Starting phenix.real_space_refine on Sun Dec 29 19:54:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8atw_15665/12_2024/8atw_15665.cif Found real_map, /net/cci-nas-00/data/ceres_data/8atw_15665/12_2024/8atw_15665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8atw_15665/12_2024/8atw_15665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8atw_15665/12_2024/8atw_15665.map" model { file = "/net/cci-nas-00/data/ceres_data/8atw_15665/12_2024/8atw_15665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8atw_15665/12_2024/8atw_15665.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 64 5.49 5 S 36 5.16 5 C 7024 2.51 5 N 1957 2.21 5 O 2202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11283 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2758 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 316} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 7235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 922, 7235 Classifications: {'peptide': 922} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 44, 'TRANS': 877} Chain breaks: 2 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 80 Chain: "N" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 582 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "T" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 567 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "C" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 109 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.95, per 1000 atoms: 0.62 Number of scatterers: 11283 At special positions: 0 Unit cell: (106.7, 114.46, 118.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 64 15.00 O 2202 8.00 N 1957 7.00 C 7024 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.02 Conformation dependent library (CDL) restraints added in 1.4 seconds 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2380 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 59.3% alpha, 8.8% beta 23 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 4.35 Creating SS restraints... Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 25 through 37 Processing helix chain 'B' and resid 44 through 47 Processing helix chain 'B' and resid 58 through 69 Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 104 through 114 removed outlier: 4.228A pdb=" N TYR B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B 109 " --> pdb=" O TRP B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 removed outlier: 3.670A pdb=" N ILE B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.772A pdb=" N PHE B 163 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 210 through 215 Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 230 through 234 removed outlier: 4.028A pdb=" N GLU B 233 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE B 234 " --> pdb=" O ALA B 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 230 through 234' Processing helix chain 'B' and resid 255 through 267 Processing helix chain 'B' and resid 273 through 278 removed outlier: 3.602A pdb=" N VAL B 277 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N MET B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 273 through 278' Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 295 through 301 removed outlier: 3.793A pdb=" N LEU B 299 " --> pdb=" O ASP B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 Processing helix chain 'B' and resid 326 through 330 removed outlier: 3.659A pdb=" N MET B 329 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP B 330 " --> pdb=" O ILE B 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 326 through 330' Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 397 through 421 removed outlier: 3.747A pdb=" N GLN A 413 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASP A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 441 Processing helix chain 'A' and resid 446 through 477 Proline residue: A 463 - end of helix Processing helix chain 'A' and resid 488 through 501 removed outlier: 4.062A pdb=" N LEU A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Proline residue: A 498 - end of helix