Starting phenix.real_space_refine on Sat Jul 20 16:00:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q63_18183/07_2024/8q63_18183.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q63_18183/07_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_18183/07_2024/8q63_18183.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q63_18183/07_2024/8q63_18183.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q63_18183/07_2024/8q63_18183.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q63_18183/07_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-5388/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: 6.98, per 1000 atoms: 0.62 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: 4.80 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: 3.90 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: 4.98 Time building geometry restraints manager: 5.17 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 2.440 nonbonded pdb=" OD1 ASP A 843 " pdb=" NE2 GLN A 916 " model vdw 2.205 2.520 nonbonded pdb=" O SER B 190 " pdb=" OG SER B 193 " model vdw 2.228 2.440 nonbonded pdb=" N LYS B 49 " pdb=" O LYS B 131 " model vdw 2.262 2.520 nonbonded pdb=" OD1 ASP A 876 " pdb=" NH1 ARG A 883 " model vdw 2.264 2.520 ... (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 ========== 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: 0.110 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 36.910 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: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.690 ------------------------------------------------------------------------------- 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 : 1.271 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: 0.2226 time to fit residues: 57.6494 Evaluate side-chains 129 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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: 10.0000 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 117 optimal weight: 30.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- 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: 0.7317 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11756 Z= 0.316 Angle : 0.672 8.750 16227 Z= 0.353 Chirality : 0.043 0.153 1800 Planarity : 0.004 0.043 1825 Dihedral : 19.570 173.639 2162 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.78 % Allowed : 9.11 % Favored : 89.11 % 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: 0.41 (0.25), residues: 1232 helix: 1.41 (0.20), residues: 676 sheet: -1.11 (0.57), residues: 74 loop : -1.14 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 159 HIS 0.007 0.001 HIS A1188 PHE 0.033 0.002 PHE A 754 TYR 0.032 0.002 TYR A 496 ARG 0.003 0.000 ARG A 800 *********************** 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 168 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 LEU cc_start: 0.7096 (tp) cc_final: 0.6796 (mt) REVERT: A 533 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7154 (ptm160) REVERT: A 656 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.9057 (tt) REVERT: A 796 ASP cc_start: 0.8123 (m-30) cc_final: 0.7860 (m-30) REVERT: A 856 LYS cc_start: 0.7232 (mmmt) cc_final: 0.7030 (mmmt) outliers start: 19 outliers final: 14 residues processed: 156 average time/residue: 0.2277 time to fit residues: 52.1434 Evaluate side-chains 158 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 533 ARG 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 736 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 1089 LEU 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 1351 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 126 optimal weight: 20.0000 chunk 104 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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: 0.7336 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11756 Z= 0.308 Angle : 0.648 8.717 16227 Z= 0.339 Chirality : 0.042 0.159 1800 Planarity : 0.004 0.043 1825 Dihedral : 19.423 168.796 2162 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.63 % Allowed : 12.58 % Favored : 84.79 % 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: 0.32 (0.25), residues: 1232 helix: 1.34 (0.20), residues: 679 sheet: -1.22 (0.53), residues: 84 loop : -1.16 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 159 HIS 0.007 0.001 HIS A1188 PHE 0.024 0.002 PHE A 936 TYR 0.029 0.002 TYR A 496 ARG 0.003 0.000 ARG A1250 *********************** 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 176 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: B 228 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8019 (tt) REVERT: B 255 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7312 (p0) REVERT: B 321 TRP cc_start: 0.8080 (t60) cc_final: 0.7525 (t60) REVERT: A 533 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7110 (ptm160) REVERT: A 727 ASN cc_start: 0.8069 (m-40) cc_final: 0.7584 (m110) REVERT: A 796 ASP cc_start: 0.8134 (m-30) cc_final: 0.7885 (m-30) REVERT: A 1103 ASP cc_start: 0.6958 (p0) cc_final: 0.6591 (p0) REVERT: A 1201 MET cc_start: 0.7526 (ttp) cc_final: 0.7021 (ttp) outliers start: 28 outliers final: 17 residues processed: 163 average time/residue: 0.2129 time to fit residues: 51.6352 Evaluate side-chains 157 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 700 THR 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 882 ASP 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 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: 30.0000 chunk 88 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 78 optimal weight: 30.0000 chunk 117 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- 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 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11756 Z= 0.297 Angle : 0.643 8.568 16227 Z= 0.333 Chirality : 0.041 0.164 1800 Planarity : 0.004 0.058 1825 Dihedral : 19.335 165.847 2162 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.38 % Allowed : 14.65 % Favored : 81.97 % 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: 1.36 (0.20), residues: 679 sheet: -1.21 (0.54), residues: 74 loop : -1.16 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 159 HIS 0.004 0.001 HIS A1188 PHE 0.025 0.002 PHE B 132 TYR 0.026 0.002 TYR A 496 ARG 0.003 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 183 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 147 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 133 LEU cc_start: 