Starting phenix.real_space_refine on Thu Sep 18 03:06:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ye9_39191/09_2025/8ye9_39191_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ye9_39191/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ye9_39191/09_2025/8ye9_39191_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ye9_39191/09_2025/8ye9_39191_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ye9_39191/09_2025/8ye9_39191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ye9_39191/09_2025/8ye9_39191.map" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 13, 'ARG:plan': 3, 'ASP:plan': 4, 'GLN:plan1': 4, 'PHE:plan': 1} 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: 3.35, per 1000 atoms: 0.25 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: 1.02 Conformation dependent library (CDL) restraints added in 796.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.52 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: 2.70 Time building geometry restraints manager: 1.43 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: 1.670 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.370 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.860 ------------------------------------------------------------------------------- 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= 0.334 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG A 69 TYR 0.028 0.003 TYR B 49 PHE 0.030 0.003 PHE A 462 TRP 0.013 0.003 TRP A1074 HIS 0.013 0.003 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00724 (13995) covalent geometry : angle 1.01364 (19311) hydrogen bonds : bond 0.14118 ( 476) hydrogen bonds : angle 8.57757 ( 1353) *********************** 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 : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7486 (t0) cc_final: 0.6968 (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: 0.7326 (mpp) REVERT: A 1258 PHE cc_start: 0.7655 (t80) cc_final: 0.7450 (t80) 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: 0.7619 (tp30) outliers start: 3 outliers final: 0 residues processed: 223 average time/residue: 0.1468 time to fit residues: 45.3597 Evaluate side-chains 110 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 A1261 GLN A1308 ASN A1311 HIS B 40 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.174656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.137120 restraints weight = 23549.642| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 4.94 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13995 Z= 0.134 Angle : 0.594 10.369 19311 Z= 0.315 Chirality : 0.041 0.238 2230 Planarity : 0.004 0.046 2145 Dihedral : 18.299 178.752 2940 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.52 % Allowed : 6.90 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.54 (0.20), residues: 1438 helix: -0.96 (0.19), residues: 664 sheet: -0.44 (0.59), residues: 88 loop : -2.63 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 71 TYR 0.010 0.001 TYR A 882 PHE 0.015 0.001 PHE A 462 TRP 0.009 0.001 TRP A1074 HIS 0.004 0.001 HIS A 982 Details of bonding type rmsd covalent geometry : bond 0.00280 (13995) covalent geometry : angle 0.59390 (19311) hydrogen bonds : bond 0.05937 ( 476) hydrogen bonds : angle 4.85757 ( 1353) *********************** 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 151 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7005 (t0) cc_final: 0.6650 (t0) REVERT: A 557 ARG cc_start: 0.7246 (tpp80) cc_final: 0.6768 (tmt170) REVERT: A 599 LYS cc_start: 0.8895 (tppt) cc_final: 0.8233 (pttp) REVERT: A 606 PHE cc_start: 0.6848 (t80) cc_final: 0.6635 (t80) REVERT: A 695 GLN cc_start: 0.7983 (mt0) cc_final: 0.6973 (tm-30) REVERT: A 781 MET cc_start: 0.6574 (ttt) cc_final: 0.6335 (mpp) REVERT: A 926 GLN cc_start: 0.5211 (OUTLIER) cc_final: 0.4994 (tp-100) REVERT: A 1021 MET cc_start: 0.7299 (ptm) cc_final: 0.7084 (ptm) REVERT: A 1189 GLU cc_start: 0.8088 (tt0) cc_final: 0.7669 (tm-30) REVERT: A 1297 HIS cc_start: 0.6990 (m-70) cc_final: 0.6370 (m170) REVERT: B 37 LYS cc_start: 0.7884 (mmmt) cc_final: 0.7023 (mttt) outliers start: 19 outliers final: 11 residues processed: 146 average time/residue: 0.1216 time to fit residues: 26.2478 Evaluate side-chains 108 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 926 GLN 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 143 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 chunk 102 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.4253 r_free = 0.4253 target = 0.171022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.134802 restraints weight = 