Starting phenix.real_space_refine on Tue Jul 29 12:34:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q63_18183/07_2025/8q63_18183.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q63_18183/07_2025/8q63_18183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q63_18183/07_2025/8q63_18183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q63_18183/07_2025/8q63_18183.map" model { file = "/net/cci-nas-00/data/ceres_data/8q63_18183/07_2025/8q63_18183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q63_18183/07_2025/8q63_18183.cif" } resolution = 3.68 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= 0.001 sd= 0.010 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 70 5.49 5 S 35 5.16 5 C 7041 2.51 5 N 1971 2.21 5 O 2229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11346 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2698 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 309} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 7200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7200 Classifications: {'peptide': 915} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 44, 'TRANS': 870} Chain breaks: 4 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 73 Chain: "N" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 642 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "T" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 630 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "C" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 152 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna3p': 6} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 6.69, per 1000 atoms: 0.59 Number of scatterers: 11346 At special positions: 0 Unit cell: (103.79, 116.4, 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 35 16.00 P 70 15.00 O 2229 8.00 N 1971 7.00 C 7041 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: 2.76 Conformation dependent library (CDL) restraints added in 1.3 seconds 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2354 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 11 sheets defined 59.8% alpha, 7.3% beta 26 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 3.81 Creating SS restraints... Processing helix chain 'B' and resid 7 through 14 removed outlier: 3.890A pdb=" N LEU B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 37 Processing helix chain 'B' and resid 38 through 41 Processing helix chain 'B' and resid 44 through 47 removed outlier: 3.762A pdb=" N GLU B 47 " --> pdb=" O HIS B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 44 through 47' Processing helix chain 'B' and resid 58 through 69 Processing helix chain 'B' and resid 79 through 90 Processing helix chain 'B' and resid 104 through 113 removed outlier: 3.834A pdb=" N TYR B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 157 removed outlier: 3.960A pdb=" N MET B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE B 154 " --> pdb=" O TRP B 150 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 removed outlier: 3.729A pdb=" N GLY B 164 " --> pdb=" O TYR B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 182 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.521A pdb=" N GLU B 212 " --> pdb=" O ASP B 209 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 214 " --> pdb=" O ASN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 230 through 234 removed outlier: 4.297A pdb=" N ILE B 234 " --> pdb=" O ALA B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 267 Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 273 through 278 removed outlier: 4.141A pdb=" N MET B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 282 Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 295 through 301 removed outlier: 3.573A pdb=" N LEU B 299 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 321 Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 397 through 421 removed outlier: 4.247A pdb=" N ASP A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 442 Processing helix chain 'A' and resid 448 through 476 removed outlier: 4.518A pdb=" N VAL A 452 " --> pdb=" O LYS A 448 " (cutoff:3.500A) Proline residue: A 463 - end of helix Processing helix chain 'A' and resid 490 through 497 removed outlier: 3.764A pdb=" N GLY A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 515 removed outlier: 4.529A pdb=" N GLY A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 552 removed outlier: 3.855A