0.7049 (tp) cc_final: 0.6792 (mt) REVERT: B 228 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8012 (tt) REVERT: B 255 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7299 (p0) REVERT: B 321 TRP cc_start: 0.8060 (t60) cc_final: 0.7542 (t60) REVERT: A 533 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7052 (ptm160) REVERT: A 727 ASN cc_start: 0.8043 (m-40) cc_final: 0.7580 (m110) REVERT: A 796 ASP cc_start: 0.8091 (m-30) cc_final: 0.7858 (m-30) REVERT: A 1201 MET cc_start: 0.7513 (ttp) cc_final: 0.7024 (ttp) outliers start: 36 outliers final: 21 residues processed: 168 average time/residue: 0.2243 time to fit residues: 56.3845 Evaluate side-chains 166 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 533 ARG 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 823 ASN Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 882 ASP 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 63 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 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 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 11756 Z= 0.263 Angle : 0.633 8.950 16227 Z= 0.326 Chirality : 0.040 0.149 1800 Planarity : 0.004 0.055 1825 Dihedral : 19.242 163.181 2162 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.10 % Allowed : 16.53 % Favored : 80.38 % 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: 0.48 (0.25), residues: 1232 helix: 1.46 (0.20), residues: 678 sheet: -1.14 (0.55), residues: 74 loop : -1.09 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 159 HIS 0.003 0.001 HIS A1188 PHE 0.028 0.002 PHE B 132 TYR 0.036 0.002 TYR B 29 ARG 0.007 0.000 ARG B 292 *********************** 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 185 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 152 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 LEU cc_start: 0.7249 (tp) cc_final: 0.7015 (mt) REVERT: B 228 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8001 (tt) REVERT: B 255 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7286 (p0) REVERT: A 533 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7048 (ptm160) REVERT: A 796 ASP cc_start: 0.8053 (m-30) cc_final: 0.7821 (m-30) REVERT: A 1103 ASP cc_start: 0.6991 (p0) cc_final: 0.6593 (p0) outliers start: 33 outliers final: 19 residues processed: 172 average time/residue: 0.2118 time to fit residues: 54.4747 Evaluate side-chains 159 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 255 ASP 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 533 ARG 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 823 ASN Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 882 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 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 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: 0.7346 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 11756 Z= 0.303 Angle : 0.653 10.212 16227 Z= 0.337 Chirality : 0.042 0.207 1800 Planarity : 0.004 0.054 1825 Dihedral : 19.262 162.106 2162 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.38 % Allowed : 18.03 % Favored : 78.59 % 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: 0.37 (0.25), residues: 1232 helix: 1.36 (0.20), residues: 680 sheet: -1.15 (0.56), residues: 74 loop : -1.13 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 159 HIS 0.004 0.001 HIS A 822 PHE 0.038 0.002 PHE A 936 TYR 0.034 0.002 TYR B 29 ARG 0.004 0.000 ARG B 292 *********************** 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 180 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 144 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 LEU cc_start: 0.7159 (tp) cc_final: 0.6936 (mt) REVERT: B 228 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7886 (tt) REVERT: B 255 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7299 (p0) REVERT: A 533 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7052 (ptm160) REVERT: A 727 ASN cc_start: 0.8026 (m-40) cc_final: 0.7577 (m110) REVERT: A 796 ASP cc_start: 0.8044 (m-30) cc_final: 0.7815 (m-30) REVERT: A 926 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7829 (tm-30) outliers start: 36 outliers final: 27 residues processed: 166 average time/residue: 0.2138 time to fit residues: 52.7250 Evaluate side-chains 169 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 211 ASN Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 255 ASP 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 533 ARG 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 823 ASN Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 899 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 11756 Z= 0.234 Angle : 0.632 9.273 16227 Z= 0.325 Chirality : 0.041 0.196 1800 Planarity : 0.004 0.052 1825 Dihedral : 19.143 162.016 2162 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.10 % Allowed : 19.91 % Favored : 77.00 % 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: 0.52 (0.25), residues: 1232 helix: 1.44 (0.21), residues: 681 sheet: -1.10 (0.53), residues: 84 loop : -0.99 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 159 HIS 0.008 0.001 HIS A 943 PHE 0.033 0.001 PHE B 132 TYR 0.025 0.002 TYR B 29 ARG 0.004 0.000 ARG B 292 *********************** 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 179 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 146 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 LEU cc_start: 0.7202 (tp) cc_final: 0.6976 (mt) REVERT: B 255 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7281 (p0) REVERT: A 533 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.6998 (ptm160) REVERT: A 796 ASP cc_start: 0.7984 (m-30) cc_final: 0.7765 (m-30) REVERT: A 1201 MET cc_start: 0.7375 (ttp) cc_final: 0.6811 (ttp) outliers start: 33 outliers final: 23 residues processed: 163 average time/residue: 0.2120 time to fit residues: 50.9727 Evaluate side-chains 170 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 533 ARG 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 823 ASN Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 882 ASP 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 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 49 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 79 optimal weight: 0.1980 chunk 84 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 40.0000 chunk 119 optimal weight: 6.