23283.912| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 4.42 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13995 Z= 0.189 Angle : 0.643 13.346 19311 Z= 0.334 Chirality : 0.043 0.236 2230 Planarity : 0.004 0.048 2145 Dihedral : 18.232 172.240 2940 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.77 % Allowed : 8.11 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.21), residues: 1438 helix: -0.26 (0.20), residues: 667 sheet: -0.41 (0.58), residues: 88 loop : -2.34 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 307 TYR 0.015 0.002 TYR A1141 PHE 0.022 0.002 PHE B 95 TRP 0.007 0.001 TRP A1126 HIS 0.007 0.001 HIS A 983 Details of bonding type rmsd covalent geometry : bond 0.00422 (13995) covalent geometry : angle 0.64330 (19311) hydrogen bonds : bond 0.06909 ( 476) hydrogen bonds : angle 4.68844 ( 1353) *********************** 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 120 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7142 (t0) cc_final: 0.6826 (t0) REVERT: A 599 LYS cc_start: 0.8928 (tppt) cc_final: 0.8333 (pttp) REVERT: A 648 MET cc_start: 0.8861 (tpp) cc_final: 0.8411 (tpp) REVERT: A 1021 MET cc_start: 0.7601 (ptm) cc_final: 0.7310 (ptm) REVERT: A 1266 LEU cc_start: 0.8419 (mm) cc_final: 0.8186 (pt) REVERT: A 1297 HIS cc_start: 0.6634 (m-70) cc_final: 0.6197 (m170) REVERT: B 26 MET cc_start: 0.7553 (mmm) cc_final: 0.7169 (mtp) REVERT: B 37 LYS cc_start: 0.8005 (mmmt) cc_final: 0.7058 (mtmm) outliers start: 22 outliers final: 14 residues processed: 115 average time/residue: 0.1119 time to fit residues: 19.7266 Evaluate side-chains 103 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 96 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 55 optimal weight: 8.9990 chunk 87 optimal weight: 30.0000 chunk 22 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 76 optimal weight: 0.0970 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 ** 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 = 0.4279 r_free = 0.4279 target = 0.173372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.135840 restraints weight = 23174.936| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 4.05 r_work: 0.3451 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3276 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= 0.123 Angle : 0.538 10.973 19311 Z= 0.284 Chirality : 0.039 0.240 2230 Planarity : 0.004 0.051 2145 Dihedral : 18.100 174.025 2940 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.85 % Allowed : 8.83 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.22), residues: 1438 helix: 0.38 (0.21), residues: 666 sheet: -0.21 (0.60), residues: 88 loop : -2.14 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.008 0.001 TYR A1141 PHE 0.011 0.001 PHE A 491 TRP 0.005 0.001 TRP A1126 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00265 (13995) covalent geometry : angle 0.53843 (19311) hydrogen bonds : bond 0.05262 ( 476) hydrogen bonds : angle 4.22478 ( 1353) *********************** 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 119 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7463 (t0) cc_final: 0.7182 (t0) REVERT: A 599 LYS cc_start: 0.8920 (tppt) cc_final: 0.8230 (pttp) REVERT: A 648 MET cc_start: 0.8979 (tpp) cc_final: 0.8508 (tpp) REVERT: A 1297 HIS cc_start: 0.6812 (m-70) cc_final: 0.6336 (m170) REVERT: B 37 LYS cc_start: 0.7769 (mmmt) cc_final: 0.6755 (mttt) outliers start: 23 outliers final: 17 residues processed: 114 average time/residue: 0.1304 time to fit residues: 21.7528 Evaluate side-chains 100 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 1241 HIS Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain A residue 1309 ILE 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 123 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4276 r_free = 0.4276 target = 0.173209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.135597 restraints weight = 23327.504| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 4.28 r_work: 0.3432 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13995 Z= 0.127 Angle : 0.538 10.825 19311 Z= 0.281 Chirality : 0.039 0.240 2230 Planarity : 0.003 0.049 2145 Dihedral : 18.041 173.467 2940 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.85 % Allowed : 9.55 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.23), residues: 1438 helix: 0.66 (0.21), residues: 669 sheet: -0.16 (0.59), residues: 88 loop : -1.99 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 629 TYR 0.010 0.001 TYR A1141 PHE 0.016 0.001 PHE A1276 TRP 0.004 0.001 TRP A1126 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00278 (13995) covalent geometry : angle 0.53750 (19311) hydrogen bonds : bond 0.05238 ( 476) hydrogen bonds : angle 4.10993 ( 1353) *********************** 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 112 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7589 (t0) cc_final: 0.7385 (t0) REVERT: A 599 LYS cc_start: 0.8915 (tppt) cc_final: 0.8225 (pttp) REVERT: A 648 MET cc_start: 0.8974 (tpp) cc_final: 0.8508 (tpp) REVERT: A 1279 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7733 (ttt180) REVERT: A 1297 HIS cc_start: 0.6882 (m-70) cc_final: 0.6386 (m170) REVERT: B 19 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7291 (mt-10) REVERT: B 26 MET cc_start: 0.8044 (mmm) cc_final: 0.7464 (mmm) REVERT: B 37 LYS cc_start: 0.7791 (mmmt) cc_final: 0.6881 (mttt) outliers start: 23 outliers final: 17 residues processed: 106 average time/residue: 0.1155 time to fit residues: 18.7894 Evaluate side-chains 103 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 564 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 1279 ARG 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 Chi-restraints excluded: chain B residue 93 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 144 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 87 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 118 optimal weight: 0.0870 chunk 6 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.0960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 612 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 = 0.4289 r_free = 0.4289 target = 0.174395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.137924 restraints weight = 23209.691| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 4.39 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13995 Z= 0.114 Angle : 0.518 10.636 19311 Z= 0.269 Chirality : 0.038 0.236 2230 Planarity : 0.003 0.046 2145 Dihedral : 17.954 174.870 2940 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.77 % Allowed : 9.87 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.23), residues: 1438 helix: 1.07 (0.21), residues: 658 sheet: -0.16 (0.59), residues: 88 loop : -1.85 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 629 TYR 0.008 0.001 TYR A1141 PHE 0.017 0.001 PHE A1276 TRP 0.005 0.001 TRP A 883 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00245 (13995) covalent geometry : angle 0.51829 (19311) hydrogen bonds : bond 0.04667 ( 476) hydrogen bonds : angle 3.89920 ( 1353) *********************** 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 114 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.7543 (mm) cc_final: 0.7143 (mt) REVERT: A 90 MET cc_start: 0.7134 (mmt) cc_final: 0.6800 (tpp) REVERT: A 599 LYS cc_start: 0.8861 (tppt) cc_final: 0.8347 (pttp) REVERT: A 648 MET cc_start: 0.8812 (tpp) cc_final: 0.8391 (tpp) REVERT: A 751 MET cc_start: 0.5189 (mtm) cc_final: 0.4964 (mtm) REVERT: A 1282 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7410 (mp) REVERT: A 1297 HIS cc_start: 0.6796 (m-70) cc_final: 0.6386 (m170) REVERT: B 26 MET cc_start: 0.7662 (mmm) cc_final: 0.6993 (mmm) REVERT: B 37 LYS cc_start: 0.8095 (mmmt) cc_final: 0.7086 (mttt) outliers start: 22 outliers final: 16 residues processed: 109 average time/residue: 0.1128 time to fit residues: 19.0863 Evaluate side-chains 105 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 642 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 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 1347 LEU Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain B residue 49 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 19 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 77 optimal weight: 40.0000 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 123 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 81 optimal weight: 30.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 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 = 0.4258 r_free = 0.4258 target = 0.171472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.132849 restraints weight = 23163.192| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 4.75 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13995 Z= 0.165 Angle : 0.580 10.317 19311 Z= 0.303 Chirality : 0.040 0.271 2230 Planarity : 0.004 0.046 2145 Dihedral : 17.982 167.388 2940 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.01 % Allowed : 10.51 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.23), residues: 1438 helix: 0.94 (0.21), residues: 663 sheet: -0.24 (0.58), residues: 88 loop : -1.84 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 