Starting phenix.real_space_refine on Wed Mar 4 10:47:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z4g_14496/03_2026/7z4g_14496.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z4g_14496/03_2026/7z4g_14496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z4g_14496/03_2026/7z4g_14496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z4g_14496/03_2026/7z4g_14496.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z4g_14496/03_2026/7z4g_14496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z4g_14496/03_2026/7z4g_14496.map" } resolution = 3.64 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= 0.001 sd= 0.006 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 140 5.49 5 S 19 5.16 5 C 7585 2.51 5 N 2223 2.21 5 O 2747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12714 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1932 Classifications: {'DNA': 1, 'RNA': 90} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 48, 'rna3p_pyr': 30} Link IDs: {'rna2p': 12, 'rna3p': 78} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 9711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1188, 9711 Classifications: {'peptide': 1188} Link IDs: {'PTRANS': 32, 'TRANS': 1155} Chain breaks: 4 Chain: "C" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 625 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Chain: "D" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 446 Inner-chain residues flagged as termini: ['pdbres=" DA D -2 "'] Classifications: {'DNA': 22} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 21} Time building chain proxies: 2.72, per 1000 atoms: 0.21 Number of scatterers: 12714 At special positions: 0 Unit cell: (86.45, 130, 122.85, 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 19 16.00 P 140 15.00 O 2747 8.00 N 2223 7.00 C 7585 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: 1.16 Conformation dependent library (CDL) restraints added in 537.8 milliseconds 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 10 sheets defined 55.3% alpha, 9.1% beta 53 base pairs and 85 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'B' and resid 22 through 26 removed outlier: 3.569A pdb=" N LYS B 26 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 86 Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 96 through 103 Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 134 through 145 removed outlier: 3.553A pdb=" N LEU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 Processing helix chain 'B' and resid 182 through 196 Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 217 through 228 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.332A pdb=" N ASN B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 286 through 306 removed outlier: 3.983A pdb=" N ASP B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 343 Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.585A pdb=" N TYR B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 368 through 383 Proline residue: B 378 - end of helix Processing helix chain 'B' and resid 387 through 395 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.869A pdb=" N ASN B 407 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY B 408 " --> pdb=" O PHE B 405 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER B 409 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 removed outlier: 4.117A pdb=" N HIS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 436 through 446 Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 483 through 494 removed outlier: 3.556A pdb=" N ILE B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 526 removed outlier: 4.146A pdb=" N LYS B 526 " --> pdb=" O ASN B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 552 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.567A pdb=" N TYR B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 603 through 609 Processing helix chain 'B' and resid 612 through 626 removed outlier: 3.520A pdb=" N THR B 622 " --> pdb=" O ASP B 618 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE B 626 " --> pdb=" O THR B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 637 Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 644 through 654 Processing helix chain 'B' and resid 664 through 669 Processing helix chain 'B' and resid 678 through 685 Processing helix chain 'B' and resid 692 through 698 Processing helix chain 'B' and resid 702 through 712 removed outlier: 4.241A pdb=" N GLU B 706 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 726 Processing helix chain 'B' and resid 730 through 751 Processing helix chain 'B' and resid 911 through 922 Processing helix chain 'B' and resid 925 through 940 removed outlier: 3.796A pdb=" N LYS B 929 " --> pdb=" O ARG B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 970 removed outlier: 3.879A pdb=" N VAL B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 1001 removed outlier: 4.112A pdb=" N ALA B 984 " --> pdb=" O ASN B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1009 Processing helix chain 'B' and resid 1043 through 1047 Processing helix chain 'B' and resid 1076 through 1088 removed outlier: 3.905A pdb=" N PHE B1080 " --> pdb=" O LYS B1076 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ALA B1081 " --> pdb=" O GLY B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1132 Processing helix chain 'B' and resid 1170 through 1177 Processing helix