowed : 18.38 % Favored : 37.58 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.01 (0.20), residues: 1115 helix: -2.75 (0.18), residues: 454 sheet: -4.25 (0.39), residues: 113 loop : -3.65 (0.22), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 747 TYR 0.022 0.002 TYR A1185 PHE 0.025 0.003 PHE A 521 TRP 0.009 0.002 TRP A 890 HIS 0.003 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00863 / 0.64 ( 9864) covalent geometry : angle 1.51244 / 1.01 (13427) hydrogen bonds : bond 0.21004 / 14.18 ( 357) hydrogen bonds : angle 9.38872 / 6.52 ( 1041) Misc. bond : bond 0.13853 / 6.65 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 429 poor density : 263 time to evaluate : 0.379 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: A 6 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6567 (mmmt) REVERT: A 48 LYS cc_start: 0.5835 (OUTLIER) cc_final: 0.5516 (tttt) REVERT: A 61 PHE cc_start: 0.6138 (OUTLIER) cc_final: 0.5313 (t80) REVERT: A 73 ASN cc_start: 0.1051 (OUTLIER) cc_final: 0.0436 (t0) REVERT: A 87 THR cc_start: 0.3857 (OUTLIER) cc_final: 0.3606 (m) REVERT: A 121 LYS cc_start: 0.6643 (OUTLIER) cc_final: 0.6152 (ptpt) REVERT: A 256 ASN cc_start: 0.6687 (OUTLIER) cc_final: 0.6030 (t0) REVERT: A 266 THR cc_start: 0.1224 (OUTLIER) cc_final: 0.0457 (p) REVERT: A 286 SER cc_start: -0.3274 (OUTLIER) cc_final: -0.3696 (t) REVERT: A 316 SER cc_start: 0.6226 (OUTLIER) cc_final: 0.5846 (t) REVERT: A 324 LEU cc_start: 0.5824 (OUTLIER) cc_final: 0.5413 (mt) REVERT: A 396 SER cc_start: 0.8511 (OUTLIER) cc_final: 0.8211 (t) REVERT: A 398 GLU cc_start: 0.5900 (OUTLIER) cc_final: 0.5567 (mt-10) REVERT: A 423 ASP cc_start: 0.6007 (m-30) cc_final: 0.5753 (m-30) REVERT: A 485 SER cc_start: 0.7817 (OUTLIER) cc_final: 0.7531 (p) REVERT: A 542 TYR cc_start: 0.2822 (OUTLIER) cc_final: 0.2271 (m-80) REVERT: A 552 LYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6630 (tppt) REVERT: A 564 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7063 (ttmt) REVERT: A 690 VAL cc_start: 0.8063 (t) cc_final: 0.7830 (t) REVERT: A 807 LYS cc_start: 0.4791 (OUTLIER) cc_final: 0.4429 (ttmt) REVERT: A 863 PHE cc_start: 0.6462 (OUTLIER) cc_final: 0.5481 (p90) REVERT: A 897 LYS cc_start: 0.7645 (mtpt) cc_final: 0.7414 (mtpt) REVERT: A 959 ASP cc_start: 0.6038 (OUTLIER) cc_final: 0.5832 (t0) REVERT: A 967 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.7363 (t) REVERT: A 1020 SER cc_start: 0.8039 (p) cc_final: 0.7803 (m) REVERT: A 1075 PHE cc_start: 0.4872 (p90) cc_final: 0.4586 (p90) REVERT: A 1097 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7577 (pt0) REVERT: A 1131 MET cc_start: 0.7853 (mmm) cc_final: 0.7558 (tpt) REVERT: A 1155 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.7054 (ptpp) REVERT: A 1214 SER cc_start: 0.7772 (OUTLIER) cc_final: 0.7358 (p) outliers start: 429 outliers final: 54 residues processed: 554 average time/residue: 0.4351 time to fit residues: 260.5986 Evaluate side-chains 226 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 148 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 73 ASN Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 542 TYR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 837 ASN Chi-restraints excluded: chain A residue 863 PHE Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1049 TYR Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1068 TYR Chi-restraints excluded: chain A residue 1097 GLU Chi-restraints excluded: chain A residue 1118 GLN Chi-restraints excluded: chain A residue 1119 SER Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1160 ILE Chi-restraints excluded: chain A residue 1214 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN A 96 ASN A 211 ASN A 226 ASN A 231 GLN A 268 GLN ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 GLN A 449 ASN A 513 GLN A 567 GLN A 703 GLN A 720 HIS ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 HIS ** A 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN A 862 ASN ** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN A 909 HIS A 941 GLN A 955 ASN ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN A1186 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.217448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.180509 