Starting phenix.real_space_refine on Sun Aug 4 20:14:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q63_18183/08_2024/8q63_18183.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q63_18183/08_2024/8q63_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q63_18183/08_2024/8q63_18183.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q63_18183/08_2024/8q63_18183.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q63_18183/08_2024/8q63_18183.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q63_18183/08_2024/8q63_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 Residue "B GLU 212": "OE1" <-> "OE2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 6.46, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 4.72 Conformation dependent library (CDL) restraints added in 1.7 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: 4.63 Time building geometry restraints manager: 5.14 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: 91.54 - 100.07: 23 100.07 - 108.61: 1255 108.61 - 117.15: 7475 117.15 - 125.69: 7025 125.69 - 134.23: 449 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: 0.010 Normalize map: mean=0, sd=1: 0.100 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 35.550 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.080 ------------------------------------------------------------------------------- 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 11756 Z= 0.388 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 1.255 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: 0.2152 time to fit residues: 56.0002 Evaluate side-chains 129 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.449 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 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 11756 Z= 0.270 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 *********************** 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 fitting. rotamer outliers: 14 poor density : 157 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 TRP cc_start: 0.7741 (t60) cc_final: 0.6791 (t60) REVERT: A 656 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.9028 (tt) REVERT: A 796 ASP cc_start: 0.8100 (m-30) cc_final: 0.7836 (m-30) REVERT: A 856 LYS cc_start: 0.7199 (mmmt) cc_final: 0.6926 (mmmt) REVERT: A 1157 LEU cc_start: 0.6635 (tp) cc_final: 0.6279 (tp) outliers start: 14 outliers final: 8 residues processed: 164 average time/residue: 0.2185 time to fit residues: 52.4087 Evaluate side-chains 151 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 142 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 65 optimal weight: 30.0000 chunk 36 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 126 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A 628 HIS ** A 868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 11756 Z= 0.416 Angle : 0.723 9.193 16227 Z= 0.379 Chirality : 0.045 0.158 1800 Planarity : 0.005 0.047 1825 Dihedral : 19.506 167.897 2162 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.54 % Allowed : 13.33 % Favored : 84.13 % 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: 0.11 (0.25), residues: 1232 helix: 1.12 (0.20), residues: 674 sheet: -1.65 (0.48), residues: 100 loop : -1.04 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 159 HIS 0.009 0.002 HIS A1188 PHE 0.027 0.002 PHE B 132 TYR 0.031 0.002 TYR A 496 ARG 0.004 0.001 ARG A 829 *********************** 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 170 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 150 TRP cc_start: 0.7418 (m-10) cc_final: 0.7108 (m-10) REVERT: B 228 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8052 (tt) REVERT: B 299 LEU cc_start: 0.8343 (tt) cc_final: 0.7780 (tp) REVERT: B 321 TRP cc_start: 0.8112 (t60) cc_final: 0.7568 (t60) REVERT: A 796 ASP cc_start: 0.8158 (m-30) cc_final: 0.7881 (m-30) REVERT: A 1128 LYS cc_start: 0.7906 (ptpt) cc_final: 0.7621 (ptmm) REVERT: A 1160 ASN cc_start: 0.8857 (m110) cc_final: 0.8499 (m110) REVERT: A 1166 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7577 (t0) outliers start: 27 outliers final: 17 residues processed: 159 average time/residue: 0.2063 time to fit residues: 49.1633 Evaluate side-chains 155 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 136 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain A residue 400 GLU 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 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 1166 ASP Chi-restraints excluded: chain A residue 1193 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 117 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 33 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: A 628 HIS ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11756 Z= 0.296 Angle : 0.646 8.715 16227 Z= 0.339 Chirality : 0.042 0.160 1800 Planarity : 0.004 0.062 1825 Dihedral : 19.350 165.831 2162 