chain 'B' and resid 1177 through 1185 removed outlier: 3.561A pdb=" N LYS B1185 " --> pdb=" O PHE B1181 " (cutoff:3.500A) Processing helix chain 'B' and resid 1229 through 1241 removed outlier: 3.570A pdb=" N HIS B1241 " --> pdb=" O TYR B1237 " (cutoff:3.500A) Processing helix chain 'B' and resid 1249 through 1264 Processing helix chain 'B' and resid 1265 through 1280 removed outlier: 3.652A pdb=" N ILE B1269 " --> pdb=" O TYR B1265 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1297 Processing helix chain 'B' and resid 1298 through 1300 No H-bonds generated for 'chain 'B' and resid 1298 through 1300' Processing helix chain 'B' and resid 1301 through 1313 Processing helix chain 'B' and resid 1340 through 1344 Processing helix chain 'B' and resid 1363 through 1365 No H-bonds generated for 'chain 'B' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'B' and resid 954 through 958 removed outlier: 6.296A pdb=" N ILE B 759 " --> pdb=" O ILE B 956 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU B 958 " --> pdb=" O ILE B 759 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 761 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 32 Processing sheet with id=AA3, first strand: chain 'B' and resid 507 through 509 removed outlier: 5.485A pdb=" N LEU B 508 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.847A pdb=" N ALA B 538 " --> pdb=" O TYR B 529 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS B 528 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 581 " --> pdb=" O LYS B 528 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1049 through 1051 Processing sheet with id=AA6, first strand: chain 'B' and resid 1063 through 1065 Processing sheet with id=AA7, first strand: chain 'B' and resid 1107 through 1111 removed outlier: 6.909A pdb=" N SER B1109 " --> pdb=" O ASP B1135 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP B1135 " --> pdb=" O SER B1109 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1156 through 1167 removed outlier: 3.557A pdb=" N LYS B1158 " --> pdb=" O VAL B1149 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B1149 " --> pdb=" O LYS B1158 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B1162 " --> pdb=" O VAL B1145 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B1145 " --> pdb=" O GLU B1162 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR B1141 " --> pdb=" O ILE B1166 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B1196 " --> pdb=" O LEU B1144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1219 through 1222 removed outlier: 6.249A pdb=" N GLU B1219 " --> pdb=" O ALA B1215 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER B1202 " --> pdb=" O LEU B1214 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU B1203 " --> pdb=" O ILE B1348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1324 through 1326 457 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 133 hydrogen bonds 262 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 85 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 1.53 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: 2820 1.33 - 1.45: 3374 1.45 - 1.57: 6738 1.57 - 1.69: 281 1.69 - 1.81: 36 Bond restraints: 13249 Sorted by residual: bond pdb=" O3' DT C 12 " pdb=" P DA C 13 " ideal model delta sigma weight residual 1.607 1.633 -0.026 1.50e-02 4.44e+03 3.10e+00 bond pdb=" CG LEU B1266 " pdb=" CD2 LEU B1266 " ideal model delta sigma weight residual 1.521 1.574 -0.053 3.30e-02 9.18e+02 2.59e+00 bond pdb=" N ARG B 655 " pdb=" CA ARG B 655 " ideal model delta sigma weight residual 1.462 1.484 -0.021 1.32e-02 5.74e+03 2.55e+00 bond pdb=" CA ARG B 655 " pdb=" C ARG B 655 " ideal model delta sigma weight residual 1.529 1.515 0.014 1.04e-02 9.25e+03 1.89e+00 bond pdb=" C GLY B 752 " pdb=" N ARG B 753 " ideal model delta sigma weight residual 1.333 1.314 0.019 1.39e-02 5.18e+03 1.80e+00 ... (remaining 13244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 18153 1.43 - 2.86: 304 2.86 - 4.28: 42 4.28 - 5.71: 5 5.71 - 7.14: 1 Bond angle restraints: 18505 Sorted by residual: angle pdb=" N ARG B 655 " pdb=" CA ARG B 655 " pdb=" C ARG B 655 " ideal model delta sigma weight residual 107.20 114.34 -7.14 1.70e+00 3.46e-01 1.76e+01 angle pdb=" O3' DT C 11 " pdb=" C3' DT C 11 " pdb=" C2' DT C 11 " ideal model delta sigma weight residual 111.50 106.48 5.02 1.50e+00 4.44e-01 1.12e+01 angle pdb=" C2' DC C 10 " pdb=" C1' DC C 10 " pdb=" N1 DC C 10 " ideal model delta sigma weight residual 113.50 118.22 -4.72 1.50e+00 4.44e-01 9.91e+00 angle pdb=" C3' DT C 11 " pdb=" C2' DT C 11 " pdb=" C1' DT C 11 " ideal model delta sigma weight residual 101.60 105.26 -3.66 1.50e+00 4.44e-01 5.96e+00 angle pdb=" C2' C A 83 " pdb=" C1' C A 83 " pdb=" N1 C A 83 " ideal model delta sigma weight residual 112.00 108.35 3.65 1.50e+00 4.44e-01 5.91e+00 ... (remaining 18500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 7067 17.09 - 34.18: 503 34.18 - 51.27: 233 51.27 - 68.35: 165 68.35 - 85.44: 20 Dihedral angle restraints: 7988 sinusoidal: 4495 harmonic: 3493 Sorted by residual: dihedral pdb=" CA LYS B1263 " pdb=" C LYS B1263 " pdb=" N HIS B1264 " pdb=" CA HIS B1264 " ideal model delta harmonic sigma weight residual 180.00 162.68 17.32 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CG ARG B 753 " pdb=" CD ARG B 753 " pdb=" NE ARG B 753 " pdb=" CZ ARG B 753 " ideal model delta sinusoidal sigma weight residual 