restraints weight = 39486.985| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 5.43 r_work: 0.4076 rms_B_bonded: 5.15 restraints_weight: 2.0000 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4101 r_free = 0.4101 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4101 r_free = 0.4101 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 9866 Z= 0.276 Angle : 1.052 14.107 13427 Z= 0.553 Chirality : 0.057 0.395 1479 Planarity : 0.007 0.088 1632 Dihedral : 18.037 170.229 1766 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 27.02 Ramachandran Plot: Outliers : 1.08 % Allowed : 12.31 % Favored : 86.61 % Rotamer: Outliers : 12.53 % Allowed : 38.30 % Favored : 49.18 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.85 (0.22), residues: 1115 helix: -1.48 (0.21), residues: 447 sheet: -4.05 (0.41), residues: 104 loop : -3.22 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 508 TYR 0.030 0.003 TYR A 854 PHE 0.030 0.003 PHE A 315 TRP 0.030 0.003 TRP A 890 HIS 0.009 0.002 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.28 ( 9864) covalent geometry : angle 1.05218 / 0.55 (13427) hydrogen bonds : bond 0.06994 / 4.68 ( 357) hydrogen bonds : angle 6.93583 / 4.77 ( 1041) Misc. bond : bond 0.01712 / 0.89 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 151 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.5526 (OUTLIER) cc_final: 0.5141 (tttt) REVERT: A 61 PHE cc_start: 0.5043 (OUTLIER) cc_final: 0.4051 (t80) REVERT: A 90 GLU cc_start: 0.4048 (OUTLIER) cc_final: 0.3739 (mm-30) REVERT: A 121 LYS cc_start: 0.6495 (OUTLIER) cc_final: 0.5798 (ptpt) REVERT: A 186 ASN cc_start: 0.5301 (OUTLIER) cc_final: 0.4837 (t0) REVERT: A 266 THR cc_start: 0.1261 (OUTLIER) cc_final: 0.1011 (m) REVERT: A 267 LYS cc_start: 0.3496 (OUTLIER) cc_final: 0.3148 (mppt) REVERT: A 276 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.5922 (mm) REVERT: A 286 SER cc_start: -0.2907 (OUTLIER) cc_final: -0.3526 (t) REVERT: A 290 TYR cc_start: -0.0664 (OUTLIER) cc_final: -0.1403 (t80) REVERT: A 324 LEU cc_start: 0.5958 (OUTLIER) cc_final: 0.5672 (mt) REVERT: A 325 PHE cc_start: 0.5284 (OUTLIER) cc_final: 0.4160 (m-10) REVERT: A 339 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8319 (mtpp) REVERT: A 423 ASP cc_start: 0.6434 (m-30) cc_final: 0.6064 (m-30) REVERT: A 552 LYS cc_start: 0.6695 (OUTLIER) cc_final: 0.6314 (mppt) REVERT: A 703 GLN cc_start: 0.5492 (OUTLIER) cc_final: 0.4249 (tt0) REVERT: A 768 LYS cc_start: 0.6527 (tptp) cc_final: 0.5679 (mttt) REVERT: A 769 ASN cc_start: 0.6565 (t0) cc_final: 0.5368 (t0) REVERT: A 807 LYS cc_start: 0.5006 (OUTLIER) cc_final: 0.4408 (ttmt) REVERT: A 835 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6944 (tp30) REVERT: A 863 PHE cc_start: 0.5718 (OUTLIER) cc_final: 0.5509 (p90) REVERT: A 1029 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.8010 (p) REVERT: A 1101 LYS cc_start: 0.7742 (tmtp) cc_final: 0.5826 (ptmt) REVERT: A 1199 LYS cc_start: 0.5509 (mttp) cc_final: 0.5287 (mtmt) outliers start: 122 outliers final: 46 residues processed: 250 average time/residue: 0.3714 time to fit residues: 101.9989 Evaluate side-chains 190 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 126 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 837 ASN Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 863 PHE Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1049 TYR Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1158 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 95 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 90 optimal weight: 0.1980 chunk 66 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 76 ASN A 200 HIS A 226 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN A 399 GLN A 513 GLN A 703 GLN ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 HIS ** A 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.218703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.182919 restraints weight = 25729.186| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 3.41 r_work: 0.4146 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4167 r_free = 0.4167 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4167 r_free = 0.4167 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.4167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 9866 Z= 0.207 Angle : 0.893 11.976 13427 Z= 0.470 Chirality : 0.051 0.375 1479 Planarity : 0.006 0.088 1632 Dihedral : 16.458 172.026 1690 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.90 % Allowed : 12.31 % Favored : 86.79 % Rotamer: Outliers : 9.65 % Allowed : 39.12 % Favored : 51.