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.72 % Allowed : 16.15 % Favored : 81.13 % 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: 0.21 (0.25), residues: 1232 helix: 1.24 (0.20), residues: 679 sheet: -1.59 (0.50), residues: 90 loop : -1.13 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 159 HIS 0.008 0.001 HIS A 628 PHE 0.027 0.002 PHE B 132 TYR 0.026 0.002 TYR A 496 ARG 0.002 0.000 ARG A 829 *********************** 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 176 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 150 TRP cc_start: 0.7374 (m-10) cc_final: 0.7161 (m-10) REVERT: B 159 TRP cc_start: 0.7955 (t60) cc_final: 0.7556 (t60) REVERT: B 228 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.7990 (tt) REVERT: B 299 LEU cc_start: 0.8321 (tt) cc_final: 0.7758 (tp) REVERT: A 796 ASP cc_start: 0.8091 (m-30) cc_final: 0.7854 (m-30) REVERT: A 865 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9039 (tt) REVERT: A 1128 LYS cc_start: 0.7857 (ptpt) cc_final: 0.7565 (ptmm) REVERT: A 1160 ASN cc_start: 0.8824 (m110) cc_final: 0.8578 (m-40) REVERT: A 1166 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7568 (t0) REVERT: A 1201 MET cc_start: 0.7650 (ttp) cc_final: 0.7334 (ttp) outliers start: 29 outliers final: 17 residues processed: 166 average time/residue: 0.2292 time to fit residues: 57.0417 Evaluate side-chains 156 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 491 THR 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 865 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 1166 ASP Chi-restraints excluded: chain A residue 1170 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 63 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11756 Z= 0.266 Angle : 0.641 10.138 16227 Z= 0.333 Chirality : 0.041 0.150 1800 Planarity : 0.004 0.060 1825 Dihedral : 19.257 162.605 2162 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.00 % Allowed : 16.90 % Favored : 80.09 % 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: 673 sheet: -1.48 (0.51), residues: 90 loop : -0.91 (0.31), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 159 HIS 0.004 0.001 HIS A1163 PHE 0.027 0.002 PHE B 132 TYR 0.026 0.002 TYR A 496 ARG 0.003 0.000 ARG A1250 *********************** 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 177 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 145 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 150 TRP cc_start: 0.7258 (m-10) cc_final: 0.7029 (m-10) REVERT: B 228 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8249 (tt) REVERT: B 292 ARG cc_start: 0.7612 (mmm-85) cc_final: 0.7391 (mmm-85) REVERT: A 796 ASP cc_start: 0.8047 (m-30) cc_final: 0.7818 (m-30) REVERT: A 865 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8991 (tt) REVERT: A 1160 ASN cc_start: 0.8823 (m110) cc_final: 0.8558 (m-40) REVERT: A 1166 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7456 (t0) REVERT: A 1201 MET cc_start: 0.7711 (ttp) cc_final: 0.7227 (ttp) outliers start: 32 outliers final: 20 residues processed: 164 average time/residue: 0.2347 time to fit residues: 57.4320 Evaluate side-chains 161 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 469 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 548 SER 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 865 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 1166 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 120 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 11756 Z= 0.319 Angle : 0.669 10.733 16227 Z= 0.348 Chirality : 0.043 0.178 1800 Planarity : 0.005 0.058 1825 Dihedral : 19.303 161.797 2162 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.66 % Allowed : 18.40 % Favored : 77.93 % 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: 0.28 (0.25), residues: 1232 helix: 1.21 (0.20), residues: 674 sheet: -1.43 (0.52), residues: 90 loop : -0.95 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 159 HIS 0.005 0.001 HIS A1163 PHE 0.036 0.002 PHE A 936 TYR 0.028 0.002 TYR B 29 ARG 0.003 0.000 ARG A 906 *********************** 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 186 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 147 time to evaluate : 1.268 Fit side-chains revert: symmetry clash REVERT: B 47 GLU cc_start: 0.7578 (mp0) cc_final: 0.7376 (mp0) REVERT: B 150 TRP cc_start: 0.7321 (m-10) cc_final: 0.7072 (m-10) REVERT: B 159 TRP cc_start: 0.8095 (t60) cc_final: 0.7753 (t60) REVERT: B 292 ARG cc_start: 0.7675 (mmm-85) cc_final: 0.7447 (mmm-85) REVERT: A 796 ASP cc_start: 0.8035 (m-30) cc_final: 0.7805 (m-30) REVERT: A 865 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8949 (tt) REVERT: A 926 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7805 (tm-30) REVERT: A 1128 LYS cc_start: 0.7861 (ptpt) cc_final: 0.7562 (ptmm) REVERT: A 1160 ASN cc_start: 0.8826 (m110) cc_final: 0.8578 (m-40) REVERT: A 