180.00 135.51 44.49 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" O5' U A 44 " pdb=" C5' U A 44 " pdb=" C4' U A 44 " pdb=" C3' U A 44 " ideal model delta sinusoidal sigma weight residual -65.00 -5.23 -59.77 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 7985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1797 0.046 - 0.092: 275 0.092 - 0.137: 53 0.137 - 0.183: 2 0.183 - 0.229: 1 Chirality restraints: 2128 Sorted by residual: chirality pdb=" CA ARG B 753 " pdb=" N ARG B 753 " pdb=" C ARG B 753 " pdb=" CB ARG B 753 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ILE B 956 " pdb=" N ILE B 956 " pdb=" C ILE B 956 " pdb=" CB ILE B 956 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" C1' A A 42 " pdb=" O4' A A 42 " pdb=" C2' A A 42 " pdb=" N9 A A 42 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.34e-01 ... (remaining 2125 not shown) Planarity restraints: 1842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 993 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.78e+00 pdb=" C VAL B 993 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL B 993 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY B 994 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 991 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C ALA B 991 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA B 991 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 992 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 83 " -0.025 2.00e-02 2.50e+03 1.39e-02 4.36e+00 pdb=" N1 C A 83 " 0.031 2.00e-02 2.50e+03 pdb=" C2 C A 83 " 0.008 2.00e-02 2.50e+03 pdb=" O2 C A 83 " -0.002 2.00e-02 2.50e+03 pdb=" N3 C A 83 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C A 83 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C A 83 " -0.006 2.00e-02 2.50e+03 pdb=" C5 C A 83 " -0.002 2.00e-02 2.50e+03 pdb=" C6 C A 83 " 0.003 2.00e-02 2.50e+03 ... (remaining 1839 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1550 2.75 - 3.29: 12666 3.29 - 3.82: 23604 3.82 - 4.36: 27947 4.36 - 4.90: 42620 Nonbonded interactions: 108387 Sorted by model distance: nonbonded pdb=" O LYS B 209 " pdb=" OG SER B 213 " model vdw 2.209 3.040 nonbonded pdb=" O2' G A 58 " pdb=" O LEU B 455 " model vdw 2.210 3.040 nonbonded pdb=" NZ LYS B 140 " pdb=" OD2 ASP B 144 " model vdw 2.210 3.120 nonbonded pdb=" NZ LYS B1161 " pdb=" OD1 ASP B1344 " model vdw 2.210 3.120 nonbonded pdb=" O GLU B1304 " pdb=" ND2 ASN B1308 " model vdw 2.219 3.120 ... (remaining 108382 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.010 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.070 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 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 : 0.003 0.053 13249 Z= 0.155 Angle : 0.478 7.138 18505 Z= 0.269 Chirality : 0.034 0.229 2128 Planarity : 0.004 0.034 1842 Dihedral : 16.648 85.443 5724 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.03 % Allowed : 4.89 % Favored : 94.08 % 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 are not related in a simple way. whole: 1.30 (0.25), residues: 1178 helix: 1.99 (0.23), residues: 590 sheet: -0.09 (0.61), residues: 78 loop : -0.29 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 654 TYR 0.015 0.001 TYR B1001 PHE 0.012 0.001 PHE B 462 TRP 0.011 0.001 TRP B 464 HIS 0.008 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00308 (13249) covalent geometry : angle 0.47792 (18505) hydrogen bonds : bond 0.12206 ( 590) hydrogen bonds : angle 5.78352 ( 1588) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 216 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.9177 (mmtt) cc_final: 0.8968 (tptt) REVERT: B 80 CYS cc_start: 0.8333 (m) cc_final: 0.8093 (m) REVERT: B 90 MET cc_start: 0.7978 (tpp) cc_final: 0.7648 (tpt) REVERT: B 100 ARG cc_start: 0.8746 (mtm-85) cc_final: 0.7821 (mtm-85) REVERT: B 151 LEU cc_start: 0.8537 (tp) cc_final: 0.8082 (pt) REVERT: B 534 MET cc_start: 0.8219 (mtp) cc_final: 0.6952 (ppp) REVERT: B 569 PHE cc_start: 0.9358 (m-80) cc_final: 0.9078 (m-80) REVERT: B 593 THR cc_start: 0.8038 (m) cc_final: 0.7803 (p) REVERT: B 625 LEU cc_start: 0.8289 (mt) cc_final: 0.8084 (mt) REVERT: B 723 HIS cc_start: 0.9258 (t70) cc_final: 0.8924 (m90) REVERT: B 1043 MET cc_start: 0.6177 (ttp) cc_final: 0.5707 (tmm) REVERT: B 1170 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8550 (mm-30) REVERT: B 1266 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9019 (tp) REVERT: B 1268 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8705 (mp0) outliers start: 11 outliers final: 2 residues processed: 222 average time/residue: 0.1495 time to fit residues: 44.8410 Evaluate side-chains 114 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 1042 ILE Chi-restraints excluded: chain B residue 1266 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 overall best weight: 6.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN B 329 HIS ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 ASN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 HIS B 721 HIS B 726 ASN B 920 GLN B 985 HIS ** B1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.069639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.055131 restraints weight = 79676.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.056747 restraints weight = 43340.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.057808 restraints weight = 29136.