Starting phenix.real_space_refine on Fri Jul 3 02:14:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k4d_62055/07_2026/9k4d_62055.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k4d_62055/07_2026/9k4d_62055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k4d_62055/07_2026/9k4d_62055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k4d_62055/07_2026/9k4d_62055.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k4d_62055/07_2026/9k4d_62055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k4d_62055/07_2026/9k4d_62055.map" } resolution = 3.53 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= 0.006 sd= 0.090 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 146 5.49 5 S 19 5.16 5 C 6745 2.51 5 N 2024 2.21 5 O 2524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11458 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 8325 Classifications: {'peptide': 1017} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 989} Chain breaks: 3 Chain: "B" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 719 Classifications: {'DNA': 35} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 34} Chain: "C" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 325 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2089 Classifications: {'RNA': 98} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 48, 'rna3p_pyr': 39} Link IDs: {'rna2p': 11, 'rna3p': 86} Time building chain proxies: 2.13, per 1000 atoms: 0.19 Number of scatterers: 11458 At special positions: 0 Unit cell: (119.658, 104.566, 143.374, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 146 15.00 O 2524 8.00 N 2024 7.00 C 6745 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: 0.77 Conformation dependent library (CDL) restraints added in 417.6 milliseconds 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 7 sheets defined 54.7% alpha, 11.3% beta 58 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.771A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.646A 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 293 through 306 removed outlier: 3.904A pdb=" N ASP A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.696A pdb=" N ALA A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 382 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: 3.809A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.281A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.786A 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 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.561A pdb=" N VAL A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 removed outlier: 4.422A pdb=" N MET A 495 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 removed outlier: 3.995A 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 568 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.533A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 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 Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 702 through 712 removed outlier: 4.470A pdb=" N GLU A 706 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 727 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.645A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 940 Processing helix chain 'A' and resid 959 through 970 removed outlier: 4.028A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 999 removed outlier: 4.557A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1191 through 1195 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 1264 through 1281 removed outlier: 3.587A pdb=" N GLU A1268 " --> pdb=" O HIS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.518A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.718A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) 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 957 removed outlier: 6.583A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 10.369A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.672A pdb=" N LYS A 528 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.586A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.586A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1326 removed outlier: 3.578A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1194 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 146 hydrogen bonds 284 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3089 1.34 - 1.46: 2808 1.46 - 1.58: 5761 1.58 - 1.69: 292 1.69 - 1.81: 36 Bond restraints: 11986 Sorted by residual: bond pdb=" C3' DC C 10 " pdb=" C2' DC C 10 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DC B 14 " pdb=" C2' DC B 14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DA B 27 " pdb=" C2' DA B 27 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.70e+00 bond pdb=" C3' DG B 12 " pdb=" C2' DG B 12 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.05e+00 bond pdb=" C3' DG B 7 " pdb=" C2' DG B 7 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.72e+00 ... (remaining 11981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 16322 1.37 - 2.74: 457 2.74 - 4.12: 46 4.12 - 5.49: 5 5.49 - 6.86: 1 Bond angle restraints: 16831 Sorted by residual: angle pdb=" O4' DG B 18 " pdb=" C4' DG B 18 " pdb=" C3' DG B 18 " ideal model delta sigma weight residual 106.00 103.13 2.87 6.00e-01 2.78e+00 2.29e+01 angle pdb=" O4' DG B 23 " pdb=" C4' DG B 23 " pdb=" C3' DG B 23 " ideal model delta sigma weight residual 106.00 103.15 2.85 6.00e-01 2.78e+00 2.26e+01 angle pdb=" O4' DA B 22 " pdb=" C4' DA B 22 " pdb=" C3' DA B 22 " ideal model delta sigma weight residual 106.00 103.33 2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" O4' DT B 19 " pdb=" C4' DT B 19 " pdb=" C3' DT B 19 " ideal model delta sigma weight residual 106.00 103.41 2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT B 4 " pdb=" C4 DT B 4 " pdb=" O4 DT B 4 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 ... (remaining 16826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 6883 35.55 - 71.10: 332 71.10 - 106.65: 24 106.65 - 142.20: 0 142.20 - 177.76: 1 Dihedral angle restraints: 7240 sinusoidal: 4253 harmonic: 2987 Sorted by residual: dihedral pdb=" C4' DG B 7 " pdb=" C3' DG B 7 " pdb=" O3' DG B 7 " pdb=" P DA B 8 " ideal model delta sinusoidal sigma weight residual 220.00 42.24 177.76 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA PHE A 446 " pdb=" C PHE A 446 " pdb=" N ARG A 447 " pdb=" CA ARG A 447 " ideal model delta harmonic sigma weight residual 180.00 163.17 16.83 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CG ARG A1359 " pdb=" CD ARG A1359 " pdb=" NE ARG A1359 " pdb=" CZ ARG A1359 " ideal model delta sinusoidal sigma