Starting phenix.real_space_refine on Sun Jan 19 09:21:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ye9_39191/01_2025/8ye9_39191_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ye9_39191/01_2025/8ye9_39191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ye9_39191/01_2025/8ye9_39191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ye9_39191/01_2025/8ye9_39191.map" model { file = "/net/cci-nas-00/data/ceres_data/8ye9_39191/01_2025/8ye9_39191_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ye9_39191/01_2025/8ye9_39191_neut.cif" } resolution = 3.43 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= 0.002 sd= 0.074 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 90 5.49 5 S 26 5.16 5 C 8260 2.51 5 N 2372 2.21 5 O 2811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 13559 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1359, 10896 Classifications: {'peptide': 1359} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 35, 'TRANS': 1323} Chain breaks: 3 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 13, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 101 Chain: "C" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1928 Classifications: {'RNA': 90} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 5, 'rna3p_pur': 42, 'rna3p_pyr': 32} Link IDs: {'rna2p': 16, 'rna3p': 73} Chain breaks: 1 Chain: "B" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 735 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Link IDs: {'TRANS': 88} Time building chain proxies: 7.24, per 1000 atoms: 0.53 Number of scatterers: 13559 At special positions: 0 Unit cell: (93.5, 121, 129.8, 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 26 16.00 P 90 15.00 O 2811 8.00 N 2372 7.00 C 8260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.3 seconds 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2756 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 7 sheets defined 49.0% alpha, 5.1% beta 13 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 60 through 94 removed outlier: 5.388A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.578A pdb=" N GLU A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 145 removed outlier: 4.297A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.556A pdb=" N ILE A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 removed outlier: 3.801A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 213 removed outlier: 3.613A pdb=" N ILE A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 227 Processing helix chain 'A' and resid 237 through 247 removed outlier: 3.620A pdb=" N GLY A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.759A pdb=" N PHE A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.811A pdb=" N ASP A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 306 removed outlier: 4.130A pdb=" N PHE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.822A pdb=" N ALA A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.510A pdb=" N ILE A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 351 " --> pdb=" O TYR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 368 through 382 removed outlier: 3.611A pdb=" N PHE A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.346A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 437 through 445 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 512 through 525 removed outlier: 3.745A pdb=" N GLU A 516 " --> pdb=" O SER A 512 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 566 Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.582A pdb=" N LYS A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.543A pdb=" N LEU A 616 " --> pdb=" O ASN A 612 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 636 removed outlier: 3.855A pdb=" N ILE A 632 " --> pdb=" O ASP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 640 Processing helix chain 'A' and resid 644 through 652 removed outlier: 4.340A pdb=" N LYS A 652 " --> pdb=" O MET A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.632A pdb=" N ILE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 