Starting phenix.real_space_refine on Wed May 14 15:54:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t79_41088/05_2025/8t79_41088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t79_41088/05_2025/8t79_41088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t79_41088/05_2025/8t79_41088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t79_41088/05_2025/8t79_41088.map" model { file = "/net/cci-nas-00/data/ceres_data/8t79_41088/05_2025/8t79_41088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t79_41088/05_2025/8t79_41088.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 118 5.49 5 S 18 5.16 5 C 7154 2.51 5 N 2083 2.21 5 O 2530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11903 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 9406 Classifications: {'peptide': 1146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 1112} Chain breaks: 6 Chain: "B" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1905 Classifications: {'RNA': 89} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 46, 'rna3p_pyr': 32} Link IDs: {'rna2p': 10, 'rna3p': 78} Chain: "C" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 401 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 191 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Time building chain proxies: 8.27, per 1000 atoms: 0.69 Number of scatterers: 11903 At special positions: 0 Unit cell: (85.8196, 123.314, 123.314, 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 18 16.00 P 118 15.00 O 2530 8.00 N 2083 7.00 C 7154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.4 seconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2186 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 7 sheets defined 52.8% alpha, 8.5% beta 40 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 4.68 Creating SS restraints... Processing helix chain 'A' and resid 59 through 91 removed outlier: 4.762A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.928A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 184 through 196 Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.525A pdb=" N SER A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 removed outlier: 4.766A pdb=" N GLU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 289 through 306 Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 345 through 352 removed outlier: 4.578A pdb=" N GLU A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.911A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.197A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.703A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 512 through 526 removed outlier: 4.810A pdb=" N TYR A 521 " --> pdb=" O TYR A 517 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 524 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 569 removed outlier: 3.912A pdb=" N TYR A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.656A pdb=" N LEU A 616 " --> pdb=" O ASN A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 643 removed outlier: 5.266A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 643 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 654 removed outlier: 3.537A pdb=" N MET A 648 " --> pdb=" O ASP A 644 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 668 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.647A pdb=" N ASN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.866A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 926 Processing helix chain 'A' and resid 927 through 929 No H-bonds generated for 'chain 'A' and resid 927 through 929' Processing helix chain 'A' and resid 930 through 940 Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.926A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.469A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 3.865A pdb=" N PHE A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1047 removed outlier: 4.194A pdb=" N PHE A1045 " --> pdb=" O ILE A1042 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A1046 " --> pdb=" O MET A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1088 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.762A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1263 through 1280 removed outlier: 4.093A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1296 Processing helix chain 'A' and resid 1301 through 1313 Processing helix chain 'A' and resid 1314 through 1316 No H-bonds generated for 'chain 'A' and resid 1314 through 1316' Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.708A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1340 through 1344' Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 958 removed outlier: 5.708A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU A 958 