Starting phenix.real_space_refine on Fri Sep 11 22:43:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6o0y_0584/09_2026/6o0y_0584.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o0y_0584/09_2026/6o0y_0584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6o0y_0584/09_2026/6o0y_0584.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6o0y_0584/09_2026/6o0y_0584.cif" model { file = "/net/cci-nas-00/data/ceres_data/6o0y_0584/09_2026/6o0y_0584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o0y_0584/09_2026/6o0y_0584.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6o0y_0584/09_2026/6o0y_0584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o0y_0584/09_2026/6o0y_0584.map" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.044 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 149 5.49 5 S 15 5.16 5 C 7059 2.51 5 N 2092 2.21 5 O 2513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11828 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 8669 Classifications: {'peptide': 1146} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 29, 'TRANS': 1116} Chain breaks: 4 Unresolved non-hydrogen bonds: 761 Unresolved non-hydrogen angles: 916 Unresolved non-hydrogen dihedrals: 609 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASP:plan': 37, 'GLU:plan': 63, 'ARG:plan': 19, 'GLN:plan1': 10, 'ASN:plan1': 9, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 490 Chain: "B" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2104 Classifications: {'RNAv2': 98} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 53, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 86} Chain: "C" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 261 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 331 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain breaks: 1 Chain: "c" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 463 Classifications: {'DNA': 23} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 22} Time building chain proxies: 2.45, per 1000 atoms: 0.21 Number of scatterers: 11828 At special positions: 0 Unit cell: (137.104, 126.236, 88.616, 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 15 16.00 P 149 15.00 O 2513 8.00 N 2092 7.00 C 7059 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: 0.79 Conformation dependent library (CDL) restraints added in 373.2 milliseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2182 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 7 sheets defined 51.7% alpha, 7.6% beta 52 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 59 through 92 removed outlier: 3.720A pdb=" N ARG A 70 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 71 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 removed outlier: 4.005A pdb=" N GLU A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 145 Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.590A pdb=" N PHE A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.737A pdb=" N ILE A 350 " --> pdb=" O LYS A 346 " (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 removed outlier: 3.600A pdb=" N MET A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.756A pdb=" N ASN A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.411A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.943A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.527A pdb=" N ILE A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 444 " --> pdb=" O ILE A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.779A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 567 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 652 removed outlier: 3.559A pdb=" N LYS A 652 " --> pdb=" O MET A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.520A pdb=" N ILE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.530A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 776 Processing helix chain 'A' and resid 779 through 791 removed outlier: 4.053A pdb=" N ARG A 783 " --> pdb=" O GLU A 779 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 785 " --> pdb=" O MET A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 798 removed outlier: 3.983A pdb=" N GLU A 798 " --> pdb=" O ILE A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 817 removed outlier: 3.755A pdb=" N LEU A 813 " --> pdb=" O GLU A 809 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR A 814 " --> pdb=" O LYS A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 866 removed outlier: 3.649A pdb=" N ASN A 863 " --> pdb=" O ARG A 859 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS A 866 " --> pdb=" O LYS A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 889 removed outlier: 6.169A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A 