698 removed outlier: 4.131A pdb=" N HIS A 698 " --> pdb=" O MET A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 711 Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.774A pdb=" N HIS A 723 " --> pdb=" O SER A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 751 removed outlier: 4.025A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 792 removed outlier: 3.514A pdb=" N GLU A 779 " --> pdb=" O LYS A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 807 removed outlier: 4.111A pdb=" N GLN A 807 " --> pdb=" O THR A 804 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 804 through 807' Processing helix chain 'A' and resid 808 through 816 Processing helix chain 'A' and resid 874 through 879 Processing helix chain 'A' and resid 879 through 889 removed outlier: 3.533A pdb=" N ALA A 889 " --> pdb=" O GLN A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 909 through 920 removed outlier: 3.689A pdb=" N LYS A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 940 removed outlier: 3.606A pdb=" N ASN A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 971 Processing helix chain 'A' and resid 981 through 1001 removed outlier: 3.595A pdb=" N ALA A 987 " --> pdb=" O HIS A 983 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR A 995 " --> pdb=" O ALA A 991 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 4.245A pdb=" N PHE A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1047 removed outlier: 3.822A pdb=" N PHE A1046 " --> pdb=" O MET A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1087 Processing helix chain 'A' and resid 1171 through 1177 removed outlier: 3.741A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 removed outlier: 3.646A pdb=" N VAL A1233 " --> pdb=" O PRO A1229 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS A1241 " --> pdb=" O TYR A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1262 removed outlier: 3.669A pdb=" N ASN A1252 " --> pdb=" O SER A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1280 Processing helix chain 'A' and resid 1284 through 1296 Processing helix chain 'A' and resid 1301 through 1311 removed outlier: 3.519A pdb=" N GLN A1305 " --> pdb=" O PRO A1301 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLU A1307 " --> pdb=" O ARG A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1315 Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.594A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 33 removed outlier: 3.617A pdb=" N ARG B 32 " --> pdb=" O ASN B 28 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 54 removed outlier: 3.824A pdb=" N HIS B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B 54 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 77 removed outlier: 3.639A pdb=" N LEU B 67 " --> pdb=" O ASP B 63 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS B 77 " --> pdb=" O VAL B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 92 removed outlier: 4.025A pdb=" N ILE B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.699A pdb=" N ARG B 98 " --> pdb=" O LEU B 94 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 10.065A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 528 through 530 Processing sheet with id=AA4, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA5, first strand: chain 'A' and resid 1064 through 1065 Processing sheet with id=AA6, first strand: chain 'A' and resid 1162 through 1167 removed outlier: 7.039A pdb=" N GLU A1162 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LEU A1144 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A1164 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A1142 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE A1166 " --> pdb=" O ALA A1140 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1325 444 hydrogen bonds defined for protein. 