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE A 761 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU A 762 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A 11 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 10.030A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLN A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 509 removed outlier: 4.998A pdb=" N LEU A 508 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 528 through 529 removed outlier: 3.848A pdb=" N ALA A 538 " --> pdb=" O TYR A 529 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1063 through 1065 Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 4.088A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A1158 " --> pdb=" O VAL A1149 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1325 removed outlier: 3.857A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 6.23 Time building geometry restraints manager: 3.72 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: 2671 1.33 - 1.45: 3151 1.45 - 1.57: 6280 1.57 - 1.70: 234 1.70 - 1.82: 35 Bond restraints: 12371 Sorted by residual: bond pdb=" CB GLN A 650 " pdb=" CG GLN A 650 " ideal model delta sigma weight residual 1.520 1.578 -0.058 3.00e-02 1.11e+03 3.73e+00 bond pdb=" CB LYS A 959 " pdb=" CG LYS A 959 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.26e+00 bond pdb=" CB ASP A 273 " pdb=" CG ASP A 273 " ideal model delta sigma weight residual 1.516 1.560 -0.044 2.50e-02 1.60e+03 3.12e+00 bond pdb=" CB ASP A 596 " pdb=" CG ASP A 596 " ideal model delta sigma weight residual 1.516 1.560 -0.044 2.50e-02 1.60e+03 3.03e+00 bond pdb=" CG ASP A 965 " pdb=" OD1 ASP A 965 " ideal model delta sigma weight residual 1.249 1.216 0.033 1.90e-02 2.77e+03 2.94e+00 ... (remaining 12366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 16978 3.59 - 7.18: 187 7.18 - 10.77: 24 10.77 - 14.36: 9 14.36 - 17.94: 3 Bond angle restraints: 17201 Sorted by residual: angle pdb=" CA GLU A1271 " pdb=" CB GLU A1271 " pdb=" CG GLU A1271 " ideal model delta sigma weight residual 114.10 125.93 -11.83 2.00e+00 2.50e-01 3.50e+01 angle pdb=" CB MET A 939 " pdb=" CG MET A 939 " pdb=" SD MET A 939 " ideal model delta sigma weight residual 112.70 130.11 -17.41 3.00e+00 1.11e-01 3.37e+01 angle pdb=" CA LEU A 651 " pdb=" CB LEU A 651 " pdb=" CG LEU A 651 " ideal model delta sigma weight residual 116.30 134.24 -17.94 3.50e+00 8.16e-02 2.63e+01 angle pdb=" CA LYS A 649 " pdb=" CB LYS A 649 " pdb=" CG LYS A 649 " ideal model delta sigma weight residual 114.10 124.04 -9.94 2.00e+00 2.50e-01 2.47e+01 angle pdb=" CA LYS A1263 " pdb=" CB LYS A1263 " pdb=" CG LYS A1263 " ideal model delta sigma weight residual 114.10 123.90 -9.80 2.00e+00 2.50e-01 2.40e+01 ... (remaining 17196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.41: 6971 30.41 - 60.82: 481 60.82 - 91.22: 80 91.22 - 121.63: 1 121.63 - 152.04: 1 Dihedral angle restraints: 7534 sinusoidal: 4164 harmonic: 3370 Sorted by residual: dihedral pdb=" CA PHE A 238 " pdb=" C PHE A 238 " pdb=" N GLY A 239 " pdb=" CA GLY A 239 " ideal model delta harmonic sigma weight residual 180.00 145.70 34.30 0 5.00e+00 4.00e-02 4.71e+01 dihedral pdb=" CA TYR A 517 " pdb=" C TYR A 517 " pdb=" N PHE A 518 " pdb=" CA PHE A 518 " ideal model delta harmonic sigma weight residual 180.00 157.69 22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA PRO A1128 " pdb=" C PRO A1128 " pdb=" N LYS A1129 " pdb=" CA LYS A1129 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 7531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1842 0.098 - 0.196: 126 0.196 - 0.294: 9 0.294 - 0.392: 2 0.392 - 0.490: 1 Chirality restraints: 1980 Sorted by residual: chirality pdb=" CB ILE A 670 " pdb=" CA ILE A 670 " pdb=" CG1 ILE A 670 " pdb=" CG2 ILE A 670 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" P DT C 23 " pdb=" OP1 DT C 23 " pdb=" OP2 DT C 23 " pdb=" O5' DT C 23 " both_signs ideal model delta sigma weight residual True 2.35 -2.73 -0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CB ILE A1309 " pdb=" CA ILE A1309 " pdb=" CG1 ILE A1309 " pdb=" CG2 ILE A1309 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 1977 not shown) Planarity restraints: 1755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A1265 " -0.022 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C TYR A1265 " 0.076 2.00e-02 2.50e+03 pdb=" O TYR A1265 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU A1266 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 14 " 0.025 2.00e-02 2.50e+03 2.73e-02 1.86e+01 pdb=" N1 DT C 14 " -0.071 2.00e-02 2.50e+03 pdb=" C2 DT C 14 " 0.036 2.00e-02 2.50e+03 pdb=" O2 DT C 14 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DT C 14 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT C 14 " -0.008 2.00e-02 2.50e+03 pdb=" O4 DT C 14 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DT C 14 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT C 14 " 0.018 2.00e-02 2.50e+03 pdb=" C6 DT C 14 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 655 " -0.317 9.50e-02 1.11e+02 1.43e-01 1.60e+01 pdb=" NE ARG A 655 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 655 " -0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG A 655 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 655 " -0.000 2.00e-02 2.50e+03 ... (remaining 1752 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2060 2.77 - 3.30: 11117 3.30 - 3.84: 21148 3.84 - 4.37: 24800 4.37 - 4.90: 38819 Nonbonded interactions: 97944 Sorted by model distance: nonbonded pdb=" OE1 GLN A 402 " pdb=" O2' U B 44 " model vdw 2.241 3.040 nonbonded pdb=" O ALA A 299 " pdb=" OG SER A 303 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR A1167 " pdb=" OE1 GLU A1170 " model vdw 2.298 3.040 nonbonded pdb=" OD2 ASP A 618 " pdb=" OH TYR A 639 " model vdw 2.300 3.040 nonbonded pdb=" OH TYR A 373 " pdb=" O LEU A 398 " model vdw 2.302 3.040 ... (remaining 97939 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 36.260 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.005 0.058 12371 Z= 0.215 Angle : 1.004 17.945 17201 Z= 0.508 Chirality : 0.054 0.490 1980 Planarity : 0.008 0.143 1755 Dihedral : 18.700 152.041 5348 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.39 % Allowed : 15.60 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.22), residues: 1132 helix: -0.63 (0.21), residues: 516 sheet: -1.17 (0.47), residues: 96 loop : -1.36 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1136 HIS 0.014 0.002 HIS A 930 PHE 0.034 0.002 PHE A 185 TYR 0.033 0.002 TYR A 988 ARG 0.033 0.001 ARG A 655 Details of bonding type rmsd hydrogen bonds : bond 0.13386 ( 506) hydrogen bonds : angle 6.38618 ( 1387) covalent geometry : bond 0.00457 (12371) covalent geometry : angle 1.00369 (17201) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TYR cc_start: 0.8531 (p90) cc_final: 0.8262 (p90) REVERT: A 1313 PHE cc_start: 0.8939 (m-80) cc_final: 0.8336 (m-80) outliers start: 4 outliers final: 2 residues processed: 97 average time/residue: 0.2326 time to fit residues: 33.6209 Evaluate side-chains 92 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 1095 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN A1264 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.119970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.076153 restraints weight = 28391.312| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.24 r_work: 0.3040 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12371 Z= 0.198 Angle : 0.612 9.738 17201 Z= 0.323 Chirality : 0.040 0.205 1980 Planarity : 0.004 0.060 1755 Dihedral : 18.963 159.328 2897 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.71 % Allowed : 11.63 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.24), residues: 1132 helix: 0.18 (0.22), residues: 533 sheet: -0.89 (0.47), residues: 105 loop : -1.04 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1136 HIS 0.004 0.001 HIS A 116 PHE 0.013 0.001 PHE A1235 TYR 0.018 0.001 TYR A 988 ARG 0.004 0.001 ARG A 215 Details of bonding type rmsd hydrogen bonds : bond 0.04481 ( 506) hydrogen bonds : angle 4.84515 ( 1387) covalent geometry : bond 0.00422 (12371) covalent geometry : angle 0.61173 (17201) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ARG cc_start: 0.7310 (mmp-170) cc_final: 0.7035 (mmp-170) REVERT: A 370 GLU cc_start: 0.9252 (tp30) cc_final: 0.9001 (tp30) REVERT: A 534 MET cc_start: 0.1470 (ptt) cc_final: 0.1250 (ptt) REVERT: A 1001 TYR cc_start: 0.6331 (m-10) cc_final: 0.5981 (m-10) REVERT: A 1297 HIS cc_start: 0.9142 (m90) cc_final: 0.8831 (m-70) REVERT: A 1313 PHE cc_start: 0.9036 (m-80) cc_final: 0.8325 (m-80) outliers start: 28 outliers final: 17 residues processed: 117 average time/residue: 0.2373 time to fit residues: 40.8055 Evaluate side-chains 109 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1242 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 88 optimal weight: 0.2980 chunk 100 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN A 497 ASN A 721 HIS A 983 HIS A1066 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.121305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.077723 restraints weight = 28605.767| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.25 r_work: 0.3070 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12371 Z= 0.119 Angle : 0.545 8.980 17201 Z= 0.287 Chirality : 0.037 0.192 1980 Planarity : 0.003 0.057 1755 Dihedral : 18.849 154.273 2894 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.33 % Allowed : 13.08 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.24), residues: 1132 helix: 0.56 (0.23), residues: 532 sheet: -0.73 (0.49), residues: 103 loop : -0.79 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1136 HIS 0.007 0.001 HIS A 723 PHE 0.012 0.001 PHE A1235 TYR 0.022 0.001 TYR A 5 ARG 0.003 0.000 ARG A 215 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 506) hydrogen bonds : angle 4.53421 ( 1387) covalent geometry : bond 0.00248 (12371) covalent geometry : angle 0.54508 (17201) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9189 (mm) REVERT: A 370 GLU cc_start: 0.9244 (tp30) cc_final: 0.8984 (tp30) REVERT: A 933 GLN cc_start: 0.8839 (mt0) cc_final: 0.8484 (mp10) REVERT: A 1297 HIS cc_start: 0.9148 (m90) cc_final: 0.8843 (m-70) REVERT: A 1313 PHE cc_start: 0.8919 (m-80) cc_final: 0.8717 (m-80) outliers start: 24 outliers final: 18 residues processed: 105 average time/residue: 0.2260 time to fit residues: 35.2886 Evaluate side-chains 106 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1253 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 105 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 109 optimal weight: 0.0970 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN A 497 ASN A 641 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.117151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.073194 restraints weight = 28812.501| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.25 r_work: 0.2974 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12371 Z= 0.278 Angle : 0.633 8.263 17201 Z= 0.332 Chirality : 0.041 0.188 1980 Planarity : 0.004 0.057 1755 Dihedral : 18.921 156.997 2894 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.00 % Allowed : 14.44 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.24), residues: 1132 helix: 0.46 (0.23), residues: 534 sheet: -0.74 (0.49), residues: 112 loop : -0.78 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1136 HIS 0.010 0.001 HIS A 511 PHE 0.032 0.002 PHE A 682 TYR 0.033 0.002 TYR A 5 ARG 0.004 0.000 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.04665 ( 506) hydrogen bonds : angle 4.70559 ( 1387) covalent geometry : bond 0.00604 (12371) covalent geometry : angle 0.63269 (17201) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9227 (mm) REVERT: A 370 GLU cc_start: 0.9304 (tp30) cc_final: 0.9071 (tp30) REVERT: A 933 GLN cc_start: 0.8866 (mt0) cc_final: 0.8486 (mp10) REVERT: A 1297 HIS cc_start: 0.9057 (m90) cc_final: 0.8797 (m-70) outliers start: 31 outliers final: 20 residues processed: 106 average time/residue: 0.2266 time to fit residues: 36.0586 Evaluate side-chains 107 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1253 GLU Chi-restraints excluded: chain A residue 1290 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 55 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 88 optimal weight: 0.1980 chunk 82 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 27 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN A 497 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.119886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.076226 restraints weight = 28386.459| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.21 r_work: 0.3044 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12371 Z= 0.118 Angle : 0.530 8.349 17201 Z= 0.278 Chirality : 0.037 0.196 1980 Planarity : 0.003 0.053 1755 Dihedral : 18.889 153.523 2894 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.42 % Allowed : 15.41 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.25), residues: 1132 helix: 0.74 (0.23), residues: 535 sheet: -0.53 (0.50), residues: 112 loop : -0.61 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 659 HIS 0.006 0.001 HIS A 723 PHE 0.028 0.001 PHE A 682 TYR 0.015 0.001 TYR A 5 ARG 0.002 0.000 ARG A 494 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 506) hydrogen bonds : angle 4.42796 ( 1387) covalent geometry : bond 0.00234 (12371) covalent geometry : angle 0.53012 (17201) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7744 (pt0) REVERT: A 156 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9192 (mm) REVERT: A 331 ASP cc_start: 0.8803 (m-30) cc_final: 0.8519 (m-30) REVERT: A 370 GLU cc_start: 0.9288 (tp30) cc_final: 0.9040 (tp30) REVERT: A 933 GLN cc_start: 0.8808 (mt0) cc_final: 0.8417 (mp10) REVERT: A 1297 HIS cc_start: 0.9049 (m90) cc_final: 0.8792 (m-70) outliers start: 25 outliers final: 16 residues processed: 107 average time/residue: 0.2329 time to fit residues: 37.3829 Evaluate side-chains 104 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1253 GLU Chi-restraints excluded: chain A residue 1290 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 27 