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.23), residues: 1115 helix: -0.93 (0.22), residues: 445 sheet: -3.70 (0.39), residues: 97 loop : -2.89 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1071 TYR 0.044 0.002 TYR A 183 PHE 0.033 0.003 PHE A 220 TRP 0.032 0.002 TRP A 890 HIS 0.010 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 ( 9864) covalent geometry : angle 0.89343 / 0.47 (13427) hydrogen bonds : bond 0.05904 / 3.92 ( 357) hydrogen bonds : angle 6.27083 / 4.30 ( 1041) Misc. bond : bond 0.00845 / 0.44 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 134 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: A 5 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7326 (pp20) REVERT: A 48 LYS cc_start: 0.5668 (OUTLIER) cc_final: 0.5241 (tttt) REVERT: A 61 PHE cc_start: 0.5129 (OUTLIER) cc_final: 0.4800 (t80) REVERT: A 86 ARG cc_start: 0.4145 (OUTLIER) cc_final: 0.2905 (mtp180) REVERT: A 121 LYS cc_start: 0.6509 (OUTLIER) cc_final: 0.5922 (ptpt) REVERT: A 186 ASN cc_start: 0.6354 (OUTLIER) cc_final: 0.5588 (t0) REVERT: A 187 MET cc_start: 0.1877 (tpt) cc_final: 0.1554 (tpt) REVERT: A 258 TYR cc_start: 0.6898 (m-10) cc_final: 0.6291 (m-10) REVERT: A 267 LYS cc_start: 0.3474 (OUTLIER) cc_final: 0.3067 (ptpp) REVERT: A 276 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.5790 (mt) REVERT: A 286 SER cc_start: -0.2779 (OUTLIER) cc_final: -0.3383 (t) REVERT: A 324 LEU cc_start: 0.5879 (OUTLIER) cc_final: 0.5639 (mt) REVERT: A 325 PHE cc_start: 0.5266 (OUTLIER) cc_final: 0.4010 (m-10) REVERT: A 339 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8357 (mtpp) REVERT: A 419 ILE cc_start: 0.7777 (mt) cc_final: 0.7180 (mp) REVERT: A 423 ASP cc_start: 0.6394 (m-30) cc_final: 0.5976 (m-30) REVERT: A 446 LEU cc_start: 0.5335 (OUTLIER) cc_final: 0.5107 (tm) REVERT: A 768 LYS cc_start: 0.6444 (tptp) cc_final: 0.5690 (mttm) REVERT: A 769 ASN cc_start: 0.6346 (t0) cc_final: 0.5650 (t0) REVERT: A 863 PHE cc_start: 0.5248 (OUTLIER) cc_final: 0.4630 (p90) REVERT: A 1101 LYS cc_start: 0.7760 (tmtp) cc_final: 0.5907 (ptmt) outliers start: 94 outliers final: 37 residues processed: 210 average time/residue: 0.3995 time to fit residues: 91.3919 Evaluate side-chains 162 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 111 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 837 ASN Chi-restraints excluded: chain A residue 863 PHE Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1158 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 30 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 90 optimal weight: 0.0170 chunk 47 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 ASN ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN A 311 ASN ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 ASN ** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.217635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.182370 restraints weight = 28204.590| |-----------------------------------------------------------------------------| r_work (start): 0.4382 rms_B_bonded: 4.01 r_work: 0.4116 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4134 r_free = 0.4134 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4134 r_free = 0.4134 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.5866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9866 Z= 0.200 Angle : 0.862 13.274 13427 Z= 0.450 Chirality : 0.050 0.339 1479 Planarity : 0.006 0.088 1632 Dihedral : 15.770 172.432 1663 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.51 % Favored : 88.77 % Rotamer: Outliers : 7.91 % Allowed : 40.35 % Favored : 51.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.23), residues: 1115 helix: -0.60 (0.23), residues: 447 sheet: -3.35 (0.42), residues: 97 loop : -2.79 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1071 TYR 0.023 0.002 TYR A 854 PHE 0.028 0.002 PHE A 220 TRP 0.034 0.002 TRP A 890 HIS 0.008 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 ( 9864) covalent geometry : angle 0.86246 / 0.45 (13427) hydrogen bonds : bond 0.05368 / 3.58 ( 357) hydrogen bonds : angle 5.92848 / 4.05 ( 1041) Misc. bond : bond 0.01199 / 0.63 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 115 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7245 (pp20) REVERT: A 16 THR cc_start: 0.7223 (p) cc_final: 0.7022 (p) REVERT: A 86 ARG cc_start: 0.4169 (OUTLIER) cc_final: 0.2817 (mtp180) REVERT: A 121 LYS cc_start: 0.6537 (OUTLIER) cc_final: 0.5984 (ptpt) REVERT: A 186 ASN cc_start: 0.5955 (OUTLIER) cc_final: 0.5483 (t0) REVERT: A 267 LYS cc_start: 0.3578 (OUTLIER) cc_final: 0.3186 (ptpp) REVERT: A 325 PHE cc_start: 0.5230 (OUTLIER) cc_final: 0.3882 (m-10) REVERT: A 419 ILE cc_start: 0.7750 (mt) cc_final: 0.7125 (mp) REVERT: A 423 ASP cc_start: 0.6513 (m-30) cc_final: 0.6103 (m-30) REVERT: A 498 LEU cc_start: 0.7027 (tm) cc_final: 0.6740 (mt) REVERT: A 703 GLN cc_start: 0.5566 (OUTLIER) cc_final: 0.3989 (tp40) REVERT: A 754 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7344 (pm20) REVERT: A 768 LYS cc_start: 0.6356 (tptp) cc_final: 0.5596 (mttm) REVERT: A 769 ASN cc_start: 0.6414 (t0) cc_final: 0.5936 (t0) REVERT: A 787 LYS cc_start: 0.6729 (OUTLIER) cc_final: 0.5675 (ptpp) REVERT: A 863 PHE cc_start: 0.5407 (OUTLIER) cc_final: 0.4848 (p90) REVERT: A 866 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7594 (mp) REVERT: A 1101 LYS cc_start: 0.7683 (tmtp) cc_final: 0.5850 (ptmt) outliers start: 77 outliers final: 34 residues processed: 179 average time/residue: 0.3622 time to fit residues: 71.5145 Evaluate side-chains 144 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 99 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 837 ASN Chi-restraints excluded: chain A residue 863 PHE Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 0 optimal weight: 5.9990 chunk 105 optimal weight: 0.1980 chunk 98 optimal weight: 0.1980 chunk 45 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.218838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.182757 restraints weight = 30782.867| |-----------------------------------------------------------------------------| r_work (start): 0.4381 rms_B_bonded: 4.80 r_work: 0.4114 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4134 r_free = 0.4134 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4134 r_free = 0.4134 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9866 Z= 0.184 Angle : 0.832 21.995 13427 Z= 0.428 Chirality : 0.048 0.324 1479 Planarity : 0.005 0.086 1632 Dihedral : 15.391 173.491 1646 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.90 % Allowed : 10.87 % Favored : 88.23 % Rotamer: Outliers : 5.95 % Allowed : 42.71 % Favored : 51.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.24), residues: 1115 helix: -0.51 (0.23), residues: 457 sheet: -3.21 (0.42), residues: 97 loop : -2.71 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1071 TYR 0.023 0.002 TYR A 903 PHE 0.023 0.002 PHE A 352 TRP 0.033 0.002 TRP A 890 HIS 0.007 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 9864) covalent geometry : angle 0.83250 / 0.43 (13427) hydrogen bonds : bond 0.05009 / 3.32 ( 357) hydrogen bonds : angle 5.68910 / 3.87 ( 1041) Misc. bond : bond 0.01171 / 0.62 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 109 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.4334 (OUTLIER) cc_final: 0.2893 (mtp180) REVERT: A 121 LYS cc_start: 0.6545 (OUTLIER) cc_final: 0.5959 (ptpt) REVERT: A 186 ASN cc_start: 0.5811 (OUTLIER) cc_final: 0.5407 (t0) REVERT: A 260 ASN cc_start: 0.7983 (t0) cc_final: 0.7442 (m-40) REVERT: A 325 PHE cc_start: 0.5166 (OUTLIER) cc_final: 0.3723 (m-10) REVERT: A 358 ILE cc_start: 0.7844 (mm) cc_final: 0.7621 (tt) REVERT: A 419 ILE cc_start: 0.7694 (mt) cc_final: 0.7211 (mm) REVERT: A 423 ASP cc_start: 0.6567 (m-30) cc_final: 0.6123 (m-30) REVERT: A 691 ASP cc_start: 0.7411 (p0) cc_final: 0.6930 (m-30) REVERT: A 768 LYS cc_start: 0.6245 (tptp) cc_final: 0.5549 (mttm) REVERT: A 769 ASN cc_start: 0.6417 (t0) cc_final: 0.5282 (t0) REVERT: A 863 PHE cc_start: 0.5263 (OUTLIER) cc_final: 0.4407 (p90) REVERT: A 866 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7474 (mp) outliers start: 58 outliers final: 32 residues processed: 153 average time/residue: 0.3475 time to fit residues: 59.0015 Evaluate side-chains 138 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 837 ASN Chi-restraints excluded: chain A residue 863 PHE Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1049 TYR Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 40 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 GLN ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1197 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.208970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.169580 restraints weight = 36623.460| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 5.20 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4245 r_free = 0.4245 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4245 r_free = 0.4245 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.6338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 9866 Z= 0.290 Angle : 0.912 19.579 13427 Z= 0.470 Chirality : 0.051 0.301 1479 Planarity : 0.006 0.085 1632 Dihedral : 15.161 164.814 1641 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 21.78 Ramachandran Plot: Outliers : 0.90 % Allowed : 12.85 % Favored : 86.25 % Rotamer: Outliers : 6.67 % Allowed : 41.79 % Favored : 51.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.23), residues: 1115 helix: -0.53 (0.23), residues: 448 sheet: -3.40 (0.40), residues: 108 loop : -2.93 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1071 TYR 0.033 0.003 TYR A 903 PHE 0.040 0.003 PHE A 304 TRP 0.040 0.003 TRP A 890 HIS 0.007 0.002 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.29 ( 9864) covalent geometry : angle 0.91205 / 0.47 (13427) hydrogen bonds : bond 0.06226 / 4.23 ( 357) hydrogen bonds : angle 5.80720 / 3.96 ( 1041) Misc. bond : bond 0.01052 / 0.55 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 110 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7145 (pp20) REVERT: A 86 ARG cc_start: 0.3971 (OUTLIER) cc_final: 0.2503 (mtp180) REVERT: A 121 LYS cc_start: 0.6683 (OUTLIER) cc_final: 0.6157 (ptpt) REVERT: A 186 ASN cc_start: 0.6425 (OUTLIER) cc_final: 0.5941 (t0) REVERT: A 260 ASN cc_start: 0.7842 (t0) cc_final: 0.7459 (m-40) REVERT: A 267 LYS cc_start: 0.3786 (OUTLIER) cc_final: 0.3426 (ptpp) REVERT: A 276 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.5994 (mt) REVERT: A 325 PHE cc_start: 0.5157 (OUTLIER) cc_final: 0.4041 (m-10) REVERT: A 687 LYS cc_start: 0.7760 (ttpp) cc_final: 0.7547 (ttpp) REVERT: A 754 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7334 (pm20) REVERT: A 768 LYS cc_start: 0.6377 (tptp) cc_final: 0.5836 (mttt) REVERT: A 835 GLU cc_start: 0.5969 (mm-30) cc_final: 0.5740 (mm-30) REVERT: A 863 PHE cc_start: 0.5727 (OUTLIER) cc_final: 0.4942 (p90) REVERT: A 866 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7539 (mp) outliers start: 65 outliers final: 34 residues processed: 166 average time/residue: 0.3913 time to fit residues: 71.5483 Evaluate side-chains 144 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 100 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 863 PHE Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1049 TYR Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1158 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 14 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 873 HIS ** 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 = 0.4699 r_free = 0.4699 target = 0.215292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.178529 restraints weight = 27202.427| |-----------------------------------------------------------------------------| r_work (start): 0.4331 rms_B_bonded: 3.92 r_work: 0.4095 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4113 r_free = 0.4113 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4113 r_free = 0.4113 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.6634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9866 Z= 0.189 Angle : 0.824 16.616 13427 Z= 0.425 Chirality : 0.048 0.286 1479 Planarity : 0.005 0.084 1632 Dihedral : 15.138 171.586 1639 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.90 % Allowed : 10.24 % Favored : 88.86 % Rotamer: Outliers : 6.06 % Allowed : 42.20 % Favored : 51.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.23), residues: 1115 helix: -0.43 (0.23), residues: 461 sheet: -2.95 (0.43), residues: 100 loop : -2.79 (0.24), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1071 TYR 0.025 0.002 TYR A 903 PHE 0.021 0.002 PHE A 220 TRP 0.039 0.002 TRP A 890 HIS 0.007 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 ( 9864) covalent geometry : angle 0.82391 / 0.43 (13427) hydrogen bonds : bond 0.05031 / 3.32 ( 357) hydrogen bonds : angle 5.62561 / 3.83 ( 1041) Misc. bond : bond 0.00849 / 0.45 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 106 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7155 (pp20) REVERT: A 61 PHE cc_start: 0.4895 (t80) cc_final: 0.4638 (t80) REVERT: A 86 ARG cc_start: 0.4390 (OUTLIER) cc_final: 0.2746 (mtp180) REVERT: A 121 LYS cc_start: 0.6551 (OUTLIER) cc_final: 0.5950 (ptpt) REVERT: A 186 ASN cc_start: 0.5663 (OUTLIER) cc_final: 0.4863 (t0) REVERT: A 260 ASN cc_start: 0.7959 (t0) cc_final: 0.7460 (m-40) REVERT: A 267 LYS cc_start: 0.3758 (OUTLIER) cc_final: 0.3517 (mppt) REVERT: A 325 PHE cc_start: 0.5356 (OUTLIER) cc_final: 0.3863 (m-10) REVERT: A 358 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7615 (tt) REVERT: A 498 LEU cc_start: 0.6945 (tm) cc_final: 0.6671 (mt) REVERT: A 552 LYS cc_start: 0.6816 (mppt) cc_final: 0.6083 (mttm) REVERT: A 686 SER cc_start: 0.5896 (OUTLIER) cc_final: 0.5021 (m) REVERT: A 687 LYS cc_start: 0.7927 (ttpp) cc_final: 0.7245 (ttpp) REVERT: A 691 ASP cc_start: 0.7493 (p0) cc_final: 0.6952 (m-30) REVERT: A 703 GLN cc_start: 0.5396 (OUTLIER) cc_final: 0.5133 (tt0) REVERT: A 754 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7271 (pm20) REVERT: A 768 LYS cc_start: 0.6352 (tptp) cc_final: 0.5791 (mttm) REVERT: A 863 PHE cc_start: 0.5572 (OUTLIER) cc_final: 0.4730 (p90) outliers start: 59 outliers final: 29 residues processed: 156 average time/residue: 0.3977 time to fit residues: 68.3513 Evaluate side-chains 137 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 754 GLU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 863 PHE Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1158 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 ASN A 306 ASN ** A 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.214826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.178521 restraints weight = 29240.606| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 4.20 r_work: 0.4076 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4096 r_free = 0.4096 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4096 r_free = 0.4096 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.6814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9866 Z= 0.199 Angle : 0.825 15.635 13427 Z= 0.429 Chirality : 0.048 0.270 1479 Planarity : 0.005 0.082 1632 Dihedral : 15.040 170.877 1637 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.96 % Favored : 88.32 % Rotamer: Outliers : 4.93 % Allowed : 42.92 % Favored : 52.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.24), residues: 1115 helix: -0.36 (0.23), residues: 460 sheet: -3.18 (0.40), residues: 110 loop : -2.74 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1071 TYR 0.027 0.002 TYR A 903 PHE 0.022 0.002 PHE A 220 TRP 0.045 0.002 TRP A 890 HIS 0.007 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 ( 9864) covalent geometry : angle 0.82537 / 0.43 (13427) hydrogen bonds : bond 0.05118 / 3.41 ( 357) hydrogen bonds : angle 5.50238 / 3.75 ( 1041) Misc. bond : bond 0.01465 / 0.77 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 108 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7149 (pp20) REVERT: A 61 PHE cc_start: 0.4913 (t80) cc_final: 0.4667 (t80) REVERT: A 121 LYS cc_start: 0.6572 (OUTLIER) cc_final: 0.6007 (ptpt) REVERT: A 186 ASN cc_start: 0.5257 (OUTLIER) cc_final: 0.4723 (t0) REVERT: A 260 ASN cc_start: 0.7947 (t0) cc_final: 0.7470 (m-40) REVERT: A 267 LYS cc_start: 0.3807 (OUTLIER) cc_final: 0.3588 (mppt) REVERT: A 276 LEU cc_start: 0.6711 (OUTLIER) cc_final: 0.6068 (mt) REVERT: A 325 PHE cc_start: 0.5413 (OUTLIER) cc_final: 0.3889 (m-10) REVERT: A 498 LEU cc_start: 0.6991 (tm) cc_final: 0.6697 (mt) REVERT: A 552 LYS cc_start: 0.6852 (mppt) cc_final: 0.6350 (mttm) REVERT: A 686 SER cc_start: 0.5941 (OUTLIER) cc_final: 0.5115 (m) REVERT: A 687 LYS cc_start: 0.7922 (ttpp) cc_final: 0.7209 (ttpp) REVERT: A 691 ASP cc_start: 0.7511 (p0) cc_final: 0.6974 (m-30) REVERT: A 703 GLN cc_start: 0.5414 (OUTLIER) cc_final: 0.5151 (tt0) REVERT: A 768 LYS cc_start: 0.6413 (tptp) cc_final: 0.5870 (mttm) REVERT: A 863 PHE cc_start: 0.5741 (OUTLIER) cc_final: 0.5015 (p90) REVERT: A 1138 ARG cc_start: 0.5809 (mmm-85) cc_final: 0.5315 (mmt-90) outliers start: 48 outliers final: 30 residues processed: 148 average time/residue: 0.3986 time to fit residues: 64.9350 Evaluate side-chains 140 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 101 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 863 PHE Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1049 TYR Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 34 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 11 optimal weight: 0.0060 chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 0.0470 chunk 105 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.4094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 ASN ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 873 HIS ** 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 = 0.4724 r_free = 0.4724 target = 0.218080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.183651 restraints weight = 30943.325| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 4.48 r_work: 0.4113 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4124 r_free = 0.4124 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4124 r_free = 0.4124 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.7101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9866 Z= 0.166 Angle : 0.790 14.628 13427 Z= 0.409 Chirality : 0.046 0.263 1479 Planarity : 0.005 0.079 1632 Dihedral : 15.033 174.695 1637 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.72 % Allowed : 9.79 % Favored : 89.49 % Rotamer: Outliers : 3.90 % Allowed : 44.76 % Favored : 51.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.24), residues: 1115 helix: -0.28 (0.23), residues: 460 sheet: -3.05 (0.41), residues: 110 loop : -2.61 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1071 TYR 0.016 0.001 TYR A 903 PHE 0.017 0.002 PHE A 219 TRP 0.046 0.002 TRP A 890 HIS 0.008 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 9864) covalent geometry : angle 0.78959 / 0.41 (13427) hydrogen bonds : bond 0.04691 / 3.10 ( 357) hydrogen bonds : angle 5.31107 / 3.63 ( 1041) Misc. bond : bond 0.01243 / 0.65 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.4942 (t80) cc_final: 0.4731 (t80) REVERT: A 121 LYS cc_start: 0.6524 (OUTLIER) cc_final: 0.5930 (ptpt) REVERT: A 186 ASN cc_start: 0.4968 (OUTLIER) cc_final: 0.4505 (t0) REVERT: A 276 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6135 (mt) REVERT: A 325 PHE cc_start: 0.5318 (OUTLIER) cc_final: 0.3737 (m-10) REVERT: A 358 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7334 (tt) REVERT: A 498 LEU cc_start: 0.6955 (tm) cc_final: 0.6680 (mt) REVERT: A 552 LYS cc_start: 0.6834 (mppt) cc_final: 0.6252 (mttm) REVERT: A 686 SER cc_start: 0.5638 (OUTLIER) cc_final: 0.4977 (m) REVERT: A 687 LYS cc_start: 0.7909 (ttpp) cc_final: 0.7240 (ttpp) REVERT: A 691 ASP cc_start: 0.7481 (p0) cc_final: 0.7015 (m-30) REVERT: A 703 GLN cc_start: 0.5357 (OUTLIER) cc_final: 0.5104 (tt0) REVERT: A 768 LYS cc_start: 0.6290 (tptp) cc_final: 0.5811 (mttm) REVERT: A 863 PHE cc_start: 0.5604 (OUTLIER) cc_final: 0.4952 (p90) REVERT: A 1116 CYS cc_start: 0.5630 (m) cc_final: 0.5371 (t) outliers start: 38 outliers final: 22 residues processed: 144 average time/residue: 0.3940 time to fit residues: 62.7757 Evaluate side-chains 131 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 863 PHE Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 577 ASN ** A 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 873 HIS ** 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 = 0.4699 r_free = 0.4699 target = 0.215193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.178860 restraints weight = 30668.252| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 4.63 r_work: 0.4090 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4106 r_free = 0.4106 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4106 r_free = 0.4106 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.7121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9866 Z= 0.200 Angle : 0.827 15.107 13427 Z= 0.428 Chirality : 0.048 0.257 1479 Planarity : 0.005 0.076 1632 Dihedral : 14.962 171.632 1637 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.42 % Favored : 88.86 % Rotamer: Outliers : 3.18 % Allowed : 45.69 % Favored : 51.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.24), residues: 1115 helix: -0.27 (0.24), residues: 458 sheet: -2.92 (0.42), residues: 110 loop : -2.66 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1071 TYR 0.035 0.002 TYR A 516 PHE 0.020 0.002 PHE A 789 TRP 0.054 0.002 TRP A 890 HIS 0.007 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 ( 9864) covalent geometry : angle 0.82700 / 0.43 (13427) hydrogen bonds : bond 0.04961 / 3.33 ( 357) hydrogen bonds : angle 5.32925 / 3.65 ( 1041) Misc. bond : bond 0.01267 / 0.67 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.4904 (t80) cc_final: 0.4701 (t80) REVERT: A 121 LYS cc_start: 0.6605 (OUTLIER) cc_final: 0.5987 (ptpt) REVERT: A 259 ILE cc_start: 0.6604 (mt) cc_final: 0.6277 (tp) REVERT: A 276 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6121 (mt) REVERT: A 325 PHE cc_start: 0.5331 (OUTLIER) cc_final: 0.3768 (m-10) REVERT: A 498 LEU cc_start: 0.6995 (tm) cc_final: 0.6703 (mt) REVERT: A 552 LYS cc_start: 0.6851 (mppt) cc_final: 0.6281 (mttm) REVERT: A 686 SER cc_start: 0.5786 (OUTLIER) cc_final: 0.5127 (m) REVERT: A 691 ASP cc_start: 0.7516 (p0) cc_final: 0.6987 (m-30) REVERT: A 703 GLN cc_start: 0.5415 (OUTLIER) cc_final: 0.5140 (tt0) REVERT: A 768 LYS cc_start: 0.6470 (tptp) cc_final: 0.6002 (mttm) REVERT: A 863 PHE cc_start: 0.5718 (OUTLIER) cc_final: 0.5214 (p90) REVERT: A 1116 CYS cc_start: 0.5684 (m) cc_final: 0.5152 (t) outliers start: 31 outliers final: 24 residues processed: 130 average time/residue: 0.3793 time to fit residues: 54.6601 Evaluate side-chains 129 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 863 PHE Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1049 TYR Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 0.4980 chunk 43 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 25 optimal weight: 0.0570 chunk 60 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 30 optimal weight: 0.0040 chunk 85 optimal weight: 0.5980 overall best weight: 0.3510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 941 GLN A 963 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.213821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.176953 restraints weight = 28010.793| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 4.02 r_work: 0.4055 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4059 r_free = 0.4059 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4059 r_free = 0.4059 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.7333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9866 Z= 0.159 Angle : 0.793 15.095 13427 Z= 0.412 Chirality : 0.046 0.255 1479 Planarity : 0.005 0.073 1632 Dihedral : 14.990 175.276 1637 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.72 % Allowed : 9.16 % Favored : 90.12 % Rotamer: Outliers : 3.49 % Allowed : 45.79 % Favored : 50.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.24), residues: 1115 helix: -0.18 (0.24), residues: 459 sheet: -2.87 (0.42), residues: 110 loop : -2.55 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1071 TYR 0.028 0.002 TYR A 516 PHE 0.017 0.002 PHE A 789 TRP 0.055 0.002 TRP A 890 HIS 0.007 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 9864) covalent geometry : angle 0.79334 / 0.41 (13427) hydrogen bonds : bond 0.04487 / 2.97 ( 357) hydrogen bonds : angle 5.18968 / 3.55 ( 1041) Misc. bond : bond 0.01130 / 0.59 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3611.89 seconds wall clock time: 62 minutes 21.50 seconds (3741.50 seconds total)