pdb=" N ILE A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 611 removed outlier: 3.747A pdb=" N VAL A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 663 removed outlier: 3.628A pdb=" N GLU A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 717 removed outlier: 3.884A pdb=" N VAL A 707 " --> pdb=" O SER A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 731 Processing helix chain 'A' and resid 737 through 751 Processing helix chain 'A' and resid 777 through 813 Processing helix chain 'A' and resid 842 through 848 Processing helix chain 'A' and resid 857 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 906 through 911 Processing helix chain 'A' and resid 913 through 930 Processing helix chain 'A' and resid 932 through 935 Processing helix chain 'A' and resid 948 through 959 removed outlier: 3.703A pdb=" N ALA A 956 " --> pdb=" O GLN A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 967 Processing helix chain 'A' and resid 977 through 997 Processing helix chain 'A' and resid 998 through 1004 Processing helix chain 'A' and resid 1009 through 1021 removed outlier: 3.729A 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 1046 through 1066 removed outlier: 4.435A pdb=" N PHE A1050 " --> pdb=" O GLU A1046 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A1053 " --> pdb=" O ASP A1049 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS A1057 " --> pdb=" O TYR A1053 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER A1060 " --> pdb=" O LYS A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1085 Processing helix chain 'A' and resid 1089 through 1094 removed outlier: 4.066A pdb=" N LYS A1094 " --> pdb=" O ASP A1090 " (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 1213 Processing helix chain 'A' and resid 1216 through 1229 Processing helix chain 'A' and resid 1242 through 1244 No H-bonds generated for 'chain 'A' and resid 1242 through 1244' Processing helix chain 'A' and resid 1245 through 1260 Processing helix chain 'A' and resid 1264 through 1281 removed outlier: 3.647A pdb=" N LEU A1279 " --> pdb=" O ARG A1275 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A1281 " --> pdb=" O GLU A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1293 Processing helix chain 'A' and resid 1295 through 1301 removed outlier: 3.774A pdb=" N LEU A1299 " --> pdb=" O THR A1295 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE A1300 " --> pdb=" O THR A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1310 Processing helix chain 'A' and resid 1339 through 1344 Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.704A pdb=" N VAL B 135 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N MET B 247 " --> pdb=" O MET B 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 206 through 207 removed outlier: 3.953A pdb=" N ILE B 207 " --> pdb=" O ILE B 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 529 through 530 removed outlier: 3.547A pdb=" N ALA A 635 " --> pdb=" O LYS A 650 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 613 through 619 Processing sheet with id=AA5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AA6, first strand: chain 'A' and resid 822 through 824 Processing sheet with id=AA7, first strand: chain 'A' and resid 855 through 856 removed outlier: 3.997A pdb=" N LYS A 855 " --> pdb=" O SER A 938 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A 938 " --> pdb=" O LYS A 855 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 942 through 944 Processing sheet with id=AA9, first strand: chain 'A' and resid 1086 through 1087 Processing sheet with id=AB1, first strand: chain 'A' and resid 1109 through 1111 removed outlier: 3.739A pdb=" N TRP A1110 " --> pdb=" O ILE A1118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1127 through 1131 removed outlier: 3.610A pdb=" N ILE A1139 " --> pdb=" O LYS A1128 " (cutoff:3.500A) 527 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 5.25 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1999 1.33 - 1.45: 3277 1.45 - 1.57: 6274 1.57 - 1.69: 146 1.69 - 1.82: 60 Bond restraints: 11756 Sorted by residual: bond pdb=" O3' DG N 136 " pdb=" P DC N 137 " ideal model delta sigma weight residual 1.607 1.449 0.158 1.50e-02 4.44e+03 1.11e+02 bond pdb=" C3' DC N 137 " pdb=" C2' DC N 137 " ideal model delta sigma weight residual 1.525 1.696 -0.171 2.00e-02 2.50e+03 7.27e+01 bond pdb=" O3A GTP C 201 " pdb=" PA GTP C 201 " ideal model delta sigma