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.058538 restraints weight = 22360.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.059011 restraints weight = 18689.260| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13249 Z= 0.314 Angle : 0.717 9.160 18505 Z= 0.376 Chirality : 0.041 0.153 2128 Planarity : 0.006 0.079 1842 Dihedral : 19.687 89.576 3221 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.23 % Allowed : 11.65 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.24), residues: 1178 helix: 1.32 (0.21), residues: 596 sheet: 0.23 (0.61), residues: 76 loop : -0.35 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 664 TYR 0.022 0.002 TYR B1265 PHE 0.022 0.003 PHE B1235 TRP 0.017 0.002 TRP B 464 HIS 0.008 0.002 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00649 (13249) covalent geometry : angle 0.71746 (18505) hydrogen bonds : bond 0.06109 ( 590) hydrogen bonds : angle 5.35036 ( 1588) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 109 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.9191 (mmtt) cc_final: 0.8973 (tptt) REVERT: B 80 CYS cc_start: 0.8347 (m) cc_final: 0.8090 (m) REVERT: B 100 ARG cc_start: 0.8745 (mtm-85) cc_final: 0.8332 (mtm180) REVERT: B 271 TYR cc_start: 0.8807 (t80) cc_final: 0.8566 (t80) REVERT: B 534 MET cc_start: 0.7728 (mtp) cc_final: 0.5431 (mtp) REVERT: B 569 PHE cc_start: 0.9401 (m-80) cc_final: 0.9058 (m-80) REVERT: B 933 GLN cc_start: 0.9558 (OUTLIER) cc_final: 0.9221 (tp-100) REVERT: B 1000 LYS cc_start: 0.8546 (tttt) cc_final: 0.8325 (ptmt) REVERT: B 1043 MET cc_start: 0.6060 (ttp) cc_final: 0.5464 (tmm) REVERT: B 1170 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8625 (mt-10) outliers start: 45 outliers final: 18 residues processed: 137 average time/residue: 0.1319 time to fit residues: 25.4346 Evaluate side-chains 101 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 933 GLN Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 974 LYS Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1172 SER Chi-restraints excluded: chain B residue 1266 LEU Chi-restraints excluded: chain B residue 1274 SER Chi-restraints excluded: chain B residue 1286 ASN Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 101 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 110 optimal weight: 0.0020 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN B 228 GLN B 459 ASN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1311 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.072134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.057584 restraints weight = 76219.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.059311 restraints weight = 40538.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.060413 restraints weight = 26708.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.061100 restraints weight = 20326.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.061629 restraints weight = 17074.101| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13249 Z= 0.140 Angle : 0.558 10.506 18505 Z= 0.290 Chirality : 0.036 0.151 2128 Planarity : 0.004 0.056 1842 Dihedral : 19.510 91.693 3219 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.82 % Allowed : 13.25 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.25), residues: 1178 helix: 1.65 (0.21), residues: 597 sheet: 0.22 (0.57), residues: 85 loop : -0.20 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 664 TYR 0.018 0.001 TYR B1265 PHE 0.013 0.001 PHE B1008 TRP 0.022 0.001 TRP B 464 HIS 0.008 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00287 (13249) covalent geometry : angle 0.55824 (18505) hydrogen bonds : bond 0.03972 ( 590) hydrogen bonds : angle 4.71492 ( 1588) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.9209 (mmtt) cc_final: 0.8893 (tptt) REVERT: B 80 CYS cc_start: 0.8255 (m) cc_final: 0.7969 (m) REVERT: B 100 ARG cc_start: 0.8625 (mtm-85) cc_final: 0.7858 (mtm-85) REVERT: B 271 TYR cc_start: 0.8772 (t80) cc_final: 0.8519 (t80) REVERT: B 483 ASP cc_start: 0.8015 (t0) cc_final: 0.7773 (t0) REVERT: B 569 PHE cc_start: 0.9389 (m-80) cc_final: 0.9070 (m-80) REVERT: B 682 PHE cc_start: 0.8581 (m-80) cc_final: 0.8277 (m-80) REVERT: B 755 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8256 (ptmm) REVERT: B 1043 MET cc_start: 0.5742 (ttp) cc_final: 0.5344 (tmm) REVERT: B 1108 GLU cc_start: 0.7631 (tt0) cc_final: 0.7303 (tt0) REVERT: B 1170 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8546 (mt-10) REVERT: B 1253 GLU cc_start: 0.9448 (tp30) cc_final: 0.8932 (mm-30) REVERT: B 1357 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8700 (mp0) outliers start: 30 outliers final: 20 residues processed: 121 average time/residue: 0.1142 time to fit residues: 20.2613 Evaluate side-chains 109 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 630 GLU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 755 LYS Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 974 LYS Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1265 TYR Chi-restraints excluded: chain B residue 1286 ASN Chi-restraints excluded: chain B residue 1325 LYS Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 69 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** 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 = 0.3787 r_free = 0.3787 target = 0.070269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.055747 restraints weight = 76838.