1293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 5.23 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3428 1.33 - 1.45: 3305 1.45 - 1.58: 7037 1.58 - 1.70: 175 1.70 - 1.82: 50 Bond restraints: 13995 Sorted by residual: bond pdb=" P A C 52 " pdb=" OP1 A C 52 " ideal model delta sigma weight residual 1.485 1.415 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" P A C 52 " pdb=" OP2 A C 52 " ideal model delta sigma weight residual 1.485 1.423 0.062 2.00e-02 2.50e+03 9.56e+00 bond pdb=" C1' A C 52 " pdb=" N9 A C 52 " ideal model delta sigma weight residual 1.475 1.439 0.036 1.50e-02 4.44e+03 5.78e+00 bond pdb=" O3' A C 52 " pdb=" P G C 53 " ideal model delta sigma weight residual 1.607 1.573 0.034 1.50e-02 4.44e+03 5.26e+00 bond pdb=" C2' A C 52 " pdb=" O2' A C 52 " ideal model delta sigma weight residual 1.420 1.386 0.034 1.50e-02 4.44e+03 5.09e+00 ... (remaining 13990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 19114 3.61 - 7.22: 184 7.22 - 10.83: 10 10.83 - 14.44: 2 14.44 - 18.05: 1 Bond angle restraints: 19311 Sorted by residual: angle pdb=" N VAL B 96 " pdb=" CA VAL B 96 " pdb=" C VAL B 96 " ideal model delta sigma weight residual 113.71 106.64 7.07 9.50e-01 1.11e+00 5.54e+01 angle pdb=" C ALA A1227 " pdb=" N LEU A1228 " pdb=" CA LEU A1228 " ideal model delta sigma weight residual 121.59 139.64 -18.05 3.54e+00 7.98e-02 2.60e+01 angle pdb=" C3' A C 52 " pdb=" C2' A C 52 " pdb=" O2' A C 52 " ideal model delta sigma weight residual 110.70 103.42 7.28 1.50e+00 4.44e-01 2.36e+01 angle pdb=" C2' A C 12 " pdb=" C1' A C 12 " pdb=" N9 A C 12 " ideal model delta sigma weight residual 112.00 119.00 -7.00 1.50e+00 4.44e-01 2.18e+01 angle pdb=" C3' A C 9 " pdb=" O3' A C 9 " pdb=" P A C 10 " ideal model delta sigma weight residual 120.20 126.73 -6.53 1.50e+00 4.44e-01 1.89e+01 ... (remaining 19306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 8321 35.35 - 70.70: 231 70.70 - 106.05: 23 106.05 - 141.39: 3 141.39 - 176.74: 3 Dihedral angle restraints: 8581 sinusoidal: 4322 harmonic: 4259 Sorted by residual: dihedral pdb=" O4' U C 24 " pdb=" C1' U C 24 " pdb=" N1 U C 24 " pdb=" C2 U C 24 " ideal model delta sinusoidal sigma weight residual -160.00 11.12 -171.12 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' U C 90 " pdb=" C1' U C 90 " pdb=" N1 U C 90 " pdb=" C2 U C 90 " ideal model delta sinusoidal sigma weight residual -128.00 48.74 -176.74 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA LYS B 37 " pdb=" C LYS B 37 " pdb=" N ASP B 38 " pdb=" CA ASP B 38 " ideal model delta harmonic sigma weight residual 180.00 144.51 35.49 0 5.00e+00 4.00e-02 5.04e+01 ... (remaining 8578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1748 0.065 - 0.129: 422 0.129 - 0.194: 51 0.194 - 0.258: 5 0.258 - 0.323: 4 Chirality restraints: 2230 Sorted by residual: chirality pdb=" C3' A C 42 " pdb=" C4' A C 42 " pdb=" O3' A C 42 " pdb=" C2' A C 42 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" C1' A C 12 " pdb=" O4' A C 12 " pdb=" C2' A C 12 " pdb=" N9 A C 12 " both_signs ideal model delta sigma weight residual False 2.46 2.14 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C3' G C 92 " pdb=" C4' G C 92 " pdb=" O3' G C 92 " pdb=" C2' G C 92 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 2227 not shown) Planarity restraints: 2145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A C 12 " 0.056 2.00e-02 2.50e+03 2.48e-02 1.70e+01 pdb=" N9 A C 12 " -0.056 2.00e-02 2.50e+03 pdb=" C8 A C 12 " -0.006 2.00e-02 2.50e+03 pdb=" N7 A C 12 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A C 12 " 0.004 2.00e-02 2.50e+03 pdb=" C6 A C 12 " 0.009 2.00e-02 2.50e+03 pdb=" N6 A C 12 " 0.011 2.00e-02 2.50e+03 pdb=" N1 A C 12 " 0.006 2.00e-02 2.50e+03 pdb=" C2 A C 12 " -0.006 2.00e-02 2.50e+03 pdb=" N3 A C 12 " -0.012 2.00e-02 2.50e+03 pdb=" C4 A C 12 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C C 18 " 0.043 2.00e-02 2.50e+03 2.20e-02 1.09e+01 pdb=" N1 C C 18 " -0.047 2.00e-02 2.50e+03 pdb=" C2 C C 18 " -0.004 2.00e-02 2.50e+03 pdb=" O2 C C 18 " -0.005 2.00e-02 2.50e+03 pdb=" N3 C C 18 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C C 18 " 0.005 2.00e-02 2.50e+03 pdb=" N4 C C 18 " 0.012 2.00e-02 2.50e+03 pdb=" C5 C C 18 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C C 18 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A1300 " 0.039 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO A1301 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A1301 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A1301 " 0.033 5.00e-02 4.00e+02 ... (remaining 2142 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1281 2.74 - 3.28: 11869 3.28 - 3.82: 20450 3.82 - 4.36: 24292 4.36 - 4.90: 40386 Nonbonded interactions: 98278 Sorted by model distance: nonbonded pdb=" OH TYR B 70 " pdb=" NZ LYS B 74 " model vdw 2.195 3.120 nonbonded pdb=" NZ LYS A1300 " pdb=" OE1 GLU A1304 " model vdw 2.202 3.120 nonbonded pdb=" NH2 ARG A 864 " pdb=" O ASN A 869 " model vdw 2.216 3.120 nonbonded pdb=" OH TYR A 373 " pdb=" O LEU A 398 " model vdw 2.268 3.040 nonbonded pdb=" OE2 GLU A 103 " pdb=" ND1 HIS A 113 " model vdw 2.305 3.120 ... (remaining 98273 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.490 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 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 0.070 13995 Z= 0.458 Angle : 1.014 18.046 19311 Z= 0.553 Chirality : 0.056 0.323 2230 Planarity : 0.006 0.060 2145 Dihedral : 15.495 176.743 5825 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.24 % Allowed : 2.97 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.35 (0.17), residues: 1438 helix: -2.93 (0.14), residues: 640 sheet: -0.86 (0.61), residues: 79 loop : -3.10 (0.19), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP A1074 HIS 0.013 0.003 HIS A 137 PHE 0.030 0.003 PHE A 462 TYR 0.028 0.003 TYR B 49 ARG 0.010 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 220 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7486 (t0) cc_final: 0.6969 (t0) REVERT: A 695 GLN cc_start: 0.7703 (mt0) cc_final: 0.6872 (tm-30) REVERT: A 781 MET cc_start: 0.7747 (ttt) cc_final: 0.7325 (mpp) REVERT: A 1297 HIS cc_start: 0.6618 (m-70) cc_final: 0.6157 (m170) REVERT: B 37 LYS cc_start: 0.7627 (mmmt) cc_final: 0.6634 (mttt) REVERT: B 66 GLU cc_start: 0.7871 (tp30) cc_final: 0.7620 (tp30) outliers start: 3 outliers final: 0 residues processed: 223 average time/residue: 0.3039 time to fit residues: 94.0680 Evaluate side-chains 109 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 61 optimal weight: 0.0060 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 511 HIS A 522 ASN A 595 HIS A 609 ASN A 709 GLN A 840 HIS A 854 ASN A 899 ASN A 920 GLN A 930 HIS A1044 ASN A1311 HIS B 40 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.174536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.137188 restraints weight = 23547.165| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 4.91 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13995 Z= 0.183 Angle : 0.594 10.388 19311 Z= 0.315 Chirality : 0.041 0.239 2230 Planarity : 0.004 0.046 2145 Dihedral : 18.301 178.851 2940 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.52 % Allowed : 6.74 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.55 (0.20), residues: 1438 helix: -0.97 (0.19), residues: 664 sheet: -0.42 (0.58), residues: 88 loop : -2.64 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1074 HIS 0.005 0.001 HIS A 930 PHE 0.015 0.001 PHE A 462 TYR 0.010 0.001 TYR A1141 ARG 0.004 0.001 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7044 (t0) cc_final: 0.6676 (t0) REVERT: A 557 ARG cc_start: 0.7261 (tpp80) cc_final: 0.6779 (tmt170) REVERT: A 599 LYS cc_start: 0.8905 (tppt) cc_final: 0.8213 (pttp) REVERT: A 606 PHE cc_start: 0.6807 (t80) cc_final: 0.6586 (t80) REVERT: A 695 GLN cc_start: 0.7971 (mt0) cc_final: 0.6969 (tm-30) REVERT: A 781 MET cc_start: 0.6536 (ttt) cc_final: 0.6248 (mpp) REVERT: A 1021 MET cc_start: 0.7284 (ptm) cc_final: 0.7013 (ptm) REVERT: A 1189 GLU cc_start: 0.8159 (tt0) cc_final: 0.7700 (tm-30) REVERT: A 1297 HIS cc_start: 0.7013 (m-70) cc_final: 0.6391 (m170) REVERT: B 37 LYS cc_start: 0.7874 (mmmt) cc_final: 0.7012 (mttt) outliers start: 19 outliers final: 11 residues processed: 144 average time/residue: 0.2581 time to fit residues: 55.8504 Evaluate side-chains 106 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain B residue 49 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 GLN A 920 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.171843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.133498 restraints weight = 23163.533| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 4.60 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13995 Z= 0.237 Angle : 0.617 13.498 19311 Z= 0.321 Chirality : 0.042 0.233 2230 Planarity : 0.004 0.044 2145 Dihedral : 18.192 172.426 2940 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.77 % Allowed : 7.54 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.21), residues: 1438 helix: -0.19 (0.20), residues: 665 sheet: -0.29 (0.59), residues: 88 loop : -2.31 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1126 HIS 0.006 0.001 HIS A 983 PHE 0.020 0.002 PHE B 95 TYR 0.015 0.001 TYR A1141 ARG 0.009 0.001 ARG A1335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 1.372 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3530 (mtt) cc_final: 0.3294 (mtt) REVERT: A 284 ASP cc_start: 0.7108 (t0) cc_final: 0.6814 (t0) REVERT: A 599 LYS cc_start: 0.8921 (tppt) cc_final: 0.8325 (pttp) REVERT: A 648 MET cc_start: 0.8883 (tpp) cc_final: 0.8450 (tpp) REVERT: A 781 MET cc_start: 0.6463 (ttt) cc_final: 0.6233 (mpp) REVERT: A 1021 MET cc_start: 0.7580 (ptm) cc_final: 0.7291 (ptm) REVERT: A 1266 LEU cc_start: 0.8483 (mm) cc_final: 0.8223 (pt) REVERT: A 1297 HIS cc_start: 0.6655 (m-70) cc_final: 0.6185 (m170) REVERT: B 26 MET cc_start: 0.7598 (mmm) cc_final: 0.7309 (mtp) REVERT: B 37 LYS cc_start: 0.8015 (mmmt) cc_final: 0.7017 (mttt) outliers start: 22 outliers final: 15 residues processed: 117 average time/residue: 0.2471 time to fit residues: 44.6734 Evaluate side-chains 104 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 96 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 132 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 920 GLN A 930 HIS ** A1224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.172651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.134823 restraints weight = 22880.311| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 4.22 r_work: 0.3439 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13995 Z= 0.177 Angle : 0.540 10.623 19311 Z= 0.284 Chirality : 0.039 0.239 2230 Planarity : 0.004 0.039 2145 Dihedral : 18.098 173.918 2940 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.01 % Allowed : 8.43 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.22), residues: 1438 helix: 0.42 (0.21), residues: 665 sheet: -0.16 (0.60), residues: 88 loop : -2.11 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1126 HIS 0.004 0.001 HIS A 137 PHE 0.014 0.001 PHE B 95 TYR 0.009 0.001 TYR A1141 ARG 0.003 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7526 (tpm170) cc_final: 0.7266 (tpm170) REVERT: A 284 ASP cc_start: 0.7502 (t0) cc_final: 0.7212 (t0) REVERT: A 383 MET cc_start: 0.7162 (mtm) cc_final: 0.6893 (mtt) REVERT: A 599 LYS cc_start: 0.8907 (tppt) cc_final: 0.8214 (pttp) REVERT: A 631 MET cc_start: 0.8265 (mmm) cc_final: 0.8026 (tpp) REVERT: A 648 MET cc_start: 0.9002 (tpp) cc_final: 0.8543 (tpp) REVERT: A 781 MET cc_start: 0.7560 (ttt) cc_final: 0.7240 (mpp) REVERT: A 1297 HIS cc_start: 0.6841 (m-70) cc_final: 0.6350 (m170) REVERT: B 37 LYS cc_start: 0.7788 (mmmt) cc_final: 0.6755 (mttt) REVERT: B 89 GLU cc_start: 0.7942 (pt0) cc_final: 0.7717 (mm-30) outliers start: 25 outliers final: 15 residues processed: 114 average time/residue: 0.2816 time to fit residues: 46.7631 Evaluate side-chains 97 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1347 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 101 optimal weight: 0.0070 chunk 76 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 90 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN A 920 GLN ** A1224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.174627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.137254 restraints weight = 23104.791| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 3.93 r_work: 