Processing helix chain 'A' and resid 504 through 519 Processing helix chain 'A' and resid 531 through 553 removed outlier: 3.646A pdb=" N ILE A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 612 Processing helix chain 'A' and resid 652 through 661 removed outlier: 4.427A pdb=" N GLY A 661 " --> pdb=" O ARG A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 717 Processing helix chain 'A' and resid 719 through 732 removed outlier: 3.975A pdb=" N THR A 732 " --> pdb=" O VAL A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 751 removed outlier: 3.537A pdb=" N GLY A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 813 Processing helix chain 'A' and resid 842 through 848 Processing helix chain 'A' and resid 860 through 873 Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 890 through 900 Processing helix chain 'A' and resid 907 through 911 Processing helix chain 'A' and resid 913 through 930 Processing helix chain 'A' and resid 932 through 935 removed outlier: 3.560A pdb=" N GLU A 935 " --> pdb=" O ASN A 932 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 932 through 935' Processing helix chain 'A' and resid 948 through 959 Processing helix chain 'A' and resid 960 through 967 Processing helix chain 'A' and resid 977 through 994 Processing helix chain 'A' and resid 998 through 1005 Processing helix chain 'A' and resid 1009 through 1021 removed outlier: 4.285A pdb=" N VAL A1021 " --> pdb=" O VAL A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1038 Processing helix chain 'A' and resid 1047 through 1066 Processing helix chain 'A' and resid 1068 through 1085 Processing helix chain 'A' and resid 1090 through 1094 removed outlier: 3.656A pdb=" N LYS A1094 " --> pdb=" O VAL A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1181 Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1197 through 1214 Processing helix chain 'A' and resid 1216 through 1229 Processing helix chain 'A' and resid 1242 through 1260 removed outlier: 3.642A pdb=" N GLN A1246 " --> pdb=" O THR A1242 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS A1247 " --> pdb=" O ASP A1243 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A1259 " --> pdb=" O LEU A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1280 Processing helix chain 'A' and resid 1283 through 1293 Processing helix chain 'A' and resid 1295 through 1302 removed outlier: 3.984A pdb=" N ASP A1302 " --> pdb=" O SER A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1310 removed outlier: 4.212A pdb=" N LEU A1309 " --> pdb=" O ASP A1305 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A1310 " --> pdb=" O LEU A1306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1305 through 1310' Processing helix chain 'A' and resid 1340 through 1346 removed outlier: 4.003A pdb=" N ASN A1345 " --> pdb=" O VAL A1342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.277A pdb=" N TYR B 73 " --> pdb=" O GLN B 96 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU B 98 " --> pdb=" O TYR B 73 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LEU B 75 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER B 74 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 76 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LYS B 167 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N LYS B 131 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 13.135A pdb=" N LEU B 169 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 10.105A pdb=" N LEU B 133 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 12.528A pdb=" N TRP B 171 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N VAL B 135 " --> pdb=" O TRP B 171 " (cutoff:3.500A) removed outlier: 11.572A pdb=" N ASN B 137 " --> pdb=" O PRO B 173 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 166 " --> pdb=" O PRO B 249 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA B 206 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU B 246 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU B 204 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASP B 248 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N