Starting phenix.real_space_refine on Mon Dec 30 02:23:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t79_41088/12_2024/8t79_41088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t79_41088/12_2024/8t79_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_41088/12_2024/8t79_41088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t79_41088/12_2024/8t79_41088.map" model { file = "/net/cci-nas-00/data/ceres_data/8t79_41088/12_2024/8t79_41088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t79_41088/12_2024/8t79_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-5532/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: 8.39, per 1000 atoms: 0.70 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: 3.05 Conformation dependent library (CDL) restraints added in 1.3 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: 4.43 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: 6.09 Time building geometry restraints manager: 3.50 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: 3.240 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 34.330 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.280 ------------------------------------------------------------------------------- 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= 0.286 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 *********************** 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 : 1.243 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: 0.2390 time to fit residues: 34.6089 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 : 1.146 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 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= 0.267 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 *********************** 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 : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ARG cc_start: 0.7323 (mmp-170) cc_final: 0.7045 (mmp-170) REVERT: A 370 GLU cc_start: 0.9322 (tp30) cc_final: 0.9047 (tp30) REVERT: A 1001 TYR cc_start: 0.6203 (m-10) cc_final: 0.5878 (m-10) REVERT: A 1297 HIS cc_start: 0.9117 (m90) cc_final: 0.8807 (m-70) REVERT: A 1313 PHE cc_start: 0.9012 (m-80) cc_final: 0.8300 (m-80) outliers start: 28 outliers final: 17 residues processed: 117 average time/residue: 0.2437 time to fit residues: 41.9115 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 : 1.197 ------------------------------------------------------------------------------- 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 62 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 76 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 983 HIS A1066 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12371 Z= 0.212 Angle : 0.560 8.879 17201 Z= 0.296 Chirality : 0.038 0.194 1980 Planarity : 0.003 0.057 1755 Dihedral : 18.868 154.748 2894 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.33 % Allowed : 13.37 % Favored : 84.30 % 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: -0.30 (0.24), residues: 1132 helix: 0.53 (0.23), residues: 532 sheet: -0.58 (0.49), residues: 105 loop : -0.84 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1136 HIS 0.006 0.001 HIS A 723 PHE 0.013 0.001 PHE A1235 TYR 0.022 0.001 TYR A 5 ARG 0.003 0.000 ARG A1078 *********************** 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 117 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9219 (mm) REVERT: A 370 GLU cc_start: 0.9311 (tp30) cc_final: 0.9052 (tp30) REVERT: A 630 GLU cc_start: 0.9015 (pm20) cc_final: 0.8709 (pm20) REVERT: A 933 GLN cc_start: 0.8824 (mt0) cc_final: 0.8480 (mp10) REVERT: A 1297 HIS cc_start: 0.9095 (m90) cc_final: 0.8810 (m170) outliers start: 24 outliers final: 19 residues processed: 104 average time/residue: 0.2405 time to fit residues: 37.5324 Evaluate side-chains 105 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 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 495 MET 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 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 111 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 58 optimal weight: 0.0570 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 30.0000 chunk 75 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12371 Z= 0.218 Angle : 0.543 8.837 17201 Z= 0.287 Chirality : 0.038 0.191 1980 Planarity : 0.003 0.056 1755 Dihedral : 18.820 154.746 2894 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.42 % Allowed : 14.63 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.16 (0.25), residues: 1132 helix: 0.64 (0.23), residues: 534 sheet: -0.64 (0.49), residues: 112 loop : -0.71 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1136 HIS 0.010 0.001 HIS A 511 PHE 0.035 0.002 PHE A 682 TYR 0.016 0.001 TYR A 988 ARG 0.003 0.000 ARG A 494 *********************** 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 116 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9225 (mm) REVERT: A 370 GLU cc_start: 0.9313 (tp30) cc_final: 0.9055 (tp30) REVERT: A 630 GLU cc_start: 0.9012 (pm20) cc_final: 0.8699 (pm20) REVERT: A 751 MET cc_start: 0.8970 (mtp) cc_final: 0.8709 (mtp) REVERT: A 933 GLN cc_start: 0.8828 (mt0) cc_final: 0.8479 (mp10) REVERT: A 1297 HIS cc_start: 0.9072 (m90) cc_final: 0.8768 (m-70) outliers start: 25 outliers final: 17 residues