888 " --> pdb=" O ARG A 884 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA A 889 " --> pdb=" O GLN A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 902 through 905 Processing helix chain 'A' and resid 917 through 940 removed outlier: 4.035A pdb=" N LEU A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A 925 " --> pdb=" O LEU A 921 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.647A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1000 Processing helix chain 'A' and resid 1080 through 1087 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 4.102A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 removed outlier: 3.632A pdb=" N PHE A1181 " --> pdb=" O ASN A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1195 removed outlier: 3.836A pdb=" N ILE A1195 " --> pdb=" O LYS A1192 " (cutoff:3.500A) 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 1240 removed outlier: 3.508A pdb=" N VAL A1233 " --> pdb=" O PRO A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1261 Processing helix chain 'A' and resid 1263 through 1278 removed outlier: 3.825A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE A1276 " --> pdb=" O GLN A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1296 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.808A pdb=" N HIS A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1317 removed outlier: 4.072A pdb=" N ASN A1317 " --> pdb=" O THR A1314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1314 through 1317' Processing helix chain 'A' and resid 1341 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 959 removed outlier: 4.459A pdb=" N GLU A 762 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE A 11 " --> pdb=" O GLU A 762 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A1095 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.827A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 528 through 530 removed outlier: 3.694A pdb=" N LYS A 528 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA6, first strand: chain 'A' and resid 1157 through 1167 removed outlier: 3.545A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1325 392 hydrogen bonds defined for protein. 1143 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 130 hydrogen bonds 252 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 3.41 Time building geometry restraints manager: 0.98 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: 1912 1.33 - 1.44: 3845 1.44 - 1.56: 6290 1.56 - 1.68: 294 1.68 - 1.80: 28 Bond restraints: 12369 Sorted by residual: bond pdb=" C1' DC c 20 " pdb=" N1 DC c 20 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.27e+01 bond pdb=" C1' DT c 14 " pdb=" N1 DT c 14 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.02e+01 bond pdb=" C3' DC c 20 " pdb=" O3' DC c 20 " ideal model delta sigma weight residual 1.435 1.397 0.038 1.30e-02 5.92e+03 8.38e+00 bond pdb=" C3' DC C 12 " pdb=" C2' DC C 12 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.95e+00 bond pdb=" C1' DT c 25 " pdb=" N1 DT c 25 " ideal model delta sigma weight residual 1.468 1.505 -0.037 1.40e-02 5.10e+03 7.14e+00 ... (remaining 12364 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 16748 2.10 - 4.19: 614 4.19 - 6.29: 63 6.29 - 8.38: 14 8.38 - 10.48: 1 Bond angle restraints: 17440 Sorted by residual: angle pdb=" O4' DC c 17 " pdb=" C4' DC c 17 " pdb=" C3' DC c 17 " ideal model delta sigma weight residual 106.00 102.62 3.38 6.00e-01 2.78e+00 3.17e+01 angle pdb=" C3' A B 8 " pdb=" O3' A B 8 " pdb=" P A B 9 " ideal model delta sigma weight residual 119.70 126.00 -6.30 1.20e+00 6.94e-01 2.76e+01 angle pdb=" C3' A B 38 " pdb=" O3' A B 38 " pdb=" P G B 39 " ideal model delta sigma weight residual 119.70 125.78 -6.08 1.20e+00 6.94e-01 2.57e+01 angle pdb=" C3' A B 42 " pdb=" O3' A B 42 " pdb=" P G B 43 " ideal model delta sigma weight residual 119.70 125.54 -5.84 1.20e+00 6.94e-01 2.37e+01 angle pdb=" O4' DT c 23 " pdb=" C4' DT c 23 " pdb=" C3' DT c 23 " ideal model delta sigma weight residual 106.00 103.14 2.86 6.00e-01 2.78e+00 2.26e+01 ... (remaining 17435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.17: 6543 31.17 - 62.34: 460 62.34 - 93.51: 22 93.51 - 124.68: 0 124.68 - 155.86: 4 Dihedral angle restraints: 7029 sinusoidal: 3660 harmonic: 3369 Sorted by residual: dihedral pdb=" C4' G B 43 " pdb=" C3' G B 43 " pdb=" C2' G B 43 " pdb=" C1' G B 43 " ideal model delta sinusoidal sigma weight residual 36.35 -36.82 73.17 1 3.10e+00 1.04e-01 7.10e+02 dihedral pdb=" C4' A B 88 " pdb=" C3' A B 88 " pdb=" C2' A B 88 " pdb=" C1' A B 88 " ideal model delta sinusoidal sigma weight residual 36.35 -35.96 72.31 1 3.10e+00 1.04e-01 6.95e+02 dihedral pdb=" C4' C B 55 " pdb=" C3' C B 55 " pdb=" C2' C B 55 " pdb=" C1' C B 55 " ideal model delta sinusoidal sigma weight residual 36.35 -35.91 72.26 1 3.10e+00 1.04e-01 6.95e+02 ... (remaining 7026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1705 0.071 - 0.142: 233 0.142 - 0.212: 68 0.212 - 0.283: 78 0.283 - 0.354: 7 Chirality restraints: 2091 Sorted by residual: chirality pdb=" C3' A B 42 " pdb=" C4' A B 42 " pdb=" O3' A B 42 " pdb=" C2' A B 42 " both_signs ideal model delta sigma weight residual False -2.50 -2.14 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" P A B 9 " pdb=" OP1 A B 9 " pdb=" OP2 A B 9 " pdb=" O5' A B 9 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C3' A B 8 " pdb=" C4' A B 8 " pdb=" O3' A B 8 " pdb=" C2' A B 8 " both_signs ideal model delta sigma weight residual False -2.50 -2.17 -0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 2088 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 622 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.35e+00 pdb=" C THR A 622 " 0.053 2.00e-02 2.50e+03 pdb=" O THR A 622 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU A 623 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 617 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.74e+00 pdb=" C GLU A 617 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU A 617 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP A 618 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 619 " -0.015 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" C ILE A 619 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE A 619 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL A 620 " -0.017 2.00e-02 2.50e+03 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3093 2.80 - 3.32: 9597 3.32 - 3.85: 20409 3.85 - 4.37: 22751 4.37 - 4.90: 35911 Nonbonded interactions: 91761 Sorted by model distance: nonbonded pdb=" O2 DC C 1 " pdb=" N2 DG D 40 " model vdw 2.272 2.496 nonbonded pdb=" O TYR A 521 " pdb=" OG1 THR A 525 " model vdw 2.306 3.040 nonbonded pdb=" OG SER A 512 " pdb=" OE2 GLU A 617 " model vdw 2.317 3.040 nonbonded pdb=" O TYR A 25 " pdb=" OH TYR A 988 " model vdw 2.330 3.040 nonbonded pdb=" OH TYR A 373 " pdb=" O LEU A 398 " model vdw 2.352 3.040 ... (remaining 91756 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.600 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 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 : 0.006 0.050 12369 Z= 0.369 Angle : 0.857 10.478 17440 Z= 0.510 Chirality : 0.074 0.354 2091 Planarity : 0.005 0.055 1656 Dihedral : 18.452 155.856 4847 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.37 % Allowed : 6.94 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.11 (0.19), residues: 1136 helix: -2.75 (0.15), residues: 537 sheet: -1.14 (0.48), residues: 117 loop : -3.01 (0.22), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 71 TYR 0.014 0.002 TYR A 155 PHE 0.015 0.001 PHE A1327 TRP 0.009 0.001 TRP A 476 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.37 (12369) covalent geometry : angle 0.85748 / 0.51 (17440) hydrogen bonds : bond 0.15367 / 10.23 ( 522) hydrogen bonds : angle 6.25252 / 4.31 ( 1395) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.324 Fit side-chains REVERT: A 465 MET cc_start: 0.8497 (tmm) cc_final: 0.8126 (tmm) REVERT: A 733 ILE cc_start: 0.8269 (pt) cc_final: 0.8044 (mm) REVERT: A 746 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8535 (tm-30) outliers start: 3 outliers final: 2 residues processed: 75 average time/residue: 0.1125 time to fit residues: 12.4137 Evaluate side-chains 52 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1190 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.0070 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 9.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 113 HIS A 402 GLN A 899 ASN A1177 ASN A1252 ASN A1295 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.077523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.056906 restraints weight = 38767.193| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.96 r_work: 0.2720 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12369 Z= 0.188 Angle : 0.929 21.092 17440 Z= 0.414 Chirality : 0.083 1.171 2091 Planarity : 0.004 0.046 1656 Dihedral : 18.023 158.031 2956 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.99 % Allowed : 10.90 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.22), residues: 1136 helix: -0.98 (0.20), residues: 556 sheet: -0.82 (0.47), residues: 115 loop : -2.53 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 864 TYR 0.020 0.001 TYR A 594 PHE 0.014 0.001 PHE A1327 TRP 0.005 0.001 TRP A 476 HIS 0.005 0.001 HIS A1264 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.19 (12369) covalent geometry : angle 0.92918 / 0.41 (17440) hydrogen bonds : bond 0.05494 / 3.47 ( 522) hydrogen bonds : angle 4.35759 / 3.05 ( 1395) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.376 Fit side-chains REVERT: A 733 ILE cc_start: 0.8292 (pt) cc_final: 0.8074 (mm) outliers start: 8 outliers final: 6 residues processed: 63 average time/residue: 0.0911 time to fit residues: 9.0078 Evaluate side-chains 58 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1313 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 chunk 56 optimal weight: 0.0770 chunk 54 optimal weight: 9.9990 chunk 88 optimal weight: 0.0050 chunk 95 optimal weight: 0.5980 chunk 104 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 overall best weight: 0.7154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 459 ASN A 721 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.079078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.058514 restraints weight = 39154.906| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.98 r_work: 0.2760 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12369 Z= 0.130 Angle : 0.704 11.277 17440 Z= 0.331 Chirality : 0.059 0.718 2091 Planarity : 0.003 0.038 1656 Dihedral : 18.100 153.716 2956 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.49 % Allowed : 11.28 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.24), residues: 1136 helix: -0.13 (0.21), residues: 559 sheet: -0.58 (0.48), residues: 114 loop : -2.24 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.015 0.001 TYR A 594 PHE 0.010 0.001 PHE A1327 TRP 0.005 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.13 (12369) covalent geometry : angle 0.70396 / 0.33 (17440) hydrogen bonds : bond 0.04712 / 2.94 ( 522) hydrogen bonds : angle 3.98787 / 2.80 ( 1395) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.412 Fit side-chains REVERT: A 733 ILE cc_start: 0.8273 (pt) cc_final: 0.8040 (mm) REVERT: A 746 GLU cc_start: 0.9237 (tm-30) cc_final: 0.8998 (tp30) outliers start: 12 outliers final: 8 residues processed: 64 average time/residue: 0.0875 time to fit residues: 9.1875 Evaluate side-chains 56 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 117 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 95 optimal weight: 0.0040 chunk 107 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 chunk 35 optimal weight: 0.0870 overall best weight: 1.2174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 459 ASN A 721 HIS A 817 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.079020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.058400 restraints weight = 39386.300| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.98 r_work: 0.2759 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12369 Z= 0.133 Angle : 0.670 10.700 17440 Z= 0.316 Chirality : 0.052 0.496 2091 Planarity : 0.003 0.034 1656 Dihedral : 18.106 151.898 2955 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.11 % Allowed : 12.64 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.25), residues: 1136 helix: 0.47 (0.22), residues: 559 sheet: -0.36 (0.47), residues: 113 loop : -2.09 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 403 TYR 0.012 0.001 TYR A 594 PHE 0.012 0.001 PHE A1258 TRP 0.006 0.001 TRP A 476 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (12369) covalent geometry : angle 0.67034 / 0.32 (17440) hydrogen bonds : bond 0.04421 / 2.78 ( 522) hydrogen bonds : angle 3.77019 / 2.67 ( 1395) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.325 Fit side-chains REVERT: A 733 ILE cc_start: 0.8258 (pt) cc_final: 0.8005 (mm) outliers start: 17 outliers final: 10 residues processed: 66 average time/residue: 0.0927 time to fit residues: 9.8675 Evaluate side-chains 60 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 35 optimal weight: 0.2980 chunk 62 optimal weight: 30.0000 chunk 25 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS A 721 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.076198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.055514 restraints weight = 39832.230| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.95 r_work: 0.2686 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12369 Z= 0.301 Angle : 0.792 12.174 17440 Z= 0.372 Chirality : 0.057 0.459 2091 Planarity : 0.003 0.039 1656 Dihedral : 18.237 154.267 2955 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.86 % Allowed : 14.25 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.25), residues: 1136 helix: 0.64 (0.22), residues: 561 sheet: -0.36 (0.48), residues: 105 loop : -2.08 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 967 TYR 0.012 0.001 TYR A 362 PHE 0.014 0.001 PHE A1327 TRP 0.009 0.001 TRP A 476 HIS 