0.3471 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13995 Z= 0.140 Angle : 0.510 10.584 19311 Z= 0.266 Chirality : 0.038 0.226 2230 Planarity : 0.003 0.037 2145 Dihedral : 17.993 176.076 2940 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.61 % Allowed : 9.39 % Favored : 89.00 % 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: -0.71 (0.23), residues: 1438 helix: 0.86 (0.21), residues: 658 sheet: -0.12 (0.59), residues: 88 loop : -1.91 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1126 HIS 0.003 0.001 HIS A 137 PHE 0.015 0.001 PHE A1276 TYR 0.007 0.001 TYR A 882 ARG 0.005 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8070 (mm) cc_final: 0.7644 (mt) REVERT: A 599 LYS cc_start: 0.8905 (tppt) cc_final: 0.8241 (pttp) REVERT: A 648 MET cc_start: 0.8960 (tpp) cc_final: 0.8488 (tpp) REVERT: A 781 MET cc_start: 0.7504 (ttt) cc_final: 0.7141 (mpp) REVERT: A 930 HIS cc_start: 0.7891 (m90) cc_final: 0.7472 (m-70) REVERT: A 1297 HIS cc_start: 0.6845 (m-70) cc_final: 0.6351 (m170) REVERT: B 26 MET cc_start: 0.7988 (mmm) cc_final: 0.7363 (mtp) REVERT: B 37 LYS cc_start: 0.7741 (mmmt) cc_final: 0.6754 (mttt) outliers start: 20 outliers final: 15 residues processed: 116 average time/residue: 0.2425 time to fit residues: 43.2337 Evaluate side-chains 102 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain B residue 49 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 67 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN A 612 ASN A 920 GLN ** A1224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1350 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.167676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.131115 restraints weight = 23563.415| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 4.91 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 13995 Z= 0.425 Angle : 0.740 10.860 19311 Z= 0.384 Chirality : 0.046 0.292 2230 Planarity : 0.005 0.051 2145 Dihedral : 18.226 172.883 2940 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.41 % Allowed : 10.03 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.22), residues: 1438 helix: 0.40 (0.20), residues: 661 sheet: -1.21 (0.53), residues: 101 loop : -2.04 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 883 HIS 0.009 0.002 HIS B 92 PHE 0.022 0.003 PHE B 99 TYR 0.028 0.002 TYR A 5 ARG 0.006 0.001 ARG A1210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 1.370 Fit side-chains revert: symmetry clash REVERT: A 7 ILE cc_start: 0.7783 (mm) cc_final: 0.7513 (mt) REVERT: A 599 LYS cc_start: 0.8951 (tppt) cc_final: 0.8368 (pttp) REVERT: A 781 MET cc_start: 0.6517 (ttt) cc_final: 0.6268 (mpp) REVERT: A 926 GLN cc_start: 0.6482 (tp-100) cc_final: 0.5866 (tp-100) REVERT: A 1297 HIS cc_start: 0.6910 (m-70) cc_final: 0.6549 (m170) REVERT: B 26 MET cc_start: 0.7754 (mmm) cc_final: 0.7487 (mtp) REVERT: B 37 LYS cc_start: 0.8087 (mmmt) cc_final: 0.7054 (mttt) outliers start: 30 outliers final: 20 residues processed: 118 average time/residue: 0.2348 time to fit residues: 43.2769 Evaluate side-chains 101 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 96 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 67 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.174013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.138221 restraints weight = 23139.813| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 4.43 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13995 Z= 0.141 Angle : 0.533 10.847 19311 Z= 0.279 Chirality : 0.039 0.250 2230 Planarity : 0.003 0.037 2145 Dihedral : 18.043 172.603 2940 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.09 % Allowed : 10.83 % Favored : 87.08 % 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: -0.54 (0.23), residues: 1438 helix: 1.02 (0.21), residues: 653 sheet: -0.42 (0.58), residues: 88 loop : -1.77 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 476 HIS 0.004 0.001 HIS B 92 PHE 0.014 0.001 PHE A1276 TYR 0.008 0.001 TYR A 450 ARG 0.004 0.000 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.7578 (mm) cc_final: 0.7211 (mt) REVERT: A 564 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7612 (tp) REVERT: A 599 LYS cc_start: 0.8845 (tppt) cc_final: 0.8380 (pttp) REVERT: A 648 MET cc_start: 0.8866 (tpp) cc_final: 0.8482 (tpp) REVERT: A 1122 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7417 (ttt-90) REVERT: A 1297 HIS cc_start: 0.6757 (m-70) cc_final: 0.6427 (m170) REVERT: B 26 MET cc_start: 0.7738 (mmm) cc_final: 0.7084 (mmm) REVERT: B 37 LYS cc_start: 0.7998 (mmmt) cc_final: 0.7008 (mttt) outliers start: 26 outliers final: 18 residues processed: 112 average time/residue: 0.2499 time to fit residues: 42.7026 Evaluate side-chains 105 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1122 ARG Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 96 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 127 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 57 optimal weight: 0.0040 chunk 83 optimal weight: 0.0020 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 GLN ** A1224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.175257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.137632 restraints weight = 23085.703| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 4.79 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13995 Z= 0.138 Angle : 0.514 9.510 19311 Z= 0.265 Chirality : 0.038 0.222 2230 Planarity : 0.003 0.036 2145 Dihedral : 17.914 168.609 2940 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.77 % Allowed : 11.48 % Favored : 86.76 % 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: -0.25 (0.23), residues: 1438 helix: 1.32 (0.22), residues: 649 sheet: -0.19 (0.58), residues: 88 loop : -1.66 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 476 HIS 0.004 0.001 HIS B 92 PHE 0.012 0.001 PHE A 491 TYR 0.008 0.001 TYR A 155 ARG 0.003 0.000 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 1.363 Fit side-chains revert: symmetry clash REVERT: A 7 ILE cc_start: 0.7602 (mm) cc_final: 0.7219 (mt) REVERT: A 564 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7955 (tp) REVERT: A 599 LYS cc_start: 0.8831 (tppt) cc_final: 0.8329 (pttp) REVERT: A 631 MET cc_start: 0.8090 (mmm) cc_final: 0.7862 (mmm) REVERT: A 648 MET cc_start: 0.8903 (tpp) cc_final: 0.8500 (tpp) REVERT: A 911 LEU cc_start: 0.4725 (OUTLIER) cc_final: 0.4312 (mt) REVERT: A 1122 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7575 (ttt-90) REVERT: A 1297 HIS cc_start: 0.6872 (m-70) cc_final: 0.6451 (m170) REVERT: B 26 MET cc_start: 0.7677 (mmm) cc_final: 0.7164 (mtp) REVERT: B 37 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7007 (mttp) outliers start: 22 outliers final: 17 residues processed: 112 average time/residue: 0.2471 time to fit residues: 41.9432 Evaluate side-chains 107 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1122 ARG Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 96 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 33 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 ASN ** A 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN A 930 HIS ** A1224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.169613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.132520 restraints weight = 23061.733| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 4.46 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13995 Z= 0.332 Angle : 0.657 10.087 19311 Z= 0.339 Chirality : 0.043 0.304 2230 Planarity : 0.004 0.038 2145 Dihedral : 18.017 169.267 2940 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.77 % Allowed : 11.96 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.23), residues: 1438 helix: 0.91 (0.21), residues: 663 sheet: -1.01 (0.50), residues: 111 loop : -1.74 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 883 HIS 0.007 0.002 HIS A 137 PHE 0.022 0.002 PHE A1276 TYR 0.018 0.002 TYR A1141 ARG 0.005 0.001 ARG A1210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 1.437 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.1312 (mtt) cc_final: 0.0921 (mtt) REVERT: A 7 ILE cc_start: 0.7723 (mm) cc_final: 0.7432 (mt) REVERT: A 564 