processed: 104 average time/residue: 0.2285 time to fit residues: 36.0170 Evaluate side-chains 103 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 495 MET 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 1242 TYR Chi-restraints excluded: chain A residue 1253 GLU Chi-restraints excluded: chain A residue 1286 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 chunk 1 optimal weight: 0.6980 chunk 89 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 102 optimal weight: 0.1980 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12371 Z= 0.149 Angle : 0.514 8.334 17201 Z= 0.271 Chirality : 0.037 0.195 1980 Planarity : 0.003 0.053 1755 Dihedral : 18.776 152.769 2894 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.62 % Allowed : 15.31 % Favored : 82.07 % 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: 0.04 (0.25), residues: 1132 helix: 0.81 (0.23), residues: 534 sheet: -0.43 (0.51), residues: 112 loop : -0.66 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 659 HIS 0.006 0.001 HIS A 723 PHE 0.025 0.001 PHE A 682 TYR 0.013 0.001 TYR A 988 ARG 0.004 0.000 ARG A 629 *********************** 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 122 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7732 (pt0) REVERT: A 156 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9215 (mm) REVERT: A 370 GLU cc_start: 0.9302 (tp30) cc_final: 0.9037 (tp30) REVERT: A 751 MET cc_start: 0.8915 (mtp) cc_final: 0.8667 (mtp) REVERT: A 933 GLN cc_start: 0.8831 (mt0) cc_final: 0.8487 (mp10) REVERT: A 1297 HIS cc_start: 0.9079 (m90) cc_final: 0.8796 (m-70) outliers start: 27 outliers final: 19 residues processed: 112 average time/residue: 0.2227 time to fit residues: 37.8904 Evaluate side-chains 106 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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 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 495 MET Chi-restraints excluded: chain A residue 630 GLU 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 1242 TYR Chi-restraints excluded: chain A residue 1253 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 23 optimal weight: 0.0010 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 30.0000 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12371 Z= 0.209 Angle : 0.540 8.927 17201 Z= 0.282 Chirality : 0.037 0.193 1980 Planarity : 0.003 0.052 1755 Dihedral : 18.714 153.247 2894 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.71 % Allowed : 15.60 % 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: 0.08 (0.25), residues: 1132 helix: 0.84 (0.23), residues: 534 sheet: -0.32 (0.52), residues: 107 loop : -0.66 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1136 HIS 0.004 0.001 HIS A 723 PHE 0.019 0.001 PHE A 682 TYR 0.016 0.001 TYR A 5 ARG 0.003 0.000 ARG A 494 *********************** 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 122 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7769 (pt0) REVERT: A 156 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9214 (mm) REVERT: A 370 GLU cc_start: 0.9327 (tp30) cc_final: 0.9070 (tp30) REVERT: A 645 ASP cc_start: 0.8684 (m-30) cc_final: 0.8310 (m-30) REVERT: A 751 MET cc_start: 0.8944 (mtp) cc_final: 0.8661 (mtp) REVERT: A 933 GLN cc_start: 0.8849 (mt0) cc_final: 0.8461 (mp10) REVERT: A 1297 HIS cc_start: 0.9055 (m90) cc_final: 0.8765 (m-70) outliers start: 28 outliers final: 21 residues processed: 110 average time/residue: 0.2273 time to fit residues: 37.5751 Evaluate side-chains 110 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 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 495 MET Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 949 LEU 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 1286 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 87 optimal weight: 0.2980 chunk 67 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 74 optimal weight: 0.0370 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 30.0000 overall best weight: 1.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12371 Z= 0.223 Angle : 0.557 8.889 17201 Z= 0.290 Chirality : 0.038 0.194 1980 Planarity : 0.003 0.050 1755 Dihedral : 18.707 153.347 2894 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.33 % Allowed : 16.86 % 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: 0.11 (0.25), residues: 1132 helix: 0.85 (0.23), residues: 534 sheet: -0.40 (0.50), residues: 112 loop : -0.60 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1136 HIS 0.003 0.001 HIS A 167 PHE 0.017 0.001 PHE A1276 TYR 0.017 0.001 TYR A 5 ARG 0.003 0.000 ARG A 629 *********************** 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 : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7748 (pt0) REVERT: A 370 GLU cc_start: 0.9329 (tp30) cc_final: 0.9073 (tp30) REVERT: A 751 MET cc_start: 0.8939 (mtp) cc_final: 0.8634 (mtp) REVERT: A 933 GLN cc_start: 0.8839 (mt0) cc_final: 0.8448 (mp10) REVERT: A 1297 HIS cc_start: 0.9049 (m90) cc_final: 0.8784 (m-70) outliers start: 24 outliers final: 18 residues processed: 103 average time/residue: 0.2380 time to fit residues: 36.5065 Evaluate side-chains 107 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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 185 PHE 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 