weight residual 1.610 1.492 0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" C2' DC N 137 " pdb=" C1' DC N 137 " ideal model delta sigma weight residual 1.525 1.409 0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" O3' DC T 18 " pdb=" P DA T 19 " ideal model delta sigma weight residual 1.607 1.524 0.083 1.50e-02 4.44e+03 3.06e+01 ... (remaining 11751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.16: 16035 4.16 - 8.32: 167 8.32 - 12.48: 17 12.48 - 16.64: 6 16.64 - 20.80: 2 Bond angle restraints: 16227 Sorted by residual: angle pdb=" O3' DG N 136 " pdb=" P DC N 137 " pdb=" O5' DC N 137 " ideal model delta sigma weight residual 104.00 124.80 -20.80 1.50e+00 4.44e-01 1.92e+02 angle pdb=" C3' DC T 18 " pdb=" O3' DC T 18 " pdb=" P DA T 19 " ideal model delta sigma weight residual 120.20 104.85 15.35 1.50e+00 4.44e-01 1.05e+02 angle pdb=" C3' DT T 20 " pdb=" O3' DT T 20 " pdb=" P DT T 21 " ideal model delta sigma weight residual 120.20 105.74 14.46 1.50e+00 4.44e-01 9.29e+01 angle pdb=" C2' DC N 137 " pdb=" C1' DC N 137 " pdb=" N1 DC N 137 " ideal model delta sigma weight residual 113.50 100.28 13.22 1.50e+00 4.44e-01 7.76e+01 angle pdb=" C3' DA N 131 " pdb=" O3' DA N 131 " pdb=" P DA N 132 " ideal model delta sigma weight residual 120.20 132.94 -12.74 1.50e+00 4.44e-01 7.22e+01 ... (remaining 16222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.16: 6546 34.16 - 68.31: 366 68.31 - 102.47: 16 102.47 - 136.62: 1 136.62 - 170.78: 2 Dihedral angle restraints: 6931 sinusoidal: 3300 harmonic: 3631 Sorted by residual: 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 -12.75 117.34 1 2.00e+01 2.50e-03 3.50e+01 dihedral pdb=" C5' G C 108 " pdb=" C4' G C 108 " pdb=" C3' G C 108 " pdb=" O3' G C 108 " ideal model delta sinusoidal sigma weight residual 147.00 112.01 34.99 1 8.00e+00 1.56e-02 2.71e+01 dihedral pdb=" O4' G C 108 " pdb=" C4' G C 108 " pdb=" C3' G C 108 " pdb=" C2' G C 108 " ideal model delta sinusoidal sigma weight residual 24.00 -7.29 31.29 1 8.00e+00 1.56e-02 2.18e+01 ... (remaining 6928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1716 0.127 - 0.253: 36 0.253 - 0.380: 4 0.380 - 0.507: 17 0.507 - 0.633: 27 Chirality restraints: 1800 Sorted by residual: chirality pdb=" P DG T 10 " pdb=" OP1 DG T 10 " pdb=" OP2 DG T 10 " pdb=" O5' DG T 10 " both_signs ideal model delta sigma weight residual True 2.35 2.98 -0.63 2.00e-01 2.50e+01 1.00e+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 -2.94 -0.59 2.00e-01 2.50e+01 8.80e+00 chirality pdb=" P DC N 137 " pdb=" OP1 DC N 137 " pdb=" OP2 DC N 137 " pdb=" O5' DC N 137 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.59 2.00e-01 2.50e+01 8.57e+00 ... (remaining 1797 not shown) Planarity restraints: 1825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT N 135 " 0.034 2.00e-02 2.50e+03 1.68e-02 7.09e+00 pdb=" N1 DT N 135 " -0.037 2.00e-02 2.50e+03 pdb=" C2 DT N 135 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DT N 135 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DT N 135 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DT N 135 " 0.012 2.00e-02 2.50e+03 pdb=" O4 DT N 135 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DT N 135 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT N 135 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT N 135 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 159 " 0.017 2.00e-02 2.50e+03 1.60e-02 6.42e+00 pdb=" CG TRP B 159 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP B 159 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 159 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 159 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 159 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 159 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 159 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 159 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 159 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 320 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C GLU B 320 " 0.033 2.00e-02 2.50e+03 pdb=" O GLU B 320 " -0.013 2.00e-02 2.50e+03 pdb=" N TRP B 321 " -0.011 2.00e-02 2.50e+03 ... (remaining 1822 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 285 2.68 - 3.23: 11044 3.23 - 3.79: 18562 3.79 - 4.34: 24480 4.34 - 4.90: 38376 Nonbonded interactions: 92747 Sorted by model distance: nonbonded pdb=" OG1 THR A1132 " pdb=" O GLN A1135 " model vdw 2.121 3.040 nonbonded pdb=" OD1 ASP A 843 " pdb=" NE2 GLN A 916 " model vdw 2.205 3.120 nonbonded pdb=" O SER B 190 " pdb=" OG SER B 193 " model vdw 2.228 3.040 nonbonded pdb=" N LYS B 49 " pdb=" O LYS B 131 " model vdw 2.262 3.120 nonbonded pdb=" OD1 ASP A 876 " pdb=" NH1 ARG A 883 " model vdw 2.264 3.120 ... (remaining 92742 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: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 31.770 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 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 : 0.007 0.171 11757 Z= 0.356 Angle : 1.034 20.795 16227 Z= 0.537 Chirality : 0.094 0.633 1800 Planarity : 0.004 0.042 1825 Dihedral : 18.500 170.778 4577 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.09 % Allowed : 0.66 % Favored : 99.25 % 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 (0.25), residues: 1232 helix: 1.59 (0.21), residues: 666 sheet: -1.19 (0.56), residues: 80 loop : -1.01 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 159 HIS 0.013 0.001 HIS A 943 PHE 0.028 0.002 PHE A 936 TYR 0.020 0.002 TYR A 954 ARG 0.003 0.000 ARG A 989 Details of bonding type rmsd hydrogen bonds : bond 0.15627 ( 586) hydrogen bonds : angle 6.37006 ( 1642) covalent geometry : bond 0.00689 (11756) covalent geometry : angle 1.03364 (16227) Misc. bond : bond 0.01190 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 727 ASN cc_start: 0.7988 (m-40) cc_final: 0.7538 (m110) REVERT: A 796 ASP cc_start: 0.8051 (m-30) cc_final: 0.7790 (m-30) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.2598 time to fit residues: 69.4818 Evaluate side-chains 129 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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: 3.9990 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 101 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 117 optimal weight: 40.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 628 HIS A 642 ASN ** A 925 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 = 0.4117 r_free = 0.4117 target = 0.152053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.120511 restraints weight = 20462.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.124454 restraints weight = 11035.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.127001 restraints weight = 7555.189| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11757 Z= 0.188 Angle : 0.654 8.376 16227 Z= 0.346 Chirality : 0.042 0.151 1800 Planarity : 0.004 0.042 1825 Dihedral : 19.476 174.143 2162 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.31 % Allowed : 9.48 % Favored : 89.20 % 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: 0.61 (0.25), residues: 1232 helix: 1.55 (0.20), residues: 673 sheet: -0.95 (0.58), residues: 74 loop : -1.02 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 159 HIS 0.006 0.001 HIS A1188 PHE 0.034 0.002 PHE A 754 TYR 0.031 0.002 TYR A 496 ARG 0.003 0.000 ARG A 829 Details of bonding type rmsd hydrogen bonds : bond 0.05390 ( 586) hydrogen bonds : angle 4.73525 ( 1642) covalent geometry : bond 0.00427 (11756) covalent geometry : angle 0.65406 (16227) Misc. bond : bond 0.00122 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 TRP cc_start: 0.7753 (t60) cc_final: 0.6817 (t60) REVERT: A 656 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9024 (tt) REVERT: A 796 ASP cc_start: 0.8052 (m-30) cc_final: 0.7799 (m-30) REVERT: A 856 LYS cc_start: 0.7208 (mmmt) cc_final: 0.6925 (mmmt) REVERT: A 1157 LEU cc_start: 0.6593 (tp) cc_final: 0.6242 (tp) outliers start: 14 outliers final: 8 residues processed: 164 average time/residue: 0.2224 time to fit residues: 53.4287 Evaluate side-chains 151 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 18 optimal weight: 40.0000 chunk 115 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 HIS ** A 925 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 = 0.4157 r_free = 0.4157 target = 0.154812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.121803 restraints weight = 20515.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.126096 restraints weight = 10735.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.128889 restraints weight = 7252.250| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11757 Z= 0.135 Angle : 0.592 7.507 16227 Z= 0.310 Chirality : 0.039 0.144 1800 Planarity : 0.004 0.039 1825 Dihedral : 19.189 168.600 2162 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.25 % Allowed : 12.58 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.69 (0.25), residues: 1232 helix: 1.67 (0.20), residues: 680 sheet: -1.28 (0.52), residues: 90 loop : -1.00 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 159 HIS 0.005 0.001 HIS A 943 PHE 0.022 0.001 PHE A 936 TYR 0.029 0.001 TYR A 496 ARG 0.002 0.000 ARG A1250 Details of bonding type rmsd hydrogen bonds : bond 0.04462 ( 586) hydrogen bonds : angle 4.34358 ( 1642) covalent geometry : bond 0.00299 (11756) covalent geometry : angle 0.59186 (16227) Misc. bond : bond 0.00068 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 228 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7888 (tt) REVERT: B 321 TRP cc_start: 0.8032 (t60) cc_final: 0.7479 (t60) REVERT: A 607 MET cc_start: 0.8051 (ttp) cc_final: 0.7827 (ttp) REVERT: A 796 ASP cc_start: 0.8017 (m-30) cc_final: 0.7788 (m-30) REVERT: A 1157 LEU cc_start: 0.6465 (tp) cc_final: 0.6196 (tp) REVERT: A 1201 MET cc_start: 0.7683 (ttp) cc_final: 0.7294 (ttp) outliers start: 24 outliers final: 14 residues processed: 171 average time/residue: 0.2213 time to fit residues: 56.0358 Evaluate side-chains 154 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 709 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 47 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 118 optimal weight: 40.0000 chunk 18 optimal weight: 40.0000 chunk 113 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 52 optimal weight: 30.0000 chunk 77 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 HIS ** A 925 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 = 0.4117 r_free = 0.4117 target = 0.151053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.117262 restraints weight = 20448.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.121330 restraints weight = 11016.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.123636 restraints weight = 7586.086| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11757 Z= 0.167 Angle : 0.604 7.817 16227 Z= 0.315 Chirality : 0.040 0.154 1800 Planarity : 0.004 0.046 1825 Dihedral : 19.137 165.364 2162 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.54 % Allowed : 14.27 % Favored : 83.19 % 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: 0.79 (0.25), residues: 1232 helix: 1.70 (0.21), residues: 669 sheet: -1.22 (0.54), residues: 80 loop : -0.84 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 159 HIS 0.006 0.001 HIS A 628 PHE 0.023 0.001 PHE B 132 TYR 0.025 0.002 TYR A 496 ARG 0.002 0.000 ARG A 906 Details of bonding type rmsd hydrogen bonds : bond 0.04545 ( 586) hydrogen bonds : angle 4.39602 ( 1642) covalent geometry : bond 0.00383 (11756) covalent geometry : angle 0.60400 (16227) Misc. bond : bond 0.00065 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 TRP cc_start: 0.8045 (t60) cc_final: 0.7828 (t60) REVERT: B 228 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7944 (tt) REVERT: A 796 ASP cc_start: 0.8115 (m-30) cc_final: 0.7871 (m-30) REVERT: A 1157 LEU cc_start: 0.6580 (tp) cc_final: 0.6013 (tp) REVERT: A 1201 MET cc_start: 0.7786 (ttp) cc_final: 0.7152 (ttp) outliers start: 27 outliers final: 16 residues processed: 169 average time/residue: 0.2193 time to fit residues: 54.5454 Evaluate side-chains 158 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 709 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1170 MET Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 7 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 20 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 925 ASN ** 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 = 0.4134 r_free = 0.4134 target = 0.152513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.118636 restraints weight = 20273.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.122587 restraints weight = 10898.