THR B 202 " --> pdb=" O ASP B 248 " (cutoff:3.500A) removed outlier: 9.616A pdb=" N ILE B 227 " --> pdb=" O LYS B 203 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ILE B 205 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 528 through 530 Processing sheet with id=AA3, first strand: chain 'A' and resid 613 through 619 removed outlier: 3.641A pdb=" N GLY A 629 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AA5, first strand: chain 'A' and resid 822 through 824 Processing sheet with id=AA6, first strand: chain 'A' and resid 855 through 856 Processing sheet with id=AA7, first strand: chain 'A' and resid 942 through 944 Processing sheet with id=AA8, first strand: chain 'A' and resid 1087 through 1088 removed outlier: 3.530A pdb=" N VAL A1323 " --> pdb=" O GLY A1236 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1109 through 1111 Processing sheet with id=AB1, first strand: chain 'A' and resid 1127 through 1131 removed outlier: 3.517A pdb=" N ILE A1139 " --> pdb=" O LYS A1128 " (cutoff:3.500A) 540 hydrogen bonds defined for protein. 1563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 4.92 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2617 1.33 - 1.45: 2671 1.45 - 1.57: 6212 1.57 - 1.69: 116 1.69 - 1.81: 61 Bond restraints: 11677 Sorted by residual: bond pdb=" O3' DT N 109 " pdb=" P DA N 110 " ideal model delta sigma weight residual 1.607 1.436 0.171 1.50e-02 4.44e+03 1.30e+02 bond pdb=" C4' DT T 20 " pdb=" O4' DT T 20 " ideal model delta sigma weight residual 1.450 1.621 -0.171 2.00e-02 2.50e+03 7.32e+01 bond pdb=" C4' DT T 21 " pdb=" O4' DT T 21 " ideal model delta sigma weight residual 1.450 1.568 -0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" O3' DT T 12 " pdb=" P DT T 13 " ideal model delta sigma weight residual 1.607 1.690 -0.083 1.50e-02 4.44e+03 3.03e+01 bond pdb=" O3' DA T 27 " pdb=" P DA T 28 " ideal model delta sigma weight residual 1.607 1.539 0.068 1.50e-02 4.44e+03 2.03e+01 ... (remaining 11672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 15885 2.78 - 5.56: 178 5.56 - 8.34: 19 8.34 - 11.12: 6 11.12 - 13.90: 6 Bond angle restraints: 16094 Sorted by residual: angle pdb=" C5' DA T 34 " pdb=" C4' DA T 34 " pdb=" O4' DA T 34 " ideal model delta sigma weight residual 109.40 123.30 -13.90 1.50e+00 4.44e-01 8.59e+01 angle pdb=" O3' DA T 28 " pdb=" C3' DA T 28 " pdb=" C2' DA T 28 " ideal model delta sigma weight residual 111.50 98.72 12.78 1.50e+00 4.44e-01 7.25e+01 angle pdb=" C5' DT N 112 " pdb=" C4' DT N 112 " pdb=" O4' DT N 112 " ideal model delta sigma weight residual 109.40 121.24 -11.84 1.50e+00 4.44e-01 6.23e+01 angle pdb=" C5' DT T 29 " pdb=" C4' DT T 29 " pdb=" O4' DT T 29 " ideal model delta sigma weight residual 109.40 119.88 -10.48 1.50e+00 4.44e-01 4.88e+01 angle pdb=" O4' DT T 20 " pdb=" C4' DT T 20 " pdb=" C3' DT T 20 " ideal model delta sigma weight residual 105.40 95.72 9.68 1.50e+00 4.44e-01 4.16e+01 ... (remaining 16089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.65: 6053 21.65 - 43.30: 641 43.30 - 64.95: 169 64.95 - 86.60: 20 86.60 - 108.26: 5 Dihedral angle restraints: 6888 sinusoidal: 3214 harmonic: 3674 Sorted by residual: dihedral pdb=" O5' GTP C 201 " pdb=" O3A GTP C 201 " pdb=" PA GTP C 201 " pdb=" PB GTP C 201 " ideal model delta sinusoidal sigma weight residual 274.12 165.87 108.26 1 2.00e+01 2.50e-03 3.15e+01 dihedral pdb=" C8 GTP C 201 " pdb=" C1' GTP C 201 " pdb=" N9 GTP C 201 " pdb=" O4' GTP C 201 " ideal model delta sinusoidal sigma weight residual 104.59 2.87 101.72 1 2.00e+01 2.50e-03 2.89e+01 dihedral pdb=" CA MET B 267 " pdb=" C MET B 267 " pdb=" N ILE B 268 " pdb=" CA ILE B 268 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 6885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1756 0.131 - 0.262: 16 0.262 - 0.393: 6 0.393 - 0.524: 2 0.524 - 0.655: 2 Chirality restraints: 1782 Sorted by residual: chirality pdb=" C4' DT T 20 " pdb=" C5' DT T 20 " pdb=" O4' DT T 20 " pdb=" C3' DT T 20 " both_signs ideal model delta sigma weight residual False -2.53 -3.18 0.66 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" P