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.057421 restraints weight = 40988.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.058535 restraints weight = 27082.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.059261 restraints weight = 20475.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.059684 restraints weight = 17070.554| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13249 Z= 0.206 Angle : 0.591 9.452 18505 Z= 0.311 Chirality : 0.037 0.146 2128 Planarity : 0.004 0.054 1842 Dihedral : 19.532 91.045 3217 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.29 % Allowed : 13.82 % Favored : 82.89 % 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 are not related in a simple way. whole: 1.01 (0.25), residues: 1178 helix: 1.53 (0.21), residues: 597 sheet: 0.05 (0.55), residues: 85 loop : -0.20 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 664 TYR 0.022 0.002 TYR B1265 PHE 0.019 0.002 PHE B1046 TRP 0.016 0.002 TRP B 464 HIS 0.007 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00427 (13249) covalent geometry : angle 0.59091 (18505) hydrogen bonds : bond 0.04747 ( 590) hydrogen bonds : angle 4.76809 ( 1588) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.9253 (mmtt) cc_final: 0.8927 (tptt) REVERT: B 80 CYS cc_start: 0.8320 (m) cc_final: 0.8037 (m) REVERT: B 100 ARG cc_start: 0.8664 (mtm-85) cc_final: 0.7965 (mtm-85) REVERT: B 271 TYR cc_start: 0.8870 (t80) cc_final: 0.8654 (t80) REVERT: B 483 ASP cc_start: 0.8035 (t0) cc_final: 0.7809 (t0) REVERT: B 569 PHE cc_start: 0.9412 (m-80) cc_final: 0.9097 (m-80) REVERT: B 755 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8379 (ptmm) REVERT: B 933 GLN cc_start: 0.9566 (tp-100) cc_final: 0.9085 (tp-100) REVERT: B 1043 MET cc_start: 0.5520 (ttp) cc_final: 0.5152 (tmm) REVERT: B 1108 GLU cc_start: 0.7732 (tt0) cc_final: 0.7444 (tt0) REVERT: B 1170 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8554 (mt-10) REVERT: B 1357 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8729 (mp0) outliers start: 35 outliers final: 24 residues processed: 113 average time/residue: 0.1100 time to fit residues: 18.5299 Evaluate side-chains 107 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 630 GLU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 755 LYS Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1106 SER Chi-restraints excluded: chain B residue 1172 SER Chi-restraints excluded: chain B residue 1265 TYR Chi-restraints excluded: chain B residue 1286 ASN Chi-restraints excluded: chain B residue 1302 ILE Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 20 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1091 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.069506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.055052 restraints weight = 78107.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.056703 restraints weight = 41266.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.057784 restraints weight = 27155.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.058508 restraints weight = 20591.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.058931 restraints weight = 17221.236| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13249 Z= 0.203 Angle : 0.590 10.225 18505 Z= 0.312 Chirality : 0.037 0.149 2128 Planarity : 0.004 0.086 1842 Dihedral : 19.586 92.234 3217 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.95 % Allowed : 14.00 % Favored : 82.05 % 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 are not related in a simple way. whole: 0.89 (0.25), residues: 1178 helix: 1.41 (0.21), residues: 597 sheet: -0.00 (0.55), residues: 85 loop : -0.22 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 629 TYR 0.018 0.002 TYR B1265 PHE 0.015 0.002 PHE B1046 TRP 0.011 0.002 TRP B 464 HIS 0.007 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00418 (13249) covalent geometry : angle 0.58977 (18505) hydrogen bonds : bond 0.04489 ( 590) hydrogen bonds : angle 4.77745 ( 1588) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 83 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.9232 (mmtt) cc_final: 0.8913 (tptt) REVERT: B 80 CYS cc_start: 0.8316 (m) cc_final: 0.8029 (m) REVERT: B 100 ARG cc_start: 0.8667 (mtm-85) cc_final: 0.7929 (mtm-85) REVERT: B 101 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8686 (mp) REVERT: B 271 TYR cc_start: 0.8903 (t80) cc_final: 0.8698 (t80) REVERT: B 483 ASP cc_start: 0.8008 (t0) cc_final: 0.7792 (t0) REVERT: B 569 PHE cc_start: 0.9439 (m-80) cc_final: 0.9153 (m-80) REVERT: B 698 HIS cc_start: 0.8914 (OUTLIER) cc_final: 0.8134 (t-90) REVERT: B 933 GLN cc_start: 0.9587 (tp-100) cc_final: 0.9100 (tp-100) REVERT: B 1043 MET cc_start: 0.5465 (ttp) cc_final: 0.5076 (tmm) REVERT: B 1108 GLU cc_start: 0.7814 (tt0) cc_final: 0.7497 (tt0) REVERT: B 1170 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8512 (mt-10) outliers start: 42 outliers final: 28 residues processed: 115 average time/residue: 0.1066 time to fit residues: 18.6069 Evaluate side-chains 103 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 698 HIS Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1106 SER Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain B residue 1172 SER Chi-restraints excluded: chain B residue 1265 TYR Chi-restraints excluded: chain B residue 1286 ASN Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 35 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 23 optimal weight: 0.3980 chunk 59 optimal weight: 0.3980 chunk 55 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 426 GLN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.070270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.055776 restraints weight = 76977.