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.125344 restraints weight = 7572.365| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11757 Z= 0.143 Angle : 0.606 9.821 16227 Z= 0.311 Chirality : 0.040 0.228 1800 Planarity : 0.004 0.041 1825 Dihedral : 19.049 162.807 2162 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.44 % Allowed : 15.68 % Favored : 81.88 % 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: 0.81 (0.25), residues: 1232 helix: 1.68 (0.20), residues: 675 sheet: -1.27 (0.52), residues: 90 loop : -0.75 (0.31), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 159 HIS 0.006 0.001 HIS B 44 PHE 0.023 0.001 PHE B 132 TYR 0.025 0.001 TYR A 496 ARG 0.002 0.000 ARG A 829 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 586) hydrogen bonds : angle 4.30463 ( 1642) covalent geometry : bond 0.00323 (11756) covalent geometry : angle 0.60625 (16227) Misc. bond : bond 0.00058 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 LYS cc_start: 0.7986 (mmtm) cc_final: 0.7528 (mmmt) REVERT: A 656 ILE cc_start: 0.9155 (tp) cc_final: 0.8942 (tt) REVERT: A 796 ASP cc_start: 0.8084 (m-30) cc_final: 0.7856 (m-30) REVERT: A 856 LYS cc_start: 0.7608 (mmtt) cc_final: 0.7222 (mmmt) REVERT: A 926 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7794 (tm-30) REVERT: A 1201 MET cc_start: 0.7802 (ttp) cc_final: 0.7127 (ttp) outliers start: 26 outliers final: 18 residues processed: 169 average time/residue: 0.2928 time to fit residues: 72.6876 Evaluate side-chains 161 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 709 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1170 MET Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 91 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 105 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 9 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 HIS A 459 ASN ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.150918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.117243 restraints weight = 20506.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.121224 restraints weight = 10977.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.123854 restraints weight = 7572.600| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11757 Z= 0.169 Angle : 0.627 9.349 16227 Z= 0.321 Chirality : 0.041 0.184 1800 Planarity : 0.004 0.039 1825 Dihedral : 19.071 163.005 2162 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.44 % Allowed : 17.28 % Favored : 80.28 % 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: 0.82 (0.25), residues: 1232 helix: 1.69 (0.20), residues: 669 sheet: -1.24 (0.52), residues: 90 loop : -0.72 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 159 HIS 0.004 0.001 HIS A1163 PHE 0.027 0.002 PHE B 132 TYR 0.022 0.002 TYR A 496 ARG 0.003 0.000 ARG A 883 Details of bonding type rmsd hydrogen bonds : bond 0.04455 ( 586) hydrogen bonds : angle 4.37663 ( 1642) covalent geometry : bond 0.00390 (11756) covalent geometry : angle 0.62660 (16227) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 HIS cc_start: 0.6745 (t-170) cc_final: 0.6519 (t-90) REVERT: B 150 TRP cc_start: 0.7063 (m-10) cc_final: 0.6862 (m-10) REVERT: B 159 TRP cc_start: 0.7973 (t60) cc_final: 0.7764 (t60) REVERT: B 296 LYS cc_start: 0.8080 (mmtm) cc_final: 0.7619 (mmmt) REVERT: A 796 ASP cc_start: 0.8095 (m-30) cc_final: 0.7862 (m-30) REVERT: A 856 LYS cc_start: 0.7700 (mmtt) cc_final: 0.7115 (mmmt) REVERT: A 1160 ASN cc_start: 0.8932 (m110) cc_final: 0.8583 (m110) REVERT: A 1201 MET cc_start: 0.7775 (ttp) cc_final: 0.7036 (ttp) outliers start: 26 outliers final: 21 residues processed: 164 average time/residue: 0.2603 time to fit residues: 63.8400 Evaluate side-chains 165 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 709 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1170 MET Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 124 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 691 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 = 0.4069 r_free = 0.4069 target = 0.146961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.113178 restraints weight = 20641.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.117042 restraints weight = 11205.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.119571 restraints weight = 7781.046| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11757 Z= 0.247 Angle : 0.698 8.565 16227 Z= 0.360 Chirality : 0.044 0.204 1800 Planarity : 0.005 0.041 1825 Dihedral : 19.267 164.675 2162 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.00 % Allowed : 17.65 % Favored : 79.34 % 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: 0.36 (0.25), residues: 1232 helix: 1.26 (0.20), residues: 674 sheet: -1.49 (0.49), residues: 100 loop : -0.83 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 159 HIS 0.009 0.001 HIS B 44 PHE 0.029 0.002 PHE B 132 TYR 0.027 0.002 TYR A 954 ARG 0.002 0.000 ARG A 883 Details of bonding type rmsd hydrogen bonds : bond 0.05341 ( 586) hydrogen bonds : angle 4.75926 ( 1642) covalent geometry : bond 0.00566 (11756) covalent geometry : angle 0.69844 (16227) Misc. bond : bond 0.00043 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 150 TRP cc_start: 0.7294 (m-10) cc_final: 0.7042 (m-10) REVERT: B 159 TRP cc_start: 0.8164 (t60) cc_final: 0.7906 (t60) REVERT: A 727 ASN cc_start: 0.8027 (m-40) cc_final: 0.7600 (m110) REVERT: A 796 ASP cc_start: 0.8050 (m-30) cc_final: 0.7824 (m-30) REVERT: A 1160 ASN cc_start: 0.8879 (m110) cc_final: 0.8614 (m-40) REVERT: A 1201 MET cc_start: 0.7769 (ttp) cc_final: 0.7357 (ttp) outliers start: 32 outliers final: 23 residues processed: 158 average time/residue: 0.3012 time to fit residues: 72.0999 Evaluate side-chains 161 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 709 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1170 MET Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 76 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 93 optimal weight: 0.0970 chunk 10 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 925 ASN ** 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 = 0.4112 r_free = 0.4112 target = 0.150494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.117078 restraints weight = 20177.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.121081 restraints weight = 10786.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.123648 restraints weight = 7404.437| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 11757 Z= 0.157 Angle : 0.643 10.223 16227 Z= 0.327 Chirality : 0.041 0.183 1800 Planarity : 0.004 0.038 1825 Dihedral : 19.041 165.282 2162 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.44 % Allowed : 18.69 % Favored : 78.87 % 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: 0.61 (0.25), residues: 1232 helix: 1.47 (0.20), residues: 674 sheet: -1.40 (0.49), residues: 100 loop : -0.71 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 159 HIS 0.004 0.001 HIS B 44 PHE 0.029 0.002 PHE B 132 TYR 0.024 0.002 TYR A 496 ARG 0.001 0.000 ARG A 800 Details of bonding type rmsd hydrogen bonds : bond 0.04503 ( 586) hydrogen bonds : angle 4.49273 ( 1642) covalent geometry : bond 0.00362 (11756) covalent geometry : angle 0.64350 (16227) Misc. bond : bond 0.00047 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 HIS cc_start: 0.7185 (t-170) cc_final: 0.6836 (t-170) REVERT: B 296 LYS cc_start: 0.8133 (mmtm) cc_final: 0.7742 (mmmt) REVERT: B 321 TRP cc_start: 0.7946 (t60) cc_final: 0.7292 (t60) REVERT: A 796 ASP cc_start: 0.8032 (m-30) cc_final: 0.7800 (m-30) REVERT: A 1160 ASN cc_start: 0.8895 (m110) cc_final: 0.8596 (m110) REVERT: A 1201 MET cc_start: 0.7793 (ttp) cc_final: 0.7137 (ttp) outliers start: 26 outliers final: 22 residues processed: 168 average time/residue: 0.3068 time to fit residues: 78.2574 Evaluate side-chains 166 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 709 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1170 MET Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 8 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 113 optimal weight: 30.0000 chunk 69 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 overall best weight: 7.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 925 ASN ** 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 = 0.4072 r_free = 0.4072 target = 0.147051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.113346 restraints weight = 20723.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.117162 restraints weight = 11219.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.119720 restraints weight = 7800.314| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 11757 Z= 0.243 Angle : 0.708 12.141 16227 Z= 0.362 Chirality : 0.044 0.208 1800 Planarity : 0.005 0.042 1825 Dihedral : 19.198 166.719 2162 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.54 % Allowed : 18.50 % Favored : 78.97 % 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: 0.35 (0.25), residues: 1232 helix: 1.25 (0.20), residues: 673 sheet: -1.39 (0.50), residues: 100 loop : -0.86 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP B 159 HIS 0.005 0.001 HIS A1163 PHE 0.034 0.002 PHE B 132 TYR 0.032 0.002 TYR A 954 ARG 0.002 0.000 ARG A 883 Details of bonding type rmsd hydrogen bonds : bond 0.05204 ( 586) hydrogen bonds : angle 4.77588 ( 1642) covalent geometry : bond 0.00563 (11756) covalent geometry : angle 0.70849 (16227) Misc. bond : bond 0.00039 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 321 TRP cc_start: 0.8031 (t60) cc_final: 0.7504 (t60) REVERT: A 461 MET cc_start: 0.6526 (mmm) cc_final: 0.6324 (mmm) REVERT: A 507 LYS cc_start: 0.8585 (mtmm) cc_final: 0.8276 (mtmm) REVERT: A 727 ASN cc_start: 0.7990 (m-40) cc_final: 0.7561 (m110) REVERT: A 796 ASP cc_start: 0.8026 (m-30) cc_final: 0.7805 (m-30) REVERT: A 1160 ASN cc_start: 0.8890 (m110) cc_final: 0.8625 (m-40) REVERT: A 1201 MET cc_start: 0.7693 (ttp) cc_final: 0.6960 (ttp) outliers start: 27 outliers final: 22 residues processed: 156 average time/residue: 0.2775 time to fit residues: 66.1008 Evaluate side-chains 164 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 709 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1170 MET Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 13 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 120 optimal weight: 0.0270 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 HIS ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1169 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.150958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.117506 restraints weight = 20427.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.121580 restraints weight = 10882.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.124146 restraints weight = 7453.364| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11757 Z= 0.149 Angle : 0.665 12.507 16227 Z= 0.337 Chirality : 0.042 0.255 1800 Planarity : 0.004 0.041 1825 Dihedral : 19.017 168.251 2162 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.35 % Allowed : 18.87 % Favored : 78.78 % 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 (0.25), residues: 1232 helix: 1.45 (0.20), residues: 670 sheet: -1.20 (0.53), residues: 90 loop : -0.77 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP B 159 HIS 0.004 0.001 HIS B 44 PHE 0.031 0.002 PHE A1350 TYR 0.028 0.002 TYR A 496 ARG 0.002 0.000 ARG B 162 Details of bonding type rmsd hydrogen bonds : bond 0.04504 ( 586) hydrogen bonds : angle 4.51239 ( 1642) covalent geometry : bond 0.00340 (11756) covalent geometry : angle 0.66489 (16227) Misc. bond : bond 0.00045 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 HIS cc_start: 0.7305 (OUTLIER) cc_final: 0.6951 (t-170) REVERT: B 137 ASN cc_start: 0.8113 (t0) cc_final: 0.7808 (t0) REVERT: B 296 LYS cc_start: 0.8052 (mmtm) cc_final: 0.7714 (mmmt) REVERT: B 321 TRP cc_start: 0.7883 (t60) cc_final: 0.7350 (t60) REVERT: A 796 ASP cc_start: 0.8022 (m-30) cc_final: 0.7797 (m-30) REVERT: A 1201 MET cc_start: 0.7782 (ttp) cc_final: 0.7106 (ttp) outliers start: 25 outliers final: 22 residues processed: 159 average time/residue: 0.3466 time to fit residues: 86.1969 Evaluate side-chains 164 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 709 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1170 MET Chi-restraints excluded: chain A residue 1193 THR Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1351 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 117 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 114 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 40.0000 chunk 42 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 925 ASN ** 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 = 0.4087 r_free = 0.4087 target = 0.148251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.114550 restraints weight = 20406.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.118462 restraints weight = 11016.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.120947 restraints weight = 7627.930| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11757 Z= 0.221 Angle : 0.702 13.825 16227 Z= 0.358 Chirality : 0.044 0.218 1800 Planarity : 0.005 0.082 1825 Dihedral : 19.141 169.524 2162 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.72 % Allowed : 18.87 % Favored : 78.40 % 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: 0.39 (0.25), residues: 1232 helix: 1.33 (0.20), residues: 668 sheet: -1.33 (0.50), residues: 100 loop : -0.91 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP B 159 HIS 0.006 0.001 HIS A1163 PHE 0.029 0.002 PHE B 132 TYR 0.032 0.002 TYR A 954 ARG 0.002 0.000 ARG A 883 Details of bonding type rmsd hydrogen bonds : bond 0.05036 ( 586) hydrogen bonds : angle 4.71293 ( 1642) covalent geometry : bond 0.00511 (11756) covalent geometry : angle 0.70219 (16227) Misc. bond : bond 0.00038 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4164.42 seconds wall clock time: 78 minutes 47.22 seconds (4727.22 seconds total)