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7250 (tp) REVERT: A 569 PHE cc_start: 0.7640 (m-10) cc_final: 0.7340 (m-80) REVERT: A 599 LYS cc_start: 0.8883 (tppt) cc_final: 0.8354 (pttp) REVERT: A 648 MET cc_start: 0.8880 (tpp) cc_final: 0.8491 (tpp) REVERT: A 911 LEU cc_start: 0.4640 (OUTLIER) cc_final: 0.4242 (mt) REVERT: A 926 GLN cc_start: 0.6499 (tp-100) cc_final: 0.5798 (tp-100) REVERT: A 1076 LYS cc_start: 0.7578 (mmtm) cc_final: 0.6628 (mmtm) REVERT: A 1297 HIS cc_start: 0.6892 (m-70) cc_final: 0.6564 (m170) REVERT: B 26 MET cc_start: 0.7737 (mmm) cc_final: 0.7354 (mtp) REVERT: B 37 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7077 (mttt) outliers start: 22 outliers final: 19 residues processed: 111 average time/residue: 0.2564 time to fit residues: 43.4010 Evaluate side-chains 107 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 87 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.169401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.132778 restraints weight = 23055.437| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 4.41 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13995 Z= 0.308 Angle : 0.655 10.713 19311 Z= 0.337 Chirality : 0.043 0.293 2230 Planarity : 0.004 0.038 2145 Dihedral : 18.038 172.131 2940 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.61 % Allowed : 12.28 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.22), residues: 1438 helix: 0.76 (0.21), residues: 664 sheet: -1.14 (0.50), residues: 111 loop : -1.76 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 883 HIS 0.008 0.001 HIS A 983 PHE 0.020 0.002 PHE A1276 TYR 0.018 0.002 TYR A 286 ARG 0.005 0.000 ARG A1210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 1.491 Fit side-chains REVERT: A 1 MET cc_start: 0.1270 (mtt) cc_final: 0.1003 (mtt) REVERT: A 7 ILE cc_start: 0.7652 (mm) cc_final: 0.7256 (mt) REVERT: A 564 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7242 (tp) REVERT: A 569 PHE cc_start: 0.7560 (m-10) cc_final: 0.7355 (m-80) REVERT: A 599 LYS cc_start: 0.8893 (tppt) cc_final: 0.8380 (pttp) REVERT: A 648 MET cc_start: 0.8883 (tpp) cc_final: 0.8514 (tpp) REVERT: A 911 LEU cc_start: 0.4844 (OUTLIER) cc_final: 0.4353 (mt) REVERT: A 930 HIS cc_start: 0.7949 (m-70) cc_final: 0.7626 (m90) REVERT: A 1122 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7342 (ttt-90) REVERT: A 1297 HIS cc_start: 0.6927 (m-70) cc_final: 0.6567 (m170) REVERT: B 26 MET cc_start: 0.7739 (mmm) cc_final: 0.7337 (mtp) REVERT: B 37 LYS cc_start: 0.8110 (mmmt) cc_final: 0.7062 (mttt) outliers start: 20 outliers final: 15 residues processed: 105 average time/residue: 0.2696 time to fit residues: 42.7668 Evaluate side-chains 105 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1122 ARG Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 49 TYR Chi-restraints excluded: chain B residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 86 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 129 optimal weight: 0.0970 chunk 138 optimal weight: 7.9990 chunk 145 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 ASN A 840 HIS ** A1224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.175063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.137699 restraints weight = 23249.853| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 4.39 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13995 Z= 0.133 Angle : 0.530 10.897 19311 Z= 0.273 Chirality : 0.038 0.234 2230 Planarity : 0.003 0.038 2145 Dihedral : 17.734 171.118 2940 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.52 % Allowed : 12.44 % Favored : 86.04 % 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: -0.24 (0.23), residues: 1438 helix: 1.25 (0.22), residues: 657 sheet: -0.29 (0.56), residues: 88 loop : -1.60 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 883 HIS 0.004 0.001 HIS B 92 PHE 0.014 0.001 PHE A1276 TYR 0.011 0.001 TYR A 450 ARG 0.003 0.000 ARG A1210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4966.62 seconds wall clock time: 89 minutes 29.95 seconds (5369.95 seconds total)