weight residual -180.00 -136.60 -43.40 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 7237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1369 0.031 - 0.062: 388 0.062 - 0.092: 124 0.092 - 0.123: 58 0.123 - 0.154: 5 Chirality restraints: 1944 Sorted by residual: chirality pdb=" C3' DG B 7 " pdb=" C4' DG B 7 " pdb=" O3' DG B 7 " pdb=" C2' DG B 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ILE A 956 " pdb=" N ILE A 956 " pdb=" C ILE A 956 " pdb=" CB ILE A 956 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA VAL A 27 " pdb=" N VAL A 27 " pdb=" C VAL A 27 " pdb=" CB VAL A 27 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 1941 not shown) Planarity restraints: 1601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D 42 " 0.022 2.00e-02 2.50e+03 1.01e-02 2.79e+00 pdb=" N9 A D 42 " -0.024 2.00e-02 2.50e+03 pdb=" C8 A D 42 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A D 42 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A D 42 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A D 42 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A D 42 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A D 42 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A D 42 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A D 42 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A D 42 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G D 54 " 0.018 2.00e-02 2.50e+03 8.10e-03 1.97e+00 pdb=" N9 G D 54 " -0.020 2.00e-02 2.50e+03 pdb=" C8 G D 54 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G D 54 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G D 54 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G D 54 " -0.000 2.00e-02 2.50e+03 pdb=" O6 G D 54 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G D 54 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G D 54 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G D 54 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G D 54 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G D 54 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 315 " 0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 316 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 316 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 316 " 0.019 5.00e-02 4.00e+02 ... (remaining 1598 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 4 2.02 - 2.74: 880 2.74 - 3.46: 15390 3.46 - 4.18: 29092 4.18 - 4.90: 46980 Nonbonded interactions: 92346 Sorted by model distance: nonbonded pdb=" NZ LYS A 510 " pdb=" OP1 G D 6 " model vdw 1.297 3.120 nonbonded pdb=" NZ LYS A 44 " pdb=" O6 G D 92 " model vdw 1.298 3.120 nonbonded pdb=" ND2 ASN A 77 " pdb=" O2 U D 59 " model vdw 1.298 3.120 nonbonded pdb=" NH1 ARG A 71 " pdb=" C5 C D 18 " model vdw 1.431 3.420 nonbonded pdb=" N2 DG B 9 " pdb=" O2 DC C 8 " model vdw 2.126 2.496 ... (remaining 92341 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.330 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11986 Z= 0.258 Angle : 0.522 6.861 16831 Z= 0.419 Chirality : 0.036 0.154 1944 Planarity : 0.003 0.034 1601 Dihedral : 16.931 177.755 5306 Min Nonbonded Distance : 1.297 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.68 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.26), residues: 1009 helix: 1.76 (0.24), residues: 506 sheet: 1.12 (0.53), residues: 105 loop : 0.17 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 494 TYR 0.009 0.001 TYR A 72 PHE 0.009 0.001 PHE A 432 TRP 0.010 0.001 TRP A1126 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.26 (11986) covalent geometry : angle 0.52162 / 0.42 (16831) hydrogen bonds : bond 0.14550 / 10.04 ( 546) hydrogen bonds : angle 5.64256 / 4.06 ( 1478) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 441 GLU cc_start: 0.8216 (mt-10) cc_final: 0.8013 (mt-10) REVERT: A 511 HIS cc_start: 0.7288 (m90) cc_final: 0.6204 (m-70) REVERT: A 534 MET cc_start: -0.0525 (mtt) cc_final: -0.2080 (tpt) REVERT: A 618 ASP cc_start: 0.8720 (t70) cc_final: 0.8348 (t0) REVERT: A 623 LEU cc_start: 0.9401 (mt) cc_final: 0.9166 (mt) REVERT: A 630 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8546 (mt-10) REVERT: A 653 ARG cc_start: 0.8049 (mtt180) cc_final: 0.7734 (mtm-85) REVERT: A 654 ARG cc_start: 0.7393 (tpt170) cc_final: 0.6702 (ttm170) REVERT: A 656 TYR cc_start: 0.8101 (m-80) cc_final: 0.7861 (m-10) REVERT: A 709 GLN cc_start: 0.7939 (mt0) cc_final: 0.7613 (mt0) REVERT: A 762 GLU cc_start: 0.7669 (pp20) cc_final: 0.7038 (tm-30) REVERT: A 954 LYS cc_start: 0.8294 (mttt) cc_final: 0.8054 (mttm) REVERT: A 962 LEU cc_start: 0.8939 (mt) cc_final: 0.8243 (tp) REVERT: A 979 ASN cc_start: 0.8427 (p0) cc_final: 0.8109 (p0) REVERT: A 1148 LYS cc_start: 0.8270 (mttt) cc_final: 0.7791 (mtpp) REVERT: A 1169 MET cc_start: 0.8891 (ttp) cc_final: 0.8617 (ttm) REVERT: A 1230 SER cc_start: 0.7697 (m) cc_final: 0.7447 (t) REVERT: A 1261 GLN cc_start: 0.9029 (mt0) cc_final: 0.8728 (mt0) REVERT: A 1325 LYS cc_start: 0.8858 (mttt) cc_final: 0.8443 (ttmm) REVERT: A 1326 TYR cc_start: 0.8507 (t80) cc_final: 0.7942 (t80) REVERT: A 1339 THR cc_start: 0.9245 (p) cc_final: 0.8948 (t) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1191 time to fit residues: 35.4387 Evaluate side-chains 111 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 30.0000 chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN A 595 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.160489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.109483 restraints weight = 18345.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107110 restraints weight = 10959.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.108177 restraints weight = 10352.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.108179 restraints weight = 7732.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.109480 restraints weight = 7190.495| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 11986 Z= 0.245 Angle : 0.595 8.020 16831 Z= 0.342 Chirality : 0.041 0.248 1944 Planarity : 0.005 0.063 1601 Dihedral : 19.447 178.632 3143 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.53 % Rotamer: Outliers : 2.30 % Allowed : 7.67 % Favored : 90.03 % 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: 1.36 (0.26), residues: 1009 helix: 1.60 (0.23), residues: 516 sheet: 1.01 (0.51), residues: 104 loop : 0.01 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 71 TYR 0.021 0.002 TYR A 5 PHE 0.017 0.002 PHE A1258 TRP 0.009 0.002 TRP A1126 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.24 (11986) covalent geometry : angle 0.59481 / 0.34 (16831) hydrogen bonds : bond 0.06221 / 4.03 ( 546) hydