Starting phenix.real_space_refine on Thu Aug 6 21:07:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kwc_62607/08_2026/9kwc_62607_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kwc_62607/08_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_62607/08_2026/9kwc_62607_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kwc_62607/08_2026/9kwc_62607_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kwc_62607/08_2026/9kwc_62607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kwc_62607/08_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-2.2rc3-6140/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: 3.87, per 1000 atoms: 0.40 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: 0.80 Conformation dependent library (CDL) restraints added in 755.9 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: 1.13 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: 1.91 Time building geometry restraints manager: 1.07 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: 1248 0.127 - 0.254: 194 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: 11.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.620 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.780 ------------------------------------------------------------------------------- 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= 0.668 Angle : 1.510 29.325 13427 Z= 1.012 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 1.51010 / 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 : 0.346 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: 0.5314 (t80) REVERT: A 73 ASN cc_start: 0.1051 (OUTLIER) cc_final: 0.0437 (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: 0.0456 (p) REVERT: A 286 SER cc_start: -0.3274 (OUTLIER) cc_final: -0.3693 (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: 0.5412 (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: 0.5752 (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: 0.2268 (m-80) REVERT: A 552 LYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6629 (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: 0.7828 (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: 0.5480 (p90) REVERT: A 897 LYS cc_start: 0.7645 (mtpt) cc_final: 0.7417 (mtpt) REVERT: A 967 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.7359 (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: 0.7576 (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: 55 residues processed: 554 average time/residue: 0.5091 time to fit residues: 304.7344 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 : 0.354 ------------------------------------------------------------------------------- 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 713 SER 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 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: 0.8980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 714 HIS A A 720 HIS ** 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 895 ASN A 909 HIS A 941 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN A1186 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.212553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.175207 restraints weight = 38343.224| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 5.44 r_work: 0.4060 rms_B_bonded: 5.08 restraints_weight: 2.0000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4087 r_free = 0.4087 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4087 r_free = 0.4087 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 9866 Z= 0.293 Angle : 1.054 13.324 13427 Z= 0.555 Chirality : 0.058 0.542 1479 Planarity : 0.007 0.090 1632 Dihedral : 18.077 169.969 1765 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 28.31 Ramachandran Plot: Outliers : 1.08 % Allowed : 12.85 % Favored : 86.07 % Rotamer: Outliers : 12.63 % Allowed : 38.40 % Favored : 48.97 % 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: -3.84 (0.22), residues: 1115 helix: -1.47 (0.21), residues: 447 sheet: -4.07 (0.41), residues: 104 loop : -3.22 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 385 TYR 0.027 0.003 TYR A 854 PHE 0.028 0.003 PHE A 395 TRP 0.029 0.003 TRP A 890 HIS 0.010 0.002 HIS A 873 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.29 ( 9864) covalent geometry : angle 1.05378 / 0.55 (13427) hydrogen bonds : bond 0.07232 / 4.83 ( 357) hydrogen bonds : angle 6.94977 / 4.78 ( 1041) Misc. bond : bond 0.01499 / 0.79 ( 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 276 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 153 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 48 LYS cc_start: 0.5579 (OUTLIER) cc_final: 0.5182 (tttt) REVERT: A 61 PHE cc_start: 0.5083 (OUTLIER) cc_final: 0.4076 (t80) REVERT: A 90 GLU cc_start: 0.4042 (OUTLIER) cc_final: 0.3752 (mm-30) REVERT: A 121 LYS cc_start: 0.6476 (OUTLIER) cc_final: 0.5745 (ptpt) REVERT: A 186 ASN cc_start: 0.5280 (OUTLIER) cc_final: 0.4482 (t0) REVERT: A 260 ASN cc_start: 0.6765 (m-40) cc_final: 0.6533 (t0) REVERT: A 266 THR cc_start: 0.1414 (OUTLIER) cc_final: 0.1174 (m) REVERT: A 267 LYS cc_start: 0.3497 (OUTLIER) cc_final: 0.3117 (mppt) REVERT: A 286 SER cc_start: -0.2879 (OUTLIER) cc_final: -0.3526 (t) REVERT: A 290 TYR cc_start: -0.0669 (OUTLIER) cc_final: -0.1391 (t80) REVERT: A 324 LEU cc_start: 0.5951 (OUTLIER) cc_final: 0.5658 (mt) REVERT: A 325 PHE cc_start: 0.5302 (OUTLIER) cc_final: 0.4173 (m-10) REVERT: A 339 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8428 (mtpp) REVERT: A 423 ASP cc_start: 0.6415 (m-30) cc_final: 0.6056 (m-30) REVERT: A 552 LYS cc_start: 0.6694 (OUTLIER) cc_final: 0.6308 (mppt) REVERT: A 703 GLN cc_start: 0.5528 (OUTLIER) cc_final: 0.4316 (tt0) REVERT: A 768 LYS cc_start: 0.6569 (tptp) cc_final: 0.5771 (mttt) REVERT: A 769 ASN cc_start: 0.6551 (t0) cc_final: 0.5994 (t0) REVERT: A 807 LYS cc_start: 0.4999 (OUTLIER) cc_final: 0.4401 (ttmt) REVERT: A 835 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6961 (tp30) REVERT: A 863 PHE cc_start: 0.5845 (OUTLIER) cc_final: 0.5548 (p90) REVERT: A 897 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7824 (mtpt) REVERT: A 1029 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.8034 (p) REVERT: A 1097 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7091 (pt0) REVERT: A 1101 LYS cc_start: 0.7755 (tmtp) cc_final: 0.5829 (ptmt) REVERT: A 1160 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7754 (tp) REVERT: A 1199 LYS cc_start: 0.5484 (mttp) cc_final: 0.5236 (mtmt) outliers start: 123 outliers final: 50 residues processed: 253 average time/residue: 0.4180 time to fit residues: 116.0044 Evaluate side-chains 198 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 129 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 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 140 LEU 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 190 PHE 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 520 LYS 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 687 LYS 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 771 ASP 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 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 1024 SER Chi-restraints excluded: chain A residue 1029 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 1097 GLU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1160 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 95 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 76 ASN A 226 ASN A 306 ASN A 311 ASN A 399 GLN A 513 GLN A 703 GLN A 706 ASN A 733 HIS ** 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 955 ASN ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.218095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.181583 restraints weight = 26168.173| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 3.54 r_work: 0.4142 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4166 r_free = 0.4166 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 = 0.4166 r_free = 0.4166 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: 0.4166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9866 Z= 0.214 Angle : 0.911 12.624 13427 Z= 0.475 Chirality : 0.052 0.454 1479 Planarity : 0.006 0.091 1632 Dihedral : 16.717 171.650 1704 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 23.71 Ramachandran Plot: Outliers : 0.90 % Allowed : 12.13 % Favored : 86.97 % Rotamer: Outliers : 9.96 % Allowed : 38.60 % Favored : 51.44 % 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: -3.26 (0.23), residues: 1115 helix: -1.00 (0.22), residues: 445 sheet: -3.69 (0.40), residues: 97 loop : -2.91 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 385 TYR 0.028 0.002 TYR A 854 PHE 0.025 0.003 PHE A 220 TRP 0.031 0.002 TRP A 890 HIS 0.009 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 ( 9864) covalent geometry : angle 0.91147 / 0.47 (13427) hydrogen bonds : bond 0.06008 / 3.99 ( 357) hydrogen bonds : angle 6.32217 / 4.33 ( 1041) Misc. bond : bond 0.01186 / 0.62 ( 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 232 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 135 time to evaluate : 0.311 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: 0.7590 (OUTLIER) cc_final: 0.7376 (pp20) REVERT: A 48 LYS cc_start: 0.5645 (OUTLIER) cc_final: 0.5213 (tttt) REVERT: A 61 PHE cc_start: 0.5069 (OUTLIER) cc_final: 0.4740 (t80) REVERT: A 86 ARG cc_start: 0.4186 (OUTLIER) cc_final: 0.2909 (mtp180) REVERT: A 121 LYS cc_start: 0.6500 (OUTLIER) cc_final: 0.5912 (ptpt) REVERT: A 260 ASN cc_start: 0.6754 (m-40) cc_final: 0.6554 (t0) REVERT: A 267 LYS cc_start: 0.3499 (OUTLIER) cc_final: 0.3119 (mppt) REVERT: A 286 SER cc_start: -0.2784 (OUTLIER) cc_final: -0.3399 (t) REVERT: A 324 LEU cc_start: 0.5882 (OUTLIER) cc_final: 0.5643 (mt) REVERT: A 325 PHE cc_start: 0.5259 (OUTLIER) cc_final: 0.4085 (m-10) REVERT: A 419 ILE cc_start: 0.7793 (mt) cc_final: 0.7191 (mp) REVERT: A 423 ASP cc_start: 0.6391 (m-30) cc_final: 0.5968 (m-30) REVERT: A 446 LEU cc_start: 0.5322 (OUTLIER) cc_final: 0.5097 (tm) REVERT: A 703 GLN cc_start: 0.5497 (OUTLIER) cc_final: 0.4390 (tt0) REVERT: A 768 LYS cc_start: 0.6485 (tptp) cc_final: 0.5761 (mttm) REVERT: A 769 ASN cc_start: 0.6372 (t0) cc_final: 0.5727 (t0) REVERT: A 787 LYS cc_start: 0.6733 (OUTLIER) cc_final: 0.5428 (ptpp) REVERT: A 863 PHE cc_start: 0.5314 (OUTLIER) cc_final: 0.4677 (p90) REVERT: A 897 LYS cc_start: 0.8034 (mtpt) cc_final: 0.7803 (mtpt) REVERT: A 900 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7205 (mtmt) REVERT: A 1101 LYS cc_start: 0.7735 (tmtp) cc_final: 0.5899 (ptmt) outliers start: 97 outliers final: 37 residues processed: 215 average time/residue: 0.4509 time to fit residues: 105.2612 Evaluate side-chains 166 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 115 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 16 THR 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 121 LYS Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 165 GLU 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 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 314 ILE 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 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 520 LYS 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 706 ASN Chi-restraints excluded: chain A residue 713 SER 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 787 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 863 PHE Chi-restraints excluded: chain A residue 900 LYS 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 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: 0.3980 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 47 optimal weight: 9.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 ASN A 340 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.217950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.181860 restraints weight = 29320.626| |-----------------------------------------------------------------------------| r_work (start): 0.4365 rms_B_bonded: 4.06 r_work: 0.4116 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4143 r_free = 0.4143 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4143 r_free = 0.4143 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.4143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 9866 Z= 0.200 Angle : 0.888 14.295 13427 Z= 0.458 Chirality : 0.051 0.418 1479 Planarity : 0.006 0.090 1632 Dihedral : 15.815 172.817 1666 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.78 % Favored : 88.50 % Rotamer: Outliers : 8.42 % Allowed : 40.14 % Favored : 51.44 % 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: -2.99 (0.23), residues: 1115 helix: -0.72 (0.23), residues: 453 sheet: -3.47 (0.42), residues: 97 loop : -2.85 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1071 TYR 0.025 0.002 TYR A 903 PHE 0.027 0.003 PHE A 220 TRP 0.032 0.002 TRP A 890 HIS 0.008 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 ( 9864) covalent geometry : angle 0.88785 / 0.46 (13427) hydrogen bonds : bond 0.05439 / 3.60 ( 357) hydrogen bonds : angle 5.97284 / 4.08 ( 1041) Misc. bond : bond 0.01527 / 0.80 ( 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 198 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 116 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7241 (pp20) REVERT: A 86 ARG cc_start: 0.4170 (OUTLIER) cc_final: 0.2782 (mtp180) REVERT: A 121 LYS cc_start: 0.6526 (OUTLIER) cc_final: 0.5958 (ptpt) REVERT: A 267 LYS cc_start: 0.3600 (OUTLIER) cc_final: 0.3203 (ptpp) REVERT: A 325 PHE cc_start: 0.5156 (OUTLIER) cc_final: 0.3899 (m-10) REVERT: A 419 ILE cc_start: 0.7765 (mt) cc_final: 0.7156 (mp) REVERT: A 423 ASP cc_start: 0.6508 (m-30) cc_final: 0.6088 (m-30) REVERT: A 754 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7377 (pm20) REVERT: A 768 LYS cc_start: 0.6371 (tptp) cc_final: 0.5611 (mttm) REVERT: A 769 ASN cc_start: 0.6412 (t0) cc_final: 0.5929 (t0) REVERT: A 787 LYS cc_start: 0.6643 (OUTLIER) cc_final: 0.5410 (ptpp) REVERT: A 863 PHE cc_start: 0.5410 (OUTLIER) cc_final: 0.4928 (p90) REVERT: A 866 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7581 (mp) REVERT: A 1101 LYS cc_start: 0.7648 (tmtp) cc_final: 0.5815 (ptmt) outliers start: 82 outliers final: 35 residues processed: 186 average time/residue: 0.4763 time to fit residues: 96.6377 Evaluate side-chains 145 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 101 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 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 86 ARG Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 183 TYR 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 226 ASN 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 520 LYS 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 704 ILE Chi-restraints excluded: chain A residue 713 SER 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 776 THR Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 809 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 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=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: 0.7980 chunk 45 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 ASN ** 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 = 0.4723 r_free = 0.4723 target = 0.217874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.180435 restraints weight = 31817.597| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 4.64 r_work: 0.4093 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4118 r_free = 0.4118 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4118 r_free = 0.4118 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: 0.4118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.6053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9866 Z= 0.191 Angle : 0.850 11.811 13427 Z= 0.439 Chirality : 0.050 0.389 1479 Planarity : 0.006 0.090 1632 Dihedral : 15.344 173.046 1645 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.72 % Allowed : 11.14 % Favored : 88.14 % Rotamer: Outliers : 6.78 % Allowed : 41.58 % Favored : 51.64 % 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: -2.78 (0.24), residues: 1115 helix: -0.47 (0.23), residues: 449 sheet: -3.29 (0.43), residues: 97 loop : -2.81 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1071 TYR 0.031 0.002 TYR A 516 PHE 0.032 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 0.00430 / 0.19 ( 9864) covalent geometry : angle 0.84959 / 0.44 (13427) hydrogen bonds : bond 0.05199 / 3.46 ( 357) hydrogen bonds : angle 5.76520 / 3.92 ( 1041) Misc. bond : bond 0.01183 / 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 170 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 104 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7207 (pp20) REVERT: A 86 ARG cc_start: 0.4299 (OUTLIER) cc_final: 0.2833 (mtp180) REVERT: A 121 LYS cc_start: 0.6540 (OUTLIER) cc_final: 0.5992 (ptpt) REVERT: A 267 LYS cc_start: 0.3598 (OUTLIER) cc_final: 0.3206 (ptpp) REVERT: A 325 PHE cc_start: 0.5203 (OUTLIER) cc_final: 0.3846 (m-10) REVERT: A 419 ILE cc_start: 0.7727 (mt) cc_final: 0.7239 (mm) REVERT: A 423 ASP cc_start: 0.6601 (m-30) cc_final: 0.6181 (m-30) REVERT: A 498 LEU cc_start: 0.6984 (tm) cc_final: 0.6696 (mt) REVERT: A 686 SER cc_start: 0.5895 (OUTLIER) cc_final: 0.4994 (m) REVERT: A 691 ASP cc_start: 0.7453 (p0) cc_final: 0.6911 (m-30) REVERT: A 754 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7380 (pm20) REVERT: A 768 LYS cc_start: 0.6290 (tptp) cc_final: 0.5588 (mttm) REVERT: A 769 ASN cc_start: 0.6482 (t0) cc_final: 0.5374 (t0) REVERT: A 787 LYS cc_start: 0.6725 (OUTLIER) cc_final: 0.5627 (ptpp) REVERT: A 863 PHE cc_start: 0.5394 (OUTLIER) cc_final: 0.4680 (p90) REVERT: A 866 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7492 (mp) REVERT: A 1036 TYR cc_start: 0.6303 (t80) cc_final: 0.5508 (t80) outliers start: 66 outliers final: 40 residues processed: 156 average time/residue: 0.4133 time to fit residues: 70.9226 Evaluate side-chains 147 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 97 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 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 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 183 TYR Chi-restraints excluded: chain A residue 196 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 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 520 LYS 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 686 SER Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 713 SER 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 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 Chi-restraints excluded: chain A residue 1158 ASP 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: 1.9990 chunk 6 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 26 optimal weight: 0.0170 chunk 58 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN A 226 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 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN A1197 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.215358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.176360 restraints weight = 38420.855| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 5.04 r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4311 r_free = 0.4311 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4311 r_free = 0.4311 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9866 Z= 0.213 Angle : 0.864 23.479 13427 Z= 0.439 Chirality : 0.050 0.372 1479 Planarity : 0.005 0.088 1632 Dihedral : 15.175 170.793 1643 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.90 % Allowed : 10.78 % Favored : 88.32 % Rotamer: Outliers : 7.08 % Allowed : 41.27 % Favored : 51.64 % 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: -2.73 (0.24), residues: 1115 helix: -0.40 (0.23), residues: 451 sheet: -3.08 (0.42), residues: 103 loop : -2.84 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1071 TYR 0.030 0.002 TYR A 903 PHE 0.033 0.003 PHE A 220 TRP 0.037 0.002 TRP A 890 HIS 0.007 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 ( 9864) covalent geometry : angle 0.86356 / 0.44 (13427) hydrogen bonds : bond 0.05251 / 3.53 ( 357) hydrogen bonds : angle 5.64069 / 3.83 ( 1041) Misc. bond : bond 0.01329 / 0.70 ( 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 173 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 104 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7124 (pp20) REVERT: A 86 ARG cc_start: 0.3996 (OUTLIER) cc_final: 0.2541 (mtp180) REVERT: A 121 LYS cc_start: 0.6629 (OUTLIER) cc_final: 0.6089 (ptpt) REVERT: A 260 ASN cc_start: 0.7959 (t0) cc_final: 0.7473 (m-40) REVERT: A 267 LYS cc_start: 0.3702 (OUTLIER) cc_final: 0.3319 (ptpp) REVERT: A 325 PHE cc_start: 0.4913 (OUTLIER) cc_final: 0.3751 (m-10) REVERT: A 358 ILE cc_start: 0.7818 (mm) cc_final: 0.7586 (tt) REVERT: A 498 LEU cc_start: 0.6793 (tm) cc_final: 0.6495 (mt) REVERT: A 686 SER cc_start: 0.5819 (OUTLIER) cc_final: 0.4920 (m) REVERT: A 754 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7247 (pm20) REVERT: A 768 LYS cc_start: 0.6284 (tptp) cc_final: 0.5716 (mttm) REVERT: A 769 ASN cc_start: 0.6054 (t0) cc_final: 0.5539 (t0) REVERT: A 787 LYS cc_start: 0.6691 (OUTLIER) cc_final: 0.6454 (pttt) REVERT: A 863 PHE cc_start: 0.5364 (OUTLIER) cc_final: 0.4320 (p90) outliers start: 69 outliers final: 38 residues processed: 162 average time/residue: 0.3770 time to fit residues: 67.6031 Evaluate side-chains 144 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 97 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 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 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 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 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 520 LYS 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 686 SER Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 713 SER 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 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 1049 TYR Chi-restraints excluded: chain A residue 1067 SER 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: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 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 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 ASN ** 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 = 0.4709 r_free = 0.4709 target = 0.216274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.179698 restraints weight = 31706.579| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 4.62 r_work: 0.4077 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4097 r_free = 0.4097 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 = 0.4097 r_free = 0.4097 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: 0.4097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.6540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9866 Z= 0.191 Angle : 0.836 21.146 13427 Z= 0.425 Chirality : 0.049 0.366 1479 Planarity : 0.005 0.086 1632 Dihedral : 15.015 172.500 1640 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.87 % Favored : 88.41 % Rotamer: Outliers : 6.16 % Allowed : 42.30 % 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: -2.65 (0.24), residues: 1115 helix: -0.31 (0.23), residues: 449 sheet: -3.29 (0.41), residues: 110 loop : -2.73 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1071 TYR 0.028 0.002 TYR A 903 PHE 0.030 0.002 PHE A 220 TRP 0.036 0.002 TRP A 890 HIS 0.007 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 ( 9864) covalent geometry : angle 0.83625 / 0.42 (13427) hydrogen bonds : bond 0.05058 / 3.37 ( 357) hydrogen bonds : angle 5.57190 / 3.79 ( 1041) Misc. bond : bond 0.01125 / 0.59 ( 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 166 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 106 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7084 (pp20) REVERT: A 61 PHE cc_start: 0.4912 (t80) cc_final: 0.4656 (t80) REVERT: A 86 ARG cc_start: 0.4376 (OUTLIER) cc_final: 0.2754 (mtp180) REVERT: A 121 LYS cc_start: 0.6550 (OUTLIER) cc_final: 0.5979 (ptpt) REVERT: A 260 ASN cc_start: 0.8020 (t0) cc_final: 0.7437 (m-40) REVERT: A 267 LYS cc_start: 0.3669 (OUTLIER) cc_final: 0.3299 (ptpp) REVERT: A 325 PHE cc_start: 0.5194 (OUTLIER) cc_final: 0.3706 (m-10) REVERT: A 358 ILE cc_start: 0.7807 (mm) cc_final: 0.7582 (tt) REVERT: A 498 LEU cc_start: 0.6979 (tm) cc_final: 0.6706 (mt) REVERT: A 686 SER cc_start: 0.5830 (OUTLIER) cc_final: 0.5087 (m) REVERT: A 691 ASP cc_start: 0.7506 (p0) cc_final: 0.6964 (m-30) REVERT: A 754 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7316 (pm20) REVERT: A 768 LYS cc_start: 0.6328 (tptp) cc_final: 0.5710 (mttm) REVERT: A 769 ASN cc_start: 0.6648 (t0) cc_final: 0.6056 (t0) REVERT: A 863 PHE cc_start: 0.5542 (OUTLIER) cc_final: 0.4667 (p90) outliers start: 60 outliers final: 35 residues processed: 156 average time/residue: 0.4530 time to fit residues: 77.7365 Evaluate side-chains 143 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 100 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 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 183 TYR Chi-restraints excluded: chain A residue 216 VAL 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 418 ILE Chi-restraints excluded: chain A residue 419 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 520 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 687 LYS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 713 SER 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 866 ILE Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 935 ARG Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 971 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 793 GLN ** 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 = 0.4696 r_free = 0.4696 target = 0.215267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.177922 restraints weight = 30118.975| |-----------------------------------------------------------------------------| r_work (start): 0.4327 rms_B_bonded: 4.41 r_work: 0.4082 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4102 r_free = 0.4102 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 = 0.4102 r_free = 0.4102 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.4102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.6750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9866 Z= 0.203 Angle : 0.857 20.901 13427 Z= 0.433 Chirality : 0.049 0.370 1479 Planarity : 0.005 0.084 1632 Dihedral : 14.960 171.515 1637 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.87 % Favored : 88.32 % Rotamer: Outliers : 5.54 % Allowed : 43.02 % Favored : 51.44 % 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: -2.55 (0.24), residues: 1115 helix: -0.21 (0.24), residues: 452 sheet: -3.19 (0.41), residues: 110 loop : -2.71 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1071 TYR 0.035 0.002 TYR A 903 PHE 0.050 0.003 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 0.00454 / 0.20 ( 9864) covalent geometry : angle 0.85672 / 0.43 (13427) hydrogen bonds : bond 0.05135 / 3.44 ( 357) hydrogen bonds : angle 5.49858 / 3.76 ( 1041) Misc. bond : bond 0.01307 / 0.69 ( 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 162 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 108 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7114 (pp20) REVERT: A 61 PHE cc_start: 0.4908 (t80) cc_final: 0.4664 (t80) REVERT: A 121 LYS cc_start: 0.6556 (OUTLIER) cc_final: 0.5953 (ptpt) REVERT: A 260 ASN cc_start: 0.8028 (t0) cc_final: 0.7472 (m-40) REVERT: A 267 LYS cc_start: 0.3789 (OUTLIER) cc_final: 0.3578 (mppt) REVERT: A 325 PHE cc_start: 0.5242 (OUTLIER) cc_final: 0.3760 (m-10) REVERT: A 358 ILE cc_start: 0.7738 (mm) cc_final: 0.7486 (tt) REVERT: A 402 GLU cc_start: 0.7916 (tp30) cc_final: 0.7698 (tp30) REVERT: A 498 LEU cc_start: 0.6953 (tm) cc_final: 0.6675 (mt) REVERT: A 686 SER cc_start: 0.5851 (OUTLIER) cc_final: 0.5040 (m) REVERT: A 691 ASP cc_start: 0.7502 (p0) cc_final: 0.6912 (m-30) REVERT: A 768 LYS cc_start: 0.6356 (tptp) cc_final: 0.5787 (mttm) REVERT: A 769 ASN cc_start: 0.6641 (t0) cc_final: 0.6212 (t0) REVERT: A 863 PHE cc_start: 0.5708 (OUTLIER) cc_final: 0.4944 (p90) REVERT: A 1138 ARG cc_start: 0.5737 (mmm-85) cc_final: 0.5325 (mmt-90) outliers start: 54 outliers final: 31 residues processed: 153 average time/residue: 0.4720 time to fit residues: 79.1602 Evaluate side-chains 134 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 216 VAL Chi-restraints excluded: chain A residue 241 ILE 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 418 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 520 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 687 LYS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 713 SER 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 863 PHE Chi-restraints excluded: chain A residue 866 ILE 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 1049 TYR Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1158 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 793 GLN ** 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 = 0.4684 r_free = 0.4684 target = 0.213182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.176478 restraints weight = 35260.719| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 5.36 r_work: 0.4023 rms_B_bonded: 5.01 restraints_weight: 2.0000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4044 r_free = 0.4044 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4044 r_free = 0.4044 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.6914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9866 Z= 0.230 Angle : 0.885 19.925 13427 Z= 0.449 Chirality : 0.051 0.376 1479 Planarity : 0.005 0.081 1632 Dihedral : 14.955 170.139 1635 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.81 % Allowed : 11.14 % Favored : 88.05 % Rotamer: Outliers : 4.31 % Allowed : 43.94 % 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: -2.60 (0.24), residues: 1115 helix: -0.27 (0.23), residues: 452 sheet: -3.15 (0.41), residues: 110 loop : -2.74 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1071 TYR 0.040 0.002 TYR A 903 PHE 0.050 0.003 PHE A 220 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 0.00522 / 0.23 ( 9864) covalent geometry : angle 0.88482 / 0.45 (13427) hydrogen bonds : bond 0.05339 / 3.61 ( 357) hydrogen bonds : angle 5.52476 / 3.78 ( 1041) Misc. bond : bond 0.01240 / 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 141 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 99 time to evaluate : 0.362 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: 0.7401 (OUTLIER) cc_final: 0.7162 (pp20) REVERT: A 61 PHE cc_start: 0.4941 (t80) cc_final: 0.4704 (t80) REVERT: A 121 LYS cc_start: 0.6593 (OUTLIER) cc_final: 0.5991 (ptpt) REVERT: A 260 ASN cc_start: 0.7988 (t0) cc_final: 0.7435 (m-40) REVERT: A 267 LYS cc_start: 0.3855 (OUTLIER) cc_final: 0.3649 (mppt) REVERT: A 325 PHE cc_start: 0.5353 (OUTLIER) cc_final: 0.3747 (m-10) REVERT: A 358 ILE cc_start: 0.7769 (mm) cc_final: 0.7514 (tt) REVERT: A 402 GLU cc_start: 0.7993 (tp30) cc_final: 0.7752 (tp30) REVERT: A 412 GLU cc_start: 0.7590 (pp20) cc_final: 0.6752 (pt0) REVERT: A 498 LEU cc_start: 0.7025 (tm) cc_final: 0.6743 (mt) REVERT: A 686 SER cc_start: 0.5845 (OUTLIER) cc_final: 0.5174 (m) REVERT: A 691 ASP cc_start: 0.7501 (p0) cc_final: 0.6957 (m-30) REVERT: A 768 LYS cc_start: 0.6503 (tptp) cc_final: 0.5910 (mttm) REVERT: A 769 ASN cc_start: 0.6786 (t0) cc_final: 0.6412 (t0) REVERT: A 863 PHE cc_start: 0.5953 (OUTLIER) cc_final: 0.5403 (p90) outliers start: 42 outliers final: 30 residues processed: 133 average time/residue: 0.4507 time to fit residues: 66.0745 Evaluate side-chains 133 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 216 VAL Chi-restraints excluded: chain A residue 241 ILE 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 418 ILE Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 520 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 687 LYS Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 713 SER 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 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 1067 SER 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: 0.9980 chunk 32 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 