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.057465 restraints weight = 39865.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.058562 restraints weight = 26117.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.059298 restraints weight = 19782.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.059716 restraints weight = 16490.628| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13249 Z= 0.149 Angle : 0.559 12.096 18505 Z= 0.291 Chirality : 0.036 0.153 2128 Planarity : 0.004 0.054 1842 Dihedral : 19.554 90.187 3217 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.29 % Allowed : 14.66 % Favored : 82.05 % 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 are not related in a simple way. whole: 1.06 (0.25), residues: 1178 helix: 1.52 (0.21), residues: 597 sheet: 0.09 (0.55), residues: 85 loop : -0.11 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 629 TYR 0.019 0.001 TYR B1265 PHE 0.012 0.001 PHE B1046 TRP 0.013 0.001 TRP B 464 HIS 0.007 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00318 (13249) covalent geometry : angle 0.55880 (18505) hydrogen bonds : bond 0.04079 ( 590) hydrogen bonds : angle 4.66882 ( 1588) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.9231 (mmtt) cc_final: 0.8898 (tptt) REVERT: B 80 CYS cc_start: 0.8310 (m) cc_final: 0.8022 (m) REVERT: B 100 ARG cc_start: 0.8666 (mtm-85) cc_final: 0.7945 (mtm-85) REVERT: B 101 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8689 (mp) REVERT: B 374 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.8726 (ptmt) REVERT: B 383 MET cc_start: 0.8828 (tpp) cc_final: 0.8617 (tpp) REVERT: B 483 ASP cc_start: 0.8008 (t0) cc_final: 0.7788 (t0) REVERT: B 534 MET cc_start: 0.4463 (OUTLIER) cc_final: 0.4023 (ptt) REVERT: B 569 PHE cc_start: 0.9418 (m-80) cc_final: 0.9166 (m-80) REVERT: B 645 ASP cc_start: 0.9169 (p0) cc_final: 0.8821 (t0) REVERT: B 755 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8216 (ptmm) REVERT: B 1043 MET cc_start: 0.5386 (ttp) cc_final: 0.5012 (tmm) REVERT: B 1207 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7969 (pm20) REVERT: B 1357 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8755 (mp0) outliers start: 35 outliers final: 26 residues processed: 111 average time/residue: 0.1033 time to fit residues: 17.6090 Evaluate side-chains 107 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 755 LYS Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1182 LEU Chi-restraints excluded: chain B residue 1207 GLU Chi-restraints excluded: chain B residue 1265 TYR Chi-restraints excluded: chain B residue 1286 ASN Chi-restraints excluded: chain B residue 1302 ILE Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1352 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 17 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 GLN ** B 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1261 GLN B1272 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.065538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.051321 restraints weight = 81746.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.052801 restraints weight = 44158.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.053810 restraints weight = 29668.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.054453 restraints weight = 22813.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.054865 restraints weight = 19252.456| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 13249 Z= 0.403 Angle : 0.831 11.331 18505 Z= 0.439 Chirality : 0.046 0.212 2128 Planarity : 0.006 0.057 1842 Dihedral : 20.150 90.739 3217 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 29.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 4.51 % Allowed : 15.70 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.24), residues: 1178 helix: 0.45 (0.20), residues: 597 sheet: -0.50 (0.54), residues: 86 loop : -0.48 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 629 TYR 0.027 0.003 TYR B 25 PHE 0.022 0.003 PHE B1235 TRP 0.023 0.003 TRP B 464 HIS 0.009 0.003 HIS B1241 Details of bonding type rmsd covalent geometry : bond 0.00829 (13249) covalent geometry : angle 0.83068 (18505) hydrogen bonds : bond 0.07539 ( 590) hydrogen bonds : angle 5.59957 ( 1588) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 72 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.9242 (mmtt) cc_final: 0.8885 (tptt) REVERT: B 100 ARG cc_start: 0.8770 (mtm-85) cc_final: 0.8106 (mtm-85) REVERT: B 101 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8764 (mp) REVERT: B 161 MET cc_start: 0.8112 (ptt) cc_final: 0.7881 (ptm) REVERT: B 374 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8660 (ptmt) REVERT: B 534 MET cc_start: 0.4837 (OUTLIER) cc_final: 0.4404 (ptt) REVERT: B 569 PHE cc_start: 0.9517 (m-80) cc_final: 0.9229 (m-80) REVERT: B 698 HIS cc_start: 0.8930 (OUTLIER) cc_final: 0.8234 (t-90) REVERT: B 933 GLN cc_start: 0.9577 (tp-100) cc_final: 0.9099 (tp-100) REVERT: B 1043 MET cc_start: 0.5547 (ttp) cc_final: 0.5170 (tmm) REVERT: B 1108 GLU cc_start: 0.7669 (tt0) cc_final: 0.7246 (tt0) outliers start: 48 outliers final: 34 residues