1166 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7488 (t0) outliers start: 39 outliers final: 26 residues processed: 171 average time/residue: 0.2291 time to fit residues: 57.0307 Evaluate side-chains 166 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 TYR 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 469 ILE Chi-restraints excluded: chain A residue 476 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 865 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 951 LEU Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1166 ASP Chi-restraints excluded: chain A residue 1170 MET Chi-restraints excluded: chain A residue 1193 THR 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 14 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 11756 Z= 0.223 Angle : 0.637 9.935 16227 Z= 0.329 Chirality : 0.041 0.228 1800 Planarity : 0.004 0.057 1825 Dihedral : 19.143 161.525 2162 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.10 % Allowed : 19.15 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.58 (0.25), residues: 1232 helix: 1.42 (0.20), residues: 674 sheet: -1.05 (0.57), residues: 80 loop : -0.82 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 159 HIS 0.007 0.001 HIS B 44 PHE 0.030 0.001 PHE B 132 TYR 0.034 0.002 TYR B 29 ARG 0.002 0.000 ARG A 883 *********************** 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 188 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 155 time to evaluate : 1.213 Fit side-chains revert: symmetry clash REVERT: B 133 LEU cc_start: 0.7129 (mt) cc_final: 0.6901 (tp) REVERT: B 150 TRP cc_start: 0.7143 (m-10) cc_final: 0.6896 (m-10) REVERT: B 159 TRP cc_start: 0.8063 (t60) cc_final: 0.7847 (t60) REVERT: B 296 LYS cc_start: 0.8178 (mmtm) cc_final: 0.7787 (mmmt) REVERT: B 321 TRP cc_start: 0.7908 (t60) cc_final: 0.7337 (t60) REVERT: A 461 MET cc_start: 0.7117 (mtp) cc_final: 0.6804 (mmm) REVERT: A 651 ILE cc_start: 0.7947 (mt) cc_final: 0.7731 (mt) REVERT: A 796 ASP cc_start: 0.8016 (m-30) cc_final: 0.7793 (m-30) REVERT: A 865 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8960 (tt) REVERT: A 1160 ASN cc_start: 0.8782 (m110) cc_final: 0.8522 (m110) REVERT: A 1166 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7455 (t0) REVERT: A 1201 MET cc_start: 0.7626 (ttp) cc_final: 0.7390 (ttp) outliers start: 33 outliers final: 24 residues processed: 173 average time/residue: 0.2230 time to fit residues: 56.1910 Evaluate side-chains 167 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 469 ILE 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 736 VAL Chi-restraints excluded: chain A residue 865 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 1019 THR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1166 ASP 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 30.0000 chunk 119 optimal weight: 0.0970 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 HIS ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 11756 Z= 0.264 Angle : 0.654 10.297 16227 Z= 0.338 Chirality : 0.041 0.194 1800 Planarity : 0.004 0.072 1825 Dihedral : 19.142 162.756 2162 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.85 % Allowed : 19.53 % Favored : 76.62 % 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: 0.51 (0.25), residues: 1232 helix: 1.36 (0.20), residues: 675 sheet: -1.02 (0.58), residues: 80 loop : -0.87 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 159 HIS 0.004 0.001 HIS A1163 PHE 0.032 0.002 PHE B 132 TYR 0.030 0.002 TYR B 29 ARG 0.002 0.000 ARG A 800 *********************** 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 184 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 143 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 133 LEU cc_start: 0.7209 (mt) cc_final: 0.6980 (tp) REVERT: B 150 TRP cc_start: 0.7168 (m-10) cc_final: 0.6888 (m-10) REVERT: B 296 LYS cc_start: 0.8206 (mmtm) cc_final: 0.7806 (mmmt) REVERT: B 321 TRP cc_start: 0.7920 (t60) cc_final: 0.7408 (t60) REVERT: A 796 ASP cc_start: 0.8021 (m-30) cc_final: 0.7804 (m-30) REVERT: A 865 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8988 (tt) REVERT: A 1160 ASN cc_start: 0.8810 (m110) cc_final: 0.8551 (m-40) REVERT: A 1166 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7494 (t0) REVERT: A 1201 MET cc_start: 0.7620 (ttp) cc_final: 0.7295 (ttp) outliers start: 41 outliers final: 29 residues processed: 167 average time/residue: 0.2184 time to fit residues: 53.9815 Evaluate side-chains 166 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 302 CYS 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 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 736 VAL Chi-restraints excluded: chain A residue 865 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 951 LEU Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1166 ASP 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 108 optimal