495 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 30.0000 chunk 75 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12371 Z= 0.260 Angle : 0.569 8.897 17201 Z= 0.295 Chirality : 0.039 0.193 1980 Planarity : 0.003 0.048 1755 Dihedral : 18.708 154.306 2894 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.03 % Allowed : 16.76 % Favored : 81.20 % 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: 0.11 (0.25), residues: 1132 helix: 0.85 (0.23), residues: 533 sheet: -0.41 (0.50), residues: 112 loop : -0.58 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1136 HIS 0.004 0.001 HIS A 167 PHE 0.018 0.002 PHE A1313 TYR 0.016 0.001 TYR A 5 ARG 0.003 0.000 ARG A 629 *********************** 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 112 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.9352 (tp30) cc_final: 0.9100 (tp30) REVERT: A 751 MET cc_start: 0.8915 (mtp) cc_final: 0.8581 (mtp) REVERT: A 933 GLN cc_start: 0.8817 (mt0) cc_final: 0.8451 (mp10) REVERT: A 968 LYS cc_start: 0.9345 (ptpp) cc_final: 0.8936 (mtmm) REVERT: A 1297 HIS cc_start: 0.9005 (m90) cc_final: 0.8779 (m-70) outliers start: 21 outliers final: 16 residues processed: 102 average time/residue: 0.2466 time to fit residues: 37.2174 Evaluate side-chains 102 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 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 495 MET 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 1253 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 67 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12371 Z= 0.164 Angle : 0.544 9.658 17201 Z= 0.280 Chirality : 0.037 0.197 1980 Planarity : 0.003 0.045 1755 Dihedral : 18.635 152.280 2894 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.74 % Allowed : 17.05 % Favored : 81.20 % 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: 0.31 (0.25), residues: 1132 helix: 1.02 (0.23), residues: 532 sheet: -0.31 (0.50), residues: 112 loop : -0.48 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1136 HIS 0.003 0.001 HIS A 329 PHE 0.043 0.001 PHE A1235 TYR 0.016 0.001 TYR A 988 ARG 0.003 0.000 ARG A 629 *********************** 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 112 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.9328 (tp30) cc_final: 0.9068 (tp30) REVERT: A 751 MET cc_start: 0.8903 (mtp) cc_final: 0.8594 (mtp) REVERT: A 933 GLN cc_start: 0.8787 (mt0) cc_final: 0.8447 (mp10) REVERT: A 968 LYS cc_start: 0.9342 (ptpp) cc_final: 0.8925 (mtmm) outliers start: 18 outliers final: 13 residues processed: 103 average time/residue: 0.2647 time to fit residues: 39.9466 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 : 1.254 ------------------------------------------------------------------------------- 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 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 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 117 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 98 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 698 HIS ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12371 Z= 0.173 Angle : 0.556 9.430 17201 Z= 0.285 Chirality : 0.037 0.196 1980 Planarity : 0.003 0.044 1755 Dihedral : 18.557 151.727 2894 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.45 % Allowed : 17.83 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1132 helix: 1.05 (0.23), residues: 533 sheet: -0.26 (0.50), residues: 112 loop : -0.45 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1136 HIS 0.003 0.001 HIS A 329 PHE 0.036 0.001 PHE A1235 TYR 0.018 0.001 TYR A 5 ARG 0.003 0.000 ARG A 629 ********************** 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 108 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.9329 (tp30) cc_final: 0.9071 (tp30) REVERT: A 751 MET cc_start: 0.8896 (mtp) cc_final: 0.8656 (mtp) REVERT: A 933 GLN cc_start: 0.8781 (mt0) cc_final: 0.8463 (mp10) outliers start: 15 outliers final: 14 residues processed: 101 average time/residue: 0.2575 time to fit residues: 38.0859 Evaluate side-chains 103 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 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 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 104 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.0030 chunk 98 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 overall best weight: 0.3590 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.120149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.077046 restraints weight = 28286.211| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.20 r_work: 0.3070 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12371 Z= 0.139 Angle : 0.544 9.665 17201 Z= 0.279 Chirality : 0.037 0.199 1980 Planarity : 0.003 0.043 1755 Dihedral : 18.466 150.158 2894 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.26 % Allowed : 18.22 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.25), residues: 1132 helix: 1.14 (0.23), residues: 532 sheet: -0.21 (0.50), residues: 112 loop : -0.41 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1136 HIS 0.003 0.001 HIS A 329 PHE 0.033 0.001 PHE A1235 TYR 0.016 0.001 TYR A 988 ARG 0.003 0.000 ARG A 629 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2489.51 seconds wall clock time: 46 minutes 40.98 seconds (2800.98 seconds total)