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- 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** ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 11756 Z= 0.256 Angle : 0.638 9.471 16227 Z= 0.327 Chirality : 0.041 0.218 1800 Planarity : 0.004 0.049 1825 Dihedral : 19.128 163.233 2162 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.47 % Allowed : 20.09 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.25), residues: 1232 helix: 1.37 (0.20), residues: 682 sheet: -1.04 (0.54), residues: 84 loop : -1.01 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 159 HIS 0.008 0.001 HIS A 943 PHE 0.034 0.002 PHE B 132 TYR 0.027 0.002 TYR A 954 ARG 0.004 0.000 ARG B 292 *********************** 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 181 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 144 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 LEU cc_start: 0.7234 (tp) cc_final: 0.6999 (mt) REVERT: B 255 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7284 (p0) REVERT: A 507 LYS cc_start: 0.8468 (mtmm) cc_final: 0.8258 (mtmm) REVERT: A 533 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7011 (ptm160) REVERT: A 796 ASP cc_start: 0.7991 (m-30) cc_final: 0.7778 (m-30) outliers start: 37 outliers final: 30 residues processed: 163 average time/residue: 0.2324 time to fit residues: 55.3103 Evaluate side-chains 172 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 255 ASP 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 487 ASN Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 533 ARG 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 823 ASN Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 951 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 7.9990 chunk 115 optimal weight: 0.1980 chunk 119 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 76 optimal weight: 0.0470 chunk 122 optimal weight: 8.9990 overall best weight: 2.2482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 943 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11756 Z= 0.195 Angle : 0.629 10.523 16227 Z= 0.318 Chirality : 0.040 0.199 1800 Planarity : 0.004 0.046 1825 Dihedral : 18.966 164.415 2162 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.72 % Allowed : 20.66 % 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: 0.70 (0.25), residues: 1232 helix: 1.56 (0.21), residues: 675 sheet: -0.93 (0.55), residues: 84 loop : -0.85 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 159 HIS 0.006 0.001 HIS A 943 PHE 0.033 0.001 PHE B 132 TYR 0.027 0.002 TYR A 496 ARG 0.003 0.000 ARG B 292 *********************** 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 190 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 161 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 255 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7275 (p0) REVERT: B 321 TRP cc_start: 0.7883 (t60) cc_final: 0.7278 (t60) REVERT: A 727 ASN cc_start: 0.7761 (m-40) cc_final: 0.7373 (m110) REVERT: A 796 ASP cc_start: 0.7976 (m-30) cc_final: 0.7767 (m-30) REVERT: A 1201 MET cc_start: 0.7177 (ttp) cc_final: 0.6550 (ttp) outliers start: 29 outliers final: 22 residues processed: 176 average time/residue: 0.2203 time to fit residues: 57.1294 Evaluate side-chains 171 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 487 ASN 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 882 ASP Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 951 LEU 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 1223 GLU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 85 optimal weight: 0.0020 chunk 128 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11756 Z= 0.227 Angle : 0.651 13.155 16227 Z= 0.326 Chirality : 0.041 0.210 1800 Planarity : 0.004 0.055 1825 Dihedral : 18.987 166.451 2162 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % 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: 0.64 (0.25), residues: 1232 helix: 1.50 (0.21), residues: 681 sheet: -0.97 (0.55), residues: 84 loop : -0.90 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 159 HIS 0.003 0.001 HIS A 943 PHE 0.032 0.002 PHE B 132 TYR 0.030 0.002 TYR A1229 ARG 0.008 0.000 ARG A 827 ********************** 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 174 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: B 255 ASP cc_start: 0.7475 (OUTLIER) cc_final: 0.7260 (p0) REVERT: B 321 TRP cc_start: 0.7910 (t60) cc_final: 0.7323 (t60) REVERT: A 533 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6963 (ptm160) REVERT: A 727 ASN cc_start: 0.7768 (m-40) cc_final: 0.7395 (m110) REVERT: A 796 ASP cc_start: 0.8075 (m-30) cc_final: 0.7869 (m-30) outliers start: 28 outliers final: 24 residues processed: 161 average time/residue: 0.2378 time to fit residues: 57.1907 Evaluate side-chains 171 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 145 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 255 ASP 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 487 ASN Chi-restraints excluded: chain A residue 533 ARG 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 823 ASN Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 882 ASP Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 951 LEU 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 1223 GLU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1343 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 12 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 89 optimal weight: 0.4980 chunk 5 optimal weight: 6.9990 overall best weight: 3.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.151277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.117690 restraints weight = 20245.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.121671 restraints weight = 10923.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.124304 restraints weight = 7510.296| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11756 Z= 0.232 Angle : 0.658 13.517 16227 Z= 0.332 Chirality : 0.041 0.230 1800 Planarity : 0.004 0.043 1825 Dihedral : 18.981 167.931 2162 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.00 % Allowed : 21.03 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.25), residues: 1232 helix: 1.54 (0.21), residues: 675 sheet: -0.98 (0.55), residues: 84 loop : -0.77 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 159 HIS 0.003 0.001 HIS A 943 PHE 0.032 0.001 PHE B 132 TYR 0.025 0.002 TYR A 496 ARG 0.005 0.000 ARG A 827 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2011.10 seconds wall clock time: 37 minutes 0.50 seconds (2220.50 seconds total)