weight: 1.9990 chunk 115 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 11756 Z= 0.251 Angle : 0.661 10.357 16227 Z= 0.338 Chirality : 0.041 0.220 1800 Planarity : 0.004 0.071 1825 Dihedral : 19.090 163.557 2162 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.00 % Allowed : 20.28 % Favored : 76.71 % 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: 0.53 (0.25), residues: 1232 helix: 1.36 (0.20), residues: 675 sheet: -0.96 (0.58), residues: 80 loop : -0.84 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 159 HIS 0.004 0.001 HIS A1163 PHE 0.033 0.002 PHE B 132 TYR 0.026 0.002 TYR B 29 ARG 0.002 0.000 ARG A 883 *********************** 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 176 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: B 133 LEU cc_start: 0.7303 (mt) cc_final: 0.7023 (tp) REVERT: B 150 TRP cc_start: 0.7106 (m-10) cc_final: 0.6877 (m-10) REVERT: B 159 TRP cc_start: 0.7982 (t60) cc_final: 0.7621 (t60) REVERT: B 296 LYS cc_start: 0.8169 (mmtm) cc_final: 0.7800 (mmmt) REVERT: B 321 TRP cc_start: 0.7893 (t60) cc_final: 0.7410 (t60) REVERT: A 607 MET cc_start: 0.7337 (ttt) cc_final: 0.7017 (ttt) REVERT: A 651 ILE cc_start: 0.7952 (mt) cc_final: 0.7723 (mt) REVERT: A 865 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8972 (tt) REVERT: A 1160 ASN cc_start: 0.8793 (m110) cc_final: 0.8540 (m-40) REVERT: A 1166 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7481 (t0) REVERT: A 1201 MET cc_start: 0.7649 (ttp) cc_final: 0.7309 (ttp) outliers start: 32 outliers final: 28 residues processed: 162 average time/residue: 0.2129 time to fit residues: 51.2719 Evaluate side-chains 168 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 469 ILE 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 736 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1166 ASP 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 74 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 102 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 HIS A 628 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 11756 Z= 0.343 Angle : 0.712 10.823 16227 Z= 0.365 Chirality : 0.043 0.234 1800 Planarity : 0.005 0.045 1825 Dihedral : 19.230 164.723 2162 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.10 % Allowed : 20.28 % Favored : 76.62 % 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: 0.29 (0.25), residues: 1232 helix: 1.27 (0.20), residues: 667 sheet: -1.22 (0.53), residues: 90 loop : -1.05 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP B 259 HIS 0.005 0.001 HIS A1163 PHE 0.036 0.002 PHE B 132 TYR 0.031 0.002 TYR A 954 ARG 0.003 0.000 ARG A 533 ********************** 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 171 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 138 time to evaluate : 1.185 Fit side-chains REVERT: B 133 LEU cc_start: 0.7193 (mt) cc_final: 0.6946 (tp) REVERT: B 150 TRP cc_start: 0.7238 (m-10) cc_final: 0.6987 (m-10) REVERT: B 159 TRP cc_start: 0.7960 (t60) cc_final: 0.7539 (t60) REVERT: B 321 TRP cc_start: 0.7941 (t60) cc_final: 0.7428 (t60) REVERT: A 461 MET cc_start: 0.6426 (mmm) cc_final: 0.6128 (mmm) REVERT: A 865 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8997 (tt) REVERT: A 1160 ASN cc_start: 0.8821 (m110) cc_final: 0.8563 (m-40) REVERT: A 1166 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7521 (t0) REVERT: A 1201 MET cc_start: 0.7639 (ttp) cc_final: 0.7291 (ttp) outliers start: 33 outliers final: 28 residues processed: 158 average time/residue: 0.2114 time to fit residues: 49.7245 Evaluate side-chains 166 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 192 CYS 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 865 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1166 ASP 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 31 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 chunk 5 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.151761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.118632 restraints weight = 20207.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.122580 restraints weight = 10731.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.125211 restraints weight = 7345.215| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 11756 Z= 0.207 Angle : 0.664 12.844 16227 Z= 0.338 Chirality : 0.041 0.236 1800 Planarity : 0.004 0.074 1825 Dihedral : 19.010 166.205 2162 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.63 % Allowed : 21.13 % Favored : 76.24 % 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: 668 sheet: -0.93 (0.54), residues: 92 loop : -0.82 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 259 HIS 0.002 0.001 HIS B 283 PHE 0.033 0.001 PHE A 936 TYR 0.030 0.002 TYR A 496 ARG 0.004 0.000 ARG A 738 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1994.29 seconds wall clock time: 36 minutes 45.26 seconds (2205.26 seconds total)