processed: 110 average time/residue: 0.0999 time to fit residues: 16.9601 Evaluate side-chains 105 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 67 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 374 LYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 698 HIS Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1106 SER Chi-restraints excluded: chain B residue 1120 ILE Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain B residue 1172 SER Chi-restraints excluded: chain B residue 1182 LEU Chi-restraints excluded: chain B residue 1203 LEU Chi-restraints excluded: chain B residue 1233 VAL Chi-restraints excluded: chain B residue 1265 TYR Chi-restraints excluded: chain B residue 1266 LEU Chi-restraints excluded: chain B residue 1286 ASN Chi-restraints excluded: chain B residue 1302 ILE Chi-restraints excluded: chain B residue 1342 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 68 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 HIS ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 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 = 0.3762 r_free = 0.3762 target = 0.068879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.054581 restraints weight = 77179.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.056179 restraints weight = 40825.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.057233 restraints weight = 27042.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.057894 restraints weight = 20587.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.058370 restraints weight = 17347.010| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13249 Z= 0.152 Angle : 0.595 12.104 18505 Z= 0.313 Chirality : 0.038 0.172 2128 Planarity : 0.006 0.224 1842 Dihedral : 19.864 90.464 3217 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.63 % Allowed : 17.67 % Favored : 79.70 % 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 are not related in a simple way. whole: 0.68 (0.25), residues: 1178 helix: 1.15 (0.21), residues: 595 sheet: -0.03 (0.57), residues: 84 loop : -0.20 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 629 TYR 0.043 0.002 TYR B 656 PHE 0.035 0.001 PHE B1008 TRP 0.014 0.001 TRP B 464 HIS 0.006 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00322 (13249) covalent geometry : angle 0.59458 (18505) hydrogen bonds : bond 0.04214 ( 590) hydrogen bonds : angle 4.84951 ( 1588) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.9168 (mmtt) cc_final: 0.8849 (tptt) REVERT: B 80 CYS cc_start: 0.8265 (m) cc_final: 0.7993 (m) REVERT: B 383 MET cc_start: 0.8773 (tpp) cc_final: 0.8471 (tpp) REVERT: B 534 MET cc_start: 0.4589 (ptt) cc_final: 0.4045 (ptt) REVERT: B 569 PHE cc_start: 0.9434 (m-80) cc_final: 0.9189 (m-80) REVERT: B 694 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.9144 (mmt) REVERT: B 698 HIS cc_start: 0.8967 (OUTLIER) cc_final: 0.8324 (t-90) REVERT: B 1043 MET cc_start: 0.5471 (ttp) cc_final: 0.5053 (tmm) REVERT: B 1357 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8753 (mp0) outliers start: 28 outliers final: 25 residues processed: 92 average time/residue: 0.0956 time to fit residues: 14.0031 Evaluate side-chains 94 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 698 HIS Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1167 THR Chi-restraints excluded: chain B residue 1172 SER Chi-restraints excluded: chain B residue 1182 LEU Chi-restraints excluded: chain B residue 1265 TYR Chi-restraints excluded: chain B residue 1286 ASN Chi-restraints excluded: chain B residue 1302 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 55 optimal weight: 0.4980 chunk 7 optimal weight: 20.0000 chunk 80 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 48 optimal weight: 0.2980 chunk 60 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 511 HIS ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 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 = 0.3750 r_free = 0.3750 target = 0.068530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.054255 restraints weight = 77284.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.055912 restraints weight = 40168.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.056978 restraints weight = 26251.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.057648 restraints weight = 19934.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.058063 restraints weight = 16768.326| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13249 Z= 0.157 Angle : 0.586 12.883 18505 Z= 0.308 Chirality : 0.037 0.167 2128 Planarity : 0.005 0.170 1842 Dihedral : 19.770 89.701 3217 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.63 % Allowed : 17.86 % Favored : 79.51 % 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 are not related in a simple way. whole: 0.71 (0.25), residues: 1178 helix: 1.19 (0.21), residues: 597 sheet: -0.30 (0.53), residues: 93 loop : -0.15 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 629 TYR 0.039 0.002 TYR B 656 PHE 0.044 0.001 PHE B1008 TRP 0.006 0.001 TRP B 476 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00333 (13249) covalent geometry : angle 0.58625 (18505) hydrogen bonds : bond 0.04337 ( 590) hydrogen bonds : angle 4.75927 ( 1588) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.9183 (mmtt) cc_final: 0.8829 (tptt) REVERT: B 80 CYS cc_start: 0.8358 (m) cc_final: 0.8065 (m) REVERT: B 383 MET cc_start: 0.8755 (tpp) cc_final: 