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 49 optimal weight: 0.0570 chunk 30 optimal weight: 0.1980 chunk 96 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 67 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.120185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.076991 restraints weight = 28849.333| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.22 r_work: 0.3057 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12371 Z= 0.107 Angle : 0.514 8.897 17201 Z= 0.270 Chirality : 0.037 0.195 1980 Planarity : 0.003 0.047 1755 Dihedral : 18.721 152.057 2894 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.03 % Allowed : 16.28 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.25), residues: 1132 helix: 0.90 (0.23), residues: 533 sheet: -0.27 (0.53), residues: 107 loop : -0.65 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1136 HIS 0.005 0.001 HIS A 723 PHE 0.029 0.001 PHE A1276 TYR 0.013 0.001 TYR A 5 ARG 0.002 0.000 ARG A 494 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 506) hydrogen bonds : angle 4.36727 ( 1387) covalent geometry : bond 0.00223 (12371) covalent geometry : angle 0.51362 (17201) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7745 (pt0) REVERT: A 156 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9221 (mm) REVERT: A 331 ASP cc_start: 0.8783 (m-30) cc_final: 0.8481 (m-30) REVERT: A 370 GLU cc_start: 0.9287 (tp30) cc_final: 0.9043 (tp30) REVERT: A 933 GLN cc_start: 0.8811 (mt0) cc_final: 0.8418 (mp10) REVERT: A 1297 HIS cc_start: 0.9088 (m90) cc_final: 0.8781 (m-70) outliers start: 21 outliers final: 13 residues processed: 106 average time/residue: 0.2255 time to fit residues: 35.9358 Evaluate side-chains 104 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1253 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 97 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 17 optimal weight: 0.1980 chunk 117 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.116885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.073292 restraints weight = 28938.523| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.22 r_work: 0.2976 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12371 Z= 0.259 Angle : 0.603 8.866 17201 Z= 0.314 Chirality : 0.040 0.189 1980 Planarity : 0.004 0.048 1755 Dihedral : 18.786 155.111 2894 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.33 % Allowed : 16.28 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.25), residues: 1132 helix: 0.80 (0.23), residues: 533 sheet: -0.26 (0.51), residues: 105 loop : -0.71 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1136 HIS 0.004 0.001 HIS A 412 PHE 0.026 0.002 PHE A1276 TYR 0.020 0.002 TYR A 5 ARG 0.004 0.000 ARG A 494 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 506) hydrogen bonds : angle 4.52492 ( 1387) covalent geometry : bond 0.00561 (12371) covalent geometry : angle 0.60252 (17201) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9224 (mm) REVERT: A 331 ASP cc_start: 0.8776 (m-30) cc_final: 0.8488 (m-30) REVERT: A 370 GLU cc_start: 0.9349 (tp30) cc_final: 0.9111 (tp30) REVERT: A 933 GLN cc_start: 0.8829 (mt0) cc_final: 0.8488 (mp10) REVERT: A 1297 HIS cc_start: 0.8990 (m90) cc_final: 0.8764 (m-70) outliers start: 24 outliers final: 17 residues processed: 100 average time/residue: 0.2410 time to fit residues: 35.8224 Evaluate side-chains 104 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1253 GLU Chi-restraints excluded: chain A residue 1290 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 50 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.118787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.075435 restraints weight = 28735.842| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.19 r_work: 0.3024 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12371 Z= 0.125 Angle : 0.538 9.178 17201 Z= 0.280 Chirality : 0.037 0.196 1980 Planarity : 0.003 0.046 1755 Dihedral : 18.724 152.975 2894 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.94 % Allowed : 16.96 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1132 helix: 0.99 (0.23), residues: 531 sheet: -0.38 (0.50), residues: 112 loop : -0.53 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 464 HIS 0.005 0.001 HIS A 723 PHE 0.023 0.001 PHE A1276 TYR 0.017 0.001 TYR A 5 ARG 0.003 0.000 ARG A 655 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 506) hydrogen bonds : angle 4.39533 ( 1387) covalent geometry : bond 0.00267 (12371) covalent geometry : angle 0.53759 (17201) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9220 (mm) REVERT: A 331 ASP cc_start: 0.8758 (m-30) cc_final: 0.8452 (m-30) REVERT: A 370 GLU cc_start: 0.9309 (tp30) cc_final: 0.9067 (tp30) REVERT: A 933 GLN cc_start: 0.8802 (mt0) cc_final: 0.8430 (mp10) REVERT: A 1297 HIS cc_start: 0.9032 (m90) cc_final: 0.8786 (m-70) outliers start: 20 outliers final: 16 residues processed: 101 average time/residue: 0.2392 time to fit residues: 35.8806 Evaluate side-chains 103 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1253 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 106 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 83 optimal weight: 0.3980 chunk 103 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.117322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.073907 restraints weight = 28557.073| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.15 r_work: 0.2994 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12371 Z= 0.197 Angle : 0.588 12.167 17201 Z= 0.302 Chirality : 0.039 0.193 1980 Planarity : 0.003 0.048 1755 Dihedral : 18.678 154.162 2894 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.84 % Allowed : 17.15 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1132 helix: 0.90 (0.23), residues: 533 sheet: -0.16 (0.51), residues: 105 loop : -0.57 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1136 HIS 0.004 0.001 HIS A 723 PHE 0.039 0.002 PHE A1235 TYR 0.022 0.001 TYR A 5 ARG 0.005 0.000 ARG A 655 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 506) hydrogen bonds : angle 4.46908 ( 1387) covalent geometry : bond 0.00429 (12371) covalent geometry : angle 0.58830 (17201) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9227 (mm) REVERT: A 331 ASP cc_start: 0.8777 (m-30) cc_final: 0.8477 (m-30) REVERT: A 370 GLU cc_start: 0.9323 (tp30) cc_final: 0.9082 (tp30) REVERT: A 933 GLN cc_start: 0.8816 (mt0) cc_final: 0.8475 (mp10) outliers start: 19 outliers final: 14 residues processed: 97 average time/residue: 0.2436 time to fit residues: 34.8875 Evaluate side-chains 101 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1253 GLU Chi-restraints excluded: chain A residue 1286 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 698 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.117838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.074357 restraints weight = 28552.523| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.15 r_work: 0.3007 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12371 Z= 0.163 Angle : 0.564 9.562 17201 Z= 0.290 Chirality : 0.038 0.195 1980 Planarity : 0.003 0.046 1755 Dihedral : 18.665 153.406 2894 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.55 % Allowed : 17.15 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1132 helix: 0.97 (0.23), residues: 533 sheet: -0.41 (0.50), residues: 112 loop : -0.49 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1136 HIS 0.004 0.001 HIS A 723 PHE 0.039 0.002 PHE A1235 TYR 0.017 0.001 TYR A 5 ARG 0.005 0.000 ARG A 655 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 506) hydrogen bonds : angle 4.41939 ( 1387) covalent geometry : bond 0.00355 (12371) covalent geometry : angle 0.56430 (17201) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ASP cc_start: 0.8735 (m-30) cc_final: 0.8427 (m-30) REVERT: A 370 GLU cc_start: 0.9306 (tp30) cc_final: 0.9076 (tp30) REVERT: A 596 ASP cc_start: 0.8509 (t0) cc_final: 0.8137 (m-30) REVERT: A 933 GLN cc_start: 0.8838 (mt0) cc_final: 0.8488 (mp10) outliers start: 16 outliers final: 13 residues processed: 98 average time/residue: 0.2487 time to fit residues: 35.6085 Evaluate side-chains 100 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1253 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 122 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 723 HIS ** 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 = 0.3982 r_free = 0.3982 target = 0.116290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.072750 restraints weight = 28553.154| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.15 r_work: 0.2973 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12371 Z= 0.229 Angle : 0.613 9.434 17201 Z= 0.314 Chirality : 0.040 0.192 1980 Planarity : 0.003 0.048 1755 Dihedral : 18.708 154.964 2894 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.94 % Allowed : 17.25 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1132 helix: 0.83 (0.23), residues: 540 sheet: -0.22 (0.51), residues: 105 loop : -0.48 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1074 HIS 0.004 0.001 HIS A 167 PHE 0.035 0.002 PHE A1235 TYR 0.023 0.002 TYR A 988 ARG 0.005 0.000 ARG A 629 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 506) hydrogen bonds : angle 4.46854 ( 1387) covalent geometry : bond 0.00501 (12371) covalent geometry : angle 0.61261 (17201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7585.23 seconds wall clock time: 131 minutes 36.18 seconds (7896.18 seconds total)