DG N 108 " pdb=" OP1 DG N 108 " pdb=" OP2 DG N 108 " pdb=" O5' DG N 108 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C4' DT T 29 " pdb=" C5' DT T 29 " pdb=" O4' DT T 29 " pdb=" C3' DT T 29 " both_signs ideal model delta sigma weight residual False -2.53 -2.02 -0.51 2.00e-01 2.50e+01 6.41e+00 ... (remaining 1779 not shown) Planarity restraints: 1838 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA T 28 " -0.022 2.00e-02 2.50e+03 1.21e-02 4.02e+00 pdb=" N9 DA T 28 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DA T 28 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA T 28 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DA T 28 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA T 28 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA T 28 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DA T 28 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA T 28 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DA T 28 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DA T 28 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 272 " -0.033 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO B 273 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 273 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 273 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 119 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 120 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 120 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 120 " 0.020 5.00e-02 4.00e+02 ... (remaining 1835 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 828 2.74 - 3.28: 11157 3.28 - 3.82: 19479 3.82 - 4.36: 22248 4.36 - 4.90: 37648 Nonbonded interactions: 91360 Sorted by model distance: nonbonded pdb=" O LEU B 23 " pdb=" OH TYR B 29 " model vdw 2.199 3.040 nonbonded pdb=" OG1 THR A1132 " pdb=" O GLN A1135 " model vdw 2.210 3.040 nonbonded pdb=" NH2 ARG A1206 " pdb=" O SER A1346 " model vdw 2.260 3.120 nonbonded pdb=" OD2 ASP A 775 " pdb=" OG SER A 777 " model vdw 2.276 3.040 nonbonded pdb=" O PRO B 102 " pdb=" OH TYR B 108 " model vdw 2.283 3.040 ... (remaining 91355 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.100 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.171 11677 Z= 0.277 Angle : 0.737 13.899 16094 Z= 0.407 Chirality : 0.054 0.655 1782 Planarity : 0.004 0.049 1838 Dihedral : 18.135 108.255 4508 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.24), residues: 1250 helix: 1.59 (0.20), residues: 708 sheet: 0.27 (0.56), residues: 85 loop : -0.58 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 159 HIS 0.004 0.001 HIS A1169 PHE 0.020 0.001 PHE A1300 TYR 0.021 0.002 TYR A 979 ARG 0.007 0.000 ARG A 984 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.242 Fit side-chains REVERT: B 52 ASP cc_start: 0.6643 (t70) cc_final: 0.6442 (t70) REVERT: B 71 ARG cc_start: 0.7645 (ptp-110) cc_final: 0.7430 (ptt180) REVERT: B 247 MET cc_start: 0.8059 (mmt) cc_final: 0.7852 (mmp) REVERT: A 398 LEU cc_start: 0.8355 (mt) cc_final: 0.8045 (mt) REVERT: A 402 LYS cc_start: 0.8556 (mptt) cc_final: 0.8352 (mptt) REVERT: A 514 LEU cc_start: 0.8787 (mt) cc_final: 0.7974 (tp) REVERT: A 1057 HIS cc_start: 0.6975 (m90) cc_final: 0.6355 (m90) REVERT: A 1325 LEU cc_start: 0.8353 (mm) cc_final: 0.8106 (mt) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2271 time to fit residues: 67.5562 Evaluate side-chains 153 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 11677 Z= 0.207 Angle : 0.571 9.386 16094 Z= 0.302 Chirality : 0.040 0.185 1782 Planarity : 0.004 0.040 1838 Dihedral : 18.418 97.987 2081 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.93 % Allowed : 9.04 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1250 helix: 1.59 (0.20), residues: 710 sheet: 0.35 (0.45), residues: 124 loop : -0.84 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 159 HIS 0.004 0.001 HIS B 265 PHE 0.018 0.001 PHE A 886 TYR 0.015 0.001 TYR A1229 ARG 0.008 0.000 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 1.171 Fit side-chains REVERT: A 514 LEU cc_start: 0.8797 (mt) cc_final: 0.8033 (tp) REVERT: A 1057 HIS cc_start: 0.6999 (m90) cc_final: 0.6575 (m90) REVERT: A 1096 PHE cc_start: 0.7627 (p90) cc_final: 0.7382 (p90) outliers start: 10 outliers final: 7 residues processed: 176 average time/residue: 0.2107 time to fit residues: 55.7030 Evaluate side-chains 157 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1233 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 97 optimal weight: 0.3980 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 104 optimal weight: 0.0770 chunk 116 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 overall best weight: 2.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS A1057 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11677 Z= 0.197 Angle : 0.548 8.610 16094 Z= 0.289 Chirality : 0.039 0.180 1782 Planarity : 0.004 0.041 1838 Dihedral : 18.424 100.106 2081 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.58 % Allowed : 12.02 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.24), residues: 1250 helix: 1.64 (0.20), residues: 702 sheet: 0.29 (0.45), residues: 126 loop : -0.70 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 24 HIS 0.006 0.001 HIS B 265 PHE 0.014 0.001 PHE A 886 TYR 0.020 0.001 TYR B 161 ARG 0.006 0.000 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 1.559 Fit side-chains REVERT: B 33 PHE cc_start: 0.7621 (m-10) cc_final: 0.7416 (m-80) REVERT: B 60 GLN cc_start: 0.7073 (tm-30) cc_final: 0.6641 (tm-30) REVERT: B 319 MET cc_start: 0.8341 (mmp) cc_final: 0.8092 (mmp) REVERT: A 1057 HIS cc_start: 0.7221 (m-70) cc_final: 0.6898 (m90) REVERT: A 1096 PHE cc_start: 0.7641 (p90) cc_final: 0.7301 (p90) outliers start: 17 outliers final: 14 residues processed: 184 average time/residue: 0.2332 time to fit residues: 63.5113 Evaluate side-chains 161 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 30.0000 chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 78 optimal weight: 0.7980 chunk 117 optimal weight: 20.0000 chunk 124 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11677 Z= 0.237 Angle : 0.561 8.550 16094 Z= 0.296 Chirality : 0.039 0.164 1782 Planarity : 0.004 0.038 1838 Dihedral : 18.477 103.171 2081 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.96 % Allowed : 14.91 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 1250 helix: 1.66 (0.20), residues: 692 sheet: 0.19 (0.45), residues: 126 loop : -0.75 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 24 HIS 0.006 0.001 HIS B 265 PHE 0.015 0.001 PHE A1300 TYR 0.019 0.001 TYR B 161 ARG 0.005 0.000 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 1.324 Fit side-chains REVERT: B 60 GLN cc_start: 0.7286 (tm-30) cc_final: 0.6664 (tm-30) REVERT: B 319 MET cc_start: 0.8323 (mmp) cc_final: 0.8112 (mmp) REVERT: A 1057 HIS cc_start: 0.7103 (m-70) cc_final: 0.6752 (m90) REVERT: A 1096 PHE cc_start: 0.7605 (p90) cc_final: 0.7256 (p90) outliers start: 21 outliers final: 13 residues processed: 167 average time/residue: 0.2273 time to fit residues: 56.8660 Evaluate side-chains 158 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 GLN B 265 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11677 Z= 0.231 Angle : 0.553 8.694 16094 Z= 0.293 Chirality : 0.039 0.163 1782 Planarity : 0.004 0.045 1838 Dihedral : 18.435 105.332 2081 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.42 % Allowed : 15.10 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1250 helix: 1.61 (0.20), residues: 698 sheet: 0.43 (0.46), residues: 120 loop : -0.83 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 24 HIS 0.006 0.001 HIS B 265 PHE 0.017 0.001 PHE A1300 TYR 0.021 0.002 TYR A1229 ARG 0.006 0.000 ARG A1275 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.243 Fit side-chains REVERT: B 60 GLN cc_start: 0.7258 (tm-30) cc_final: 0.6779 (tm-30) REVERT: A 1057 HIS cc_start: 0.6955 (m-70) cc_final: 0.6638 (m90) REVERT: A 1096 PHE cc_start: 0.7546 (p90) cc_final: 0.7106 (p90) REVERT: A 1229 TYR cc_start: 0.7893 (m-10) cc_final: 0.6987 (m-10) outliers start: 26 outliers final: 23 residues processed: 165 average time/residue: 0.2261 time to fit residues: 55.5725 Evaluate side-chains 163 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 754 PHE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 120 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11677 Z= 0.235 Angle : 0.557 8.417 16094 Z= 0.294 Chirality : 0.039 0.158 1782 Planarity : 0.004 0.049 1838 Dihedral : 18.427 107.134 2081 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.61 % Allowed : 16.78 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.24), residues: 1250 helix: 1.62 (0.20), residues: 692 sheet: 0.29 (0.46), residues: 122 loop : -0.75 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 24 HIS 0.006 0.001 HIS B 265 PHE 0.016 0.001 PHE A1300 TYR 0.019 0.002 TYR B 161 ARG 0.006 0.000 ARG A1275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 1.303 Fit side-chains REVERT: A 1057 HIS cc_start: 0.6948 (m-70) cc_final: 0.6655 (m-70) REVERT: A 1096 PHE cc_start: 0.7551 (p90) cc_final: 0.7132 (p90) REVERT: A 1229 TYR cc_start: 0.7959 (m-10) cc_final: 0.7668 (m-80) outliers start: 28 outliers final: 22 residues processed: 175 average time/residue: 0.2347 time to fit residues: 60.7011 Evaluate side-chains 162 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 91 optimal weight: 30.0000 chunk 70 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11677 Z= 0.319 Angle : 0.612 8.472 16094 Z= 0.324 Chirality : 0.041 0.161 1782 Planarity : 0.004 0.048 1838 Dihedral : 18.583 109.962 2081 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.61 % Allowed : 17.33 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.24), residues: 1250 helix: 1.39 (0.20), residues: 699 sheet: 0.07 (0.46), residues: 118 loop : -0.88 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 24 HIS 0.008 0.001 HIS B 265 PHE 0.019 0.002 PHE A1300 TYR 0.019 0.002 TYR B 161 ARG 0.005 0.000 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.259 Fit side-chains REVERT: A 529 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.7942 (ppp) REVERT: A 926 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7359 (mm-30) REVERT: A 930 MET cc_start: 0.7529 (ttm) cc_final: 0.7302 (ttt) REVERT: A 1057 HIS cc_start: 0.6984 (m-70) cc_final: 0.6658 (m-70) REVERT: A 1096 PHE cc_start: 0.7532 (p90) cc_final: 0.7019 (p90) outliers start: 28 outliers final: 22 residues processed: 161 average time/residue: 0.2111 time to fit residues: 51.7194 Evaluate side-chains 158 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 754 PHE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 61 optimal weight: 0.4980 chunk 11 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 11677 Z= 0.324 Angle : 0.617 8.350 16094 Z= 0.327 Chirality : 0.041 0.158 1782 Planarity : 0.004 0.049 1838 Dihedral : 18.663 113.920 2081 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.89 % Allowed : 17.99 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.24), residues: 1250 helix: 1.36 (0.20), residues: 699 sheet: -0.14 (0.45), residues: 121 loop : -0.94 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 235 HIS 0.004 0.001 HIS B 127 PHE 0.025 0.002 PHE B 85 TYR 0.020 0.002 TYR B 161 ARG 0.009 0.000 ARG A1275 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.239 Fit side-chains REVERT: B 329 MET cc_start: 0.6818 (mtm) cc_final: 0.6322 (mmm) REVERT: A 529 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.7988 (ppp) REVERT: A 926 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7381 (mm-30) REVERT: A 930 MET cc_start: 0.7560 (ttm) cc_final: 0.7347 (ttt) REVERT: A 1057 HIS cc_start: 0.6995 (m-70) cc_final: 0.6684 (m-70) REVERT: A 1096 PHE cc_start: 0.7473 (p90) cc_final: 0.6980 (p90) REVERT: A 1170 MET cc_start: 0.8236 (tmm) cc_final: 0.8034 (tmm) outliers start: 31 outliers final: 23 residues processed: 164 average time/residue: 0.2264 time to fit residues: 55.2621 Evaluate side-chains 157 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 754 PHE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 7.9990 chunk 115 optimal weight: 30.0000 chunk 119 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 122 optimal weight: 0.5980 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 