0.8380 (tpp) REVERT: B 483 ASP cc_start: 0.8031 (t0) cc_final: 0.7281 (p0) REVERT: B 534 MET cc_start: 0.4593 (ptt) cc_final: 0.4091 (ptt) REVERT: B 569 PHE cc_start: 0.9465 (m-80) cc_final: 0.9226 (m-80) REVERT: B 694 MET cc_start: 0.9432 (OUTLIER) cc_final: 0.9200 (mmt) REVERT: B 698 HIS cc_start: 0.9002 (OUTLIER) cc_final: 0.8318 (t-90) REVERT: B 1043 MET cc_start: 0.5491 (ttp) cc_final: 0.5085 (tmm) REVERT: B 1357 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8780 (mp0) outliers start: 28 outliers final: 24 residues processed: 94 average time/residue: 0.0978 time to fit residues: 14.5730 Evaluate side-chains 91 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 698 HIS Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 980 ASN Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1182 LEU Chi-restraints excluded: chain B residue 1265 TYR Chi-restraints excluded: chain B residue 1286 ASN Chi-restraints excluded: chain B residue 1302 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 125 optimal weight: 0.0010 chunk 102 optimal weight: 0.4980 chunk 112 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 GLN ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.070375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.056135 restraints weight = 76741.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.057838 restraints weight = 39425.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.058966 restraints weight = 25704.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.059698 restraints weight = 19332.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.060107 restraints weight = 16098.584| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13249 Z= 0.120 Angle : 0.570 15.454 18505 Z= 0.294 Chirality : 0.036 0.168 2128 Planarity : 0.004 0.113 1842 Dihedral : 19.623 88.834 3217 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.97 % Allowed : 18.80 % Favored : 79.23 % 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 are not related in a simple way. whole: 0.90 (0.25), residues: 1178 helix: 1.32 (0.22), residues: 596 sheet: -0.00 (0.58), residues: 90 loop : -0.08 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 100 TYR 0.030 0.001 TYR B 656 PHE 0.051 0.001 PHE B1008 TRP 0.007 0.001 TRP B 464 HIS 0.012 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00259 (13249) covalent geometry : angle 0.56974 (18505) hydrogen bonds : bond 0.03680 ( 590) hydrogen bonds : angle 4.57797 ( 1588) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.9136 (mmtt) cc_final: 0.8764 (tptt) REVERT: B 80 CYS cc_start: 0.8278 (m) cc_final: 0.8005 (m) REVERT: B 383 MET cc_start: 0.8734 (tpp) cc_final: 0.8372 (tpp) REVERT: B 483 ASP cc_start: 0.8002 (t0) cc_final: 0.7345 (p0) REVERT: B 534 MET cc_start: 0.4519 (ptt) cc_final: 0.3991 (ptt) REVERT: B 569 PHE cc_start: 0.9440 (m-80) cc_final: 0.9206 (m-80) REVERT: B 645 ASP cc_start: 0.9265 (p0) cc_final: 0.8654 (t0) REVERT: B 679 ILE cc_start: 0.9230 (mm) cc_final: 0.9029 (mm) REVERT: B 694 MET cc_start: 0.9423 (OUTLIER) cc_final: 0.9192 (mmt) REVERT: B 698 HIS cc_start: 0.9010 (OUTLIER) cc_final: 0.8000 (t-90) REVERT: B 1043 MET cc_start: 0.5491 (ttp) cc_final: 0.5139 (tmm) REVERT: B 1357 GLU cc_start: 0.9249 (mt-10) cc_final: 0.8795 (mp0) outliers start: 21 outliers final: 18 residues processed: 92 average time/residue: 0.0906 time to fit residues: 13.6725 Evaluate side-chains 90 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 698 HIS Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 946 ASN Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1182 LEU Chi-restraints excluded: chain B residue 1265 TYR Chi-restraints excluded: chain B residue 1302 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 58 optimal weight: 0.4980 chunk 106 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 34 optimal weight: 0.0000 chunk 24 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 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 = 0.3779 r_free = 0.3779 target = 0.069926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.055693 restraints weight = 77464.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.057377 restraints weight = 40108.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.058467 restraints weight = 26076.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.059129 restraints weight = 19758.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.059588 restraints weight = 16641.976| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13249 Z= 0.125 Angle : 0.576 13.680 18505 Z= 0.296 Chirality : 0.036 0.184 2128 Planarity : 0.004 0.053 1842 Dihedral : 19.550 87.615 3217 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.88 % Allowed : 19.17 % Favored : 78.95 % 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 are not related in a simple way. whole: 0.94 (0.25), residues: 1178 helix: 1.39 (0.22), residues: 597 sheet: -0.34 (0.54), residues: 99 loop : -0.03 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 654 TYR 0.028 0.001 TYR B 271 PHE 0.048 0.001 PHE B1008 TRP 0.009 0.001 TRP B 464 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00270 (13249) covalent geometry : angle 0.57578 (18505) hydrogen bonds : bond 0.03774 ( 590) hydrogen bonds : angle 4.56589 ( 1588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2500.43 seconds wall clock time: 44 minutes 4.62 seconds (2644.62 seconds total)