0.010 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.30 (12369) covalent geometry : angle 0.79237 / 0.37 (17440) hydrogen bonds : bond 0.05460 / 3.53 ( 522) hydrogen bonds : angle 3.96378 / 2.81 ( 1395) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.353 Fit side-chains REVERT: A 733 ILE cc_start: 0.8305 (pt) cc_final: 0.8033 (mm) REVERT: A 746 GLU cc_start: 0.9316 (tp30) cc_final: 0.8996 (tp30) outliers start: 15 outliers final: 12 residues processed: 59 average time/residue: 0.0954 time to fit residues: 8.9965 Evaluate side-chains 57 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 96 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 98 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.078336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.057421 restraints weight = 39061.856| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.03 r_work: 0.2724 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12369 Z= 0.133 Angle : 0.667 9.598 17440 Z= 0.316 Chirality : 0.052 0.378 2091 Planarity : 0.003 0.030 1656 Dihedral : 18.152 152.802 2955 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.11 % Allowed : 14.25 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.25), residues: 1136 helix: 0.86 (0.23), residues: 563 sheet: -0.33 (0.47), residues: 114 loop : -1.92 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 71 TYR 0.011 0.001 TYR A 594 PHE 0.011 0.001 PHE A1258 TRP 0.007 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (12369) covalent geometry : angle 0.66726 / 0.32 (17440) hydrogen bonds : bond 0.04615 / 2.88 ( 522) hydrogen bonds : angle 3.69214 / 2.63 ( 1395) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.387 Fit side-chains REVERT: A 733 ILE cc_start: 0.8224 (pt) cc_final: 0.7927 (mm) REVERT: A 746 GLU cc_start: 0.9271 (tp30) cc_final: 0.9012 (tp30) outliers start: 17 outliers final: 12 residues processed: 65 average time/residue: 0.0888 time to fit residues: 9.2063 Evaluate side-chains 65 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 40 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 24 optimal weight: 0.0470 chunk 87 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 123 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.077860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.056953 restraints weight = 39065.791| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.02 r_work: 0.2712 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12369 Z= 0.164 Angle : 0.671 9.377 17440 Z= 0.319 Chirality : 0.052 0.349 2091 Planarity : 0.003 0.030 1656 Dihedral : 18.150 152.525 2955 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.23 % Allowed : 14.75 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.25), residues: 1136 helix: 0.96 (0.23), residues: 563 sheet: -0.30 (0.47), residues: 114 loop : -1.89 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1333 TYR 0.017 0.001 TYR A 594 PHE 0.010 0.001 PHE A1327 TRP 0.007 0.001 TRP A 476 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (12369) covalent geometry : angle 0.67111 / 0.32 (17440) hydrogen bonds : bond 0.04691 / 2.97 ( 522) hydrogen bonds : angle 3.68088 / 2.62 ( 1395) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.404 Fit side-chains REVERT: A 733 ILE cc_start: 0.8225 (pt) cc_final: 0.7908 (mm) REVERT: A 746 GLU cc_start: 0.9292 (tp30) cc_final: 0.8998 (tp30) outliers start: 18 outliers final: 15 residues processed: 67 average time/residue: 0.0852 time to fit residues: 9.3633 Evaluate side-chains 67 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 58 optimal weight: 0.4980 chunk 96 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 111 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 95 optimal weight: 0.0870 chunk 20 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 overall best weight: 2.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.077914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.057052 restraints weight = 38883.975| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.00 r_work: 0.2714 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12369 Z= 0.160 Angle : 0.668 9.165 17440 Z= 0.318 Chirality : 0.052 0.333 2091 Planarity : 0.003 0.029 1656 Dihedral : 18.135 152.424 2955 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.98 % Allowed : 15.24 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.25), residues: 1136 helix: 0.99 (0.23), residues: 563 sheet: -0.17 (0.48), residues: 105 loop : -1.87 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 340 TYR 0.020 0.001 TYR A 594 PHE 0.014 0.001 PHE A1258 TRP 0.007 0.001 TRP A 476 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 (12369) covalent geometry : angle 0.66757 / 0.32 (17440) hydrogen bonds : bond 0.04660 / 2.94 ( 522) hydrogen bonds : angle 3.66644 / 2.61 ( 1395) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.409 Fit side-chains REVERT: A 733 ILE cc_start: 0.8221 (pt) cc_final: 0.7909 (mm) REVERT: A 746 GLU cc_start: 0.9305 (tp30) cc_final: 0.9019 (tp30) outliers start: 16 outliers final: 14 residues processed: 66 average time/residue: 0.0851 time to fit residues: 9.0719 Evaluate side-chains 66 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 100 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.078381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.057541 restraints weight = 38659.211| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.00 r_work: 0.2725 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12369 Z= 0.136 Angle : 0.653 8.772 17440 Z= 0.312 Chirality : 0.052 0.306 2091 Planarity : 0.003 0.029 1656 Dihedral : 18.097 152.002 2955 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.98 % Allowed : 15.24 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.25), residues: 1136 helix: 1.06 (0.23), residues: 563 sheet: -0.15 (0.48), residues: 113 loop : -1.82 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 71 TYR 0.018 0.001 TYR A 594 PHE 0.010 0.001 PHE A 432 TRP 0.006 0.001 TRP A 476 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (12369) covalent geometry : angle 0.65350 / 0.31 (17440) hydrogen bonds : bond 0.04562 / 2.86 ( 522) hydrogen bonds : angle 3.61087 / 2.58 ( 1395) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.412 Fit side-chains REVERT: A 733 ILE cc_start: 0.8203 (pt) cc_final: 0.7888 (mm) REVERT: A 746 GLU cc_start: 0.9259 (tp30) cc_final: 0.8932 (tp30) outliers start: 16 outliers final: 14 residues processed: 66 average time/residue: 0.0876 time to fit residues: 9.4062 Evaluate side-chains 65 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 2 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 64 optimal weight: 0.0570 chunk 72 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.077579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.056706 restraints weight = 39192.765| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.01 r_work: 0.2704 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12369 Z= 0.193 Angle : 0.683 9.544 17440 Z= 0.325 Chirality : 0.052 0.314 2091 Planarity : 0.003 0.029 1656 Dihedral : 18.112 152.311 2955 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.86 % Allowed : 15.49 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.25), residues: 1136 helix: 1.12 (0.23), residues: 563 sheet: -0.11 (0.49), residues: 105 loop : -1.84 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1333 TYR 0.017 0.001 TYR A 594 PHE 0.011 0.001 PHE A1327 TRP 0.007 0.001 TRP A 476 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (12369) covalent geometry : angle 0.68278 / 0.32 (17440) hydrogen bonds : bond 0.04762 / 3.03 ( 522) hydrogen bonds : angle 3.65683 / 2.61 ( 1395) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.370 Fit side-chains REVERT: A 733 ILE cc_start: 0.8227 (pt) cc_final: 0.7905 (mm) REVERT: A 746 GLU cc_start: 0.9276 (tp30) cc_final: 0.8978 (tp30) outliers start: 15 outliers final: 14 residues processed: 62 average time/residue: 0.0887 time to fit residues: 8.6342 Evaluate side-chains 63 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1313 PHE Chi-restraints excluded: chain A residue 1337 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 99 optimal weight: 7.9990 chunk 39 optimal weight: 0.0980 chunk 120 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 81 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.077562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.056657 restraints weight = 39129.239| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.02 r_work: 0.2705 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12369 Z= 0.181 Angle : 0.682 10.156 17440 Z= 0.324 Chirality : 0.052 0.311 2091 Planarity : 0.003 0.028 1656 Dihedral : 18.102 152.420 2955 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.73 % Allowed : 15.61 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.25), residues: 1136 helix: 1.12 (0.23), residues: 563 sheet: -0.11 (0.49), residues: 105 loop : -1.83 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 967 TYR 0.017 0.001 TYR A 594 PHE 0.010 0.001 PHE A 432 TRP 0.007 0.001 TRP A 476 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 (12369) covalent geometry : angle 0.68184 / 0.32 (17440) hydrogen bonds : bond 0.04736 / 3.00 ( 522) hydrogen bonds : angle 3.65139 / 2.61 ( 1395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2616.38 seconds wall clock time: 45 minutes 45.17 seconds (2745.17 seconds total)