98 TYR 0.014 0.001 TYR A1141 PHE 0.019 0.002 PHE A1276 TRP 0.006 0.001 TRP A 883 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00368 (13995) covalent geometry : angle 0.57973 (19311) hydrogen bonds : bond 0.06062 ( 476) hydrogen bonds : angle 4.13843 ( 1353) *********************** 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 114 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.7631 (mm) cc_final: 0.7254 (mt) REVERT: A 599 LYS cc_start: 0.8877 (tppt) cc_final: 0.8373 (pttp) REVERT: A 648 MET cc_start: 0.8913 (tpp) cc_final: 0.8435 (tpp) REVERT: A 1122 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7469 (ttt-90) REVERT: A 1297 HIS cc_start: 0.6879 (m-70) cc_final: 0.6527 (m170) REVERT: B 26 MET cc_start: 0.7693 (mmm) cc_final: 0.7257 (mtp) REVERT: B 37 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7076 (mttt) outliers start: 25 outliers final: 19 residues processed: 110 average time/residue: 0.1118 time to fit residues: 18.7070 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 : 0.497 ------------------------------------------------------------------------------- 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 564 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 627 GLU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 85 optimal weight: 40.0000 chunk 138 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 117 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.172422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.134546 restraints weight = 22924.300| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 4.46 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4044 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= 0.148 Angle : 0.560 9.583 19311 Z= 0.292 Chirality : 0.040 0.270 2230 Planarity : 0.004 0.045 2145 Dihedral : 17.928 166.956 2940 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.93 % Allowed : 10.59 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.23), residues: 1438 helix: 1.01 (0.21), residues: 663 sheet: -0.32 (0.57), residues: 88 loop : -1.81 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 395 TYR 0.011 0.001 TYR A1141 PHE 0.019 0.001 PHE A1276 TRP 0.006 0.001 TRP A 883 HIS 0.005 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00328 (13995) covalent geometry : angle 0.55954 (19311) hydrogen bonds : bond 0.05465 ( 476) hydrogen bonds : angle 4.03918 ( 1353) *********************** 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 118 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.7571 (mm) cc_final: 0.7214 (mt) REVERT: A 564 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7903 (tp) REVERT: A 599 LYS cc_start: 0.8855 (tppt) cc_final: 0.8349 (pttp) REVERT: A 648 MET cc_start: 0.8964 (tpp) cc_final: 0.8582 (tpp) REVERT: A 698 HIS cc_start: 0.7728 (m-70) cc_final: 0.7387 (m-70) REVERT: A 911 LEU cc_start: 0.4719 (OUTLIER) cc_final: 0.4296 (mt) REVERT: A 1122 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7441 (ttt-90) REVERT: A 1297 HIS cc_start: 0.6989 (m-70) cc_final: 0.6559 (m170) outliers start: 24 outliers final: 19 residues processed: 113 average time/residue: 0.0981 time to fit residues: 16.7492 Evaluate side-chains 109 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 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 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 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.4283 r_free = 0.4283 target = 0.173833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.135813 restraints weight = 23305.231| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 4.56 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13995 Z= 0.118 Angle : 0.532 10.035 19311 Z= 0.276 Chirality : 0.039 0.251 2230 Planarity : 0.003 0.045 2145 Dihedral : 17.812 169.160 2940 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.69 % Allowed : 11.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.23), residues: 1438 helix: 1.24 (0.21), residues: 660 sheet: -0.21 (0.57), residues: 88 loop : -1.72 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 220 TYR 0.012 0.001 TYR A 5 PHE 0.017 0.001 PHE A1276 TRP 0.006 0.001 TRP A 883 HIS 0.005 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00257 (13995) covalent geometry : angle 0.53249 (19311) hydrogen bonds : bond 0.04748 ( 476) hydrogen bonds : angle 3.85859 ( 1353) *********************** 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 111 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 7 ILE cc_start: 0.7585 (mm) cc_final: 0.7188 (mt) REVERT: A 564 