101 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.216950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.179804 restraints weight = 39020.989| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 5.08 r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4356 r_free = 0.4356 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4356 r_free = 0.4356 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.7124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9866 Z= 0.176 Angle : 0.823 16.844 13427 Z= 0.420 Chirality : 0.048 0.363 1479 Planarity : 0.005 0.079 1632 Dihedral : 14.946 174.575 1635 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.06 % Favored : 89.22 % Rotamer: Outliers : 3.39 % Allowed : 44.87 % Favored : 51.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.38 (0.24), residues: 1115 helix: -0.09 (0.24), residues: 451 sheet: -3.03 (0.42), residues: 110 loop : -2.61 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1071 TYR 0.032 0.002 TYR A 903 PHE 0.040 0.002 PHE A 220 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 0.00387 / 0.18 ( 9864) covalent geometry : angle 0.82296 / 0.42 (13427) hydrogen bonds : bond 0.04742 / 3.15 ( 357) hydrogen bonds : angle 5.32509 / 3.64 ( 1041) Misc. bond : bond 0.01185 / 0.62 ( 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 141 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.367 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: 0.7230 (OUTLIER) cc_final: 0.6982 (pp20) REVERT: A 61 PHE cc_start: 0.5501 (t80) cc_final: 0.5242 (t80) REVERT: A 121 LYS cc_start: 0.6575 (OUTLIER) cc_final: 0.5975 (ptpt) REVERT: A 260 ASN cc_start: 0.7864 (t0) cc_final: 0.7542 (m-40) REVERT: A 276 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6052 (mt) REVERT: A 325 PHE cc_start: 0.4986 (OUTLIER) cc_final: 0.3615 (m-10) REVERT: A 358 ILE cc_start: 0.7697 (mm) cc_final: 0.7463 (tt) REVERT: A 412 GLU cc_start: 0.7186 (pp20) cc_final: 0.6512 (pt0) REVERT: A 440 PHE cc_start: 0.4910 (t80) cc_final: 0.4666 (t80) REVERT: A 498 LEU cc_start: 0.6852 (tm) cc_final: 0.6586 (mt) REVERT: A 552 LYS cc_start: 0.6531 (mppt) cc_final: 0.5817 (mttm) REVERT: A 686 SER cc_start: 0.5411 (OUTLIER) cc_final: 0.4813 (m) REVERT: A 691 ASP cc_start: 0.7308 (p0) cc_final: 0.6856 (m-30) REVERT: A 768 LYS cc_start: 0.6135 (tptp) cc_final: 0.5695 (mttm) REVERT: A 769 ASN cc_start: 0.6116 (t0) cc_final: 0.5811 (t0) outliers start: 33 outliers final: 24 residues processed: 135 average time/residue: 0.4630 time to fit residues: 68.7988 Evaluate side-chains 130 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 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 316 SER Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 520 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 687 LYS Chi-restraints excluded: chain A residue 713 SER 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 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 1155 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 30 optimal weight: 0.0270 chunk 85 optimal weight: 2.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 793 GLN ** 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 = 0.4726 r_free = 0.4726 target = 0.218136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.181876 restraints weight = 32720.656| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 4.72 r_work: 0.4122 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4136 r_free = 0.4136 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4136 r_free = 0.4136 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.7299 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 : 0.808 14.754 13427 Z= 0.413 Chirality : 0.048 0.364 1479 Planarity : 0.005 0.077 1632 Dihedral : 14.883 174.195 1633 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.15 % Favored : 89.13 % Rotamer: Outliers : 3.49 % Allowed : 45.07 % Favored : 51.44 % 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: -2.30 (0.24), residues: 1115 helix: -0.09 (0.24), residues: 458 sheet: -2.92 (0.43), residues: 110 loop : -2.55 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1071 TYR 0.031 0.002 TYR A 903 PHE 0.035 0.002 PHE A 220 TRP 0.058 0.002 TRP A 890 HIS 0.007 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 9864) covalent geometry : angle 0.80766 / 0.41 (13427) hydrogen bonds : bond 0.04616 / 3.07 ( 357) hydrogen bonds : angle 5.20145 / 3.56 ( 1041) Misc. bond : bond 0.01144 / 0.60 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3982.39 seconds wall clock time: 68 minutes 45.10 seconds (4125.10 seconds total)