11677 Z= 0.285 Angle : 0.613 10.768 16094 Z= 0.322 Chirality : 0.041 0.303 1782 Planarity : 0.004 0.045 1838 Dihedral : 18.657 115.155 2081 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.70 % Allowed : 18.17 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.24), residues: 1250 helix: 1.36 (0.20), residues: 698 sheet: -0.00 (0.46), residues: 118 loop : -1.04 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 24 HIS 0.004 0.001 HIS B 127 PHE 0.017 0.002 PHE A1300 TYR 0.020 0.002 TYR B 161 ARG 0.007 0.000 ARG A 984 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 1.290 Fit side-chains REVERT: B 329 MET cc_start: 0.6810 (mtm) cc_final: 0.6316 (mmm) REVERT: A 529 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.7923 (ppp) REVERT: A 926 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7381 (mm-30) REVERT: A 930 MET cc_start: 0.7578 (ttm) cc_final: 0.7356 (ttt) REVERT: A 1057 HIS cc_start: 0.6954 (m-70) cc_final: 0.6687 (m-70) REVERT: A 1096 PHE cc_start: 0.7496 (p90) cc_final: 0.6955 (p90) outliers start: 29 outliers final: 25 residues processed: 157 average time/residue: 0.2191 time to fit residues: 51.6997 Evaluate side-chains 162 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 754 PHE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 102 optimal weight: 0.0050 chunk 10 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 overall best weight: 4.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 11677 Z= 0.278 Angle : 0.615 10.311 16094 Z= 0.321 Chirality : 0.040 0.163 1782 Planarity : 0.004 0.047 1838 Dihedral : 18.638 116.422 2081 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.61 % Allowed : 18.55 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.24), residues: 1250 helix: 1.37 (0.20), residues: 697 sheet: 0.04 (0.45), residues: 120 loop : -0.99 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 24 HIS 0.004 0.001 HIS B 127 PHE 0.016 0.001 PHE A1300 TYR 0.038 0.002 TYR A1229 ARG 0.006 0.000 ARG A 984 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 1.456 Fit side-chains REVERT: B 329 MET cc_start: 0.6809 (mtm) cc_final: 0.6288 (mmm) REVERT: A 529 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.7916 (ppp) REVERT: A 926 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7407 (mm-30) REVERT: A 930 MET cc_start: 0.7568 (ttm) cc_final: 0.7358 (ttt) REVERT: A 1057 HIS cc_start: 0.6964 (m-70) cc_final: 0.6701 (m-70) REVERT: A 1096 PHE cc_start: 0.7471 (p90) cc_final: 0.6983 (p90) outliers start: 28 outliers final: 26 residues processed: 158 average time/residue: 0.2096 time to fit residues: 50.8605 Evaluate side-chains 164 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 754 PHE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1103 ASP Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1332 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 42 optimal weight: 30.0000 chunk 105 optimal weight: 7.9990 chunk 12 optimal weight: 30.0000 chunk 18 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 overall best weight: 6.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.139131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.107688 restraints weight = 18057.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.111106 restraints weight = 10165.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.113350 restraints weight = 7197.915| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 11677 Z= 0.354 Angle : 0.651 9.982 16094 Z= 0.341 Chirality : 0.042 0.236 1782 Planarity : 0.004 0.045 1838 Dihedral : 18.788 118.597 2081 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.89 % Allowed : 18.64 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.24), residues: 1250 helix: 1.23 (0.20), residues: 697 sheet: -0.16 (0.46), residues: 121 loop : -1.04 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 24 HIS 0.004 0.001 HIS B 127 PHE 0.022 0.002 PHE A1300 TYR 0.021 0.002 TYR B 161 ARG 0.009 0.001 ARG A1275 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1981.70 seconds wall clock time: 37 minutes 46.65 seconds (2266.65 seconds total)