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7957 (tp) REVERT: A 599 LYS cc_start: 0.8799 (tppt) cc_final: 0.8302 (pttp) REVERT: A 648 MET cc_start: 0.8889 (tpp) cc_final: 0.8423 (tpp) REVERT: A 911 LEU cc_start: 0.4754 (OUTLIER) cc_final: 0.4315 (mt) REVERT: A 1122 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7477 (ttt-90) REVERT: A 1282 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7439 (mp) REVERT: A 1297 HIS cc_start: 0.6978 (m-70) cc_final: 0.6559 (m170) REVERT: B 26 MET cc_start: 0.7584 (mmm) cc_final: 0.7249 (mtp) outliers start: 21 outliers final: 15 residues processed: 107 average time/residue: 0.1139 time to fit residues: 18.4401 Evaluate side-chains 107 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 564 LEU 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 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 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 117 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 0.0980 chunk 118 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 143 optimal weight: 10.0000 chunk 102 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** A1252 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.175190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.137453 restraints weight = 23043.098| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 4.44 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4407 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= 0.103 Angle : 0.510 10.793 19311 Z= 0.264 Chirality : 0.038 0.236 2230 Planarity : 0.003 0.045 2145 Dihedral : 17.717 172.830 2940 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.52 % Allowed : 11.48 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.23), residues: 1438 helix: 1.39 (0.22), residues: 661 sheet: -0.20 (0.57), residues: 88 loop : -1.63 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 629 TYR 0.008 0.001 TYR A 5 PHE 0.012 0.001 PHE A 119 TRP 0.005 0.001 TRP A 883 HIS 0.005 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00222 (13995) covalent geometry : angle 0.50984 (19311) hydrogen bonds : bond 0.04223 ( 476) hydrogen bonds : angle 3.73121 ( 1353) ********************** 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 113 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.7592 (mm) cc_final: 0.7169 (mt) REVERT: A 564 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7839 (tp) REVERT: A 599 LYS cc_start: 0.8793 (tppt) cc_final: 0.8306 (pttp) REVERT: A 648 MET cc_start: 0.8845 (tpp) cc_final: 0.8455 (tpp) REVERT: A 911 LEU cc_start: 0.4721 (OUTLIER) cc_final: 0.4333 (mt) REVERT: A 939 MET cc_start: 0.6576 (mmm) cc_final: 0.6121 (mmt) REVERT: A 1122 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7516 (ttt-90) REVERT: A 1282 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7311 (mp) REVERT: A 1297 HIS cc_start: 0.6967 (m-70) cc_final: 0.6539 (m170) REVERT: B 26 MET cc_start: 0.7584 (mmm) cc_final: 0.6975 (mmm) outliers start: 19 outliers final: 14 residues processed: 109 average time/residue: 0.1118 time to fit residues: 18.3580 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 : 0.487 ------------------------------------------------------------------------------- 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 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 49 TYR Chi-restraints excluded: chain B residue 66 GLU 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 135 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** A 920 GLN ** A1224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.170082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.132777 restraints weight = 23216.434| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 4.45 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13995 Z= 0.204 Angle : 0.634 10.634 19311 Z= 0.327 Chirality : 0.042 0.304 2230 Planarity : 0.004 0.047 2145 Dihedral : 17.826 172.334 2940 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.69 % Allowed : 12.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.23), residues: 1438 helix: 0.97 (0.21), residues: 676 sheet: -0.90 (0.51), residues: 111 loop : -1.73 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1210 TYR 0.016 0.002 TYR A1141 PHE 0.021 0.002 PHE A1276 TRP 0.008 0.001 TRP A 883 HIS 0.006 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00462 (13995) covalent geometry : angle 0.63356 (19311) hydrogen bonds : bond 0.06562 ( 476) hydrogen bonds : angle 4.21506 ( 1353) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2612.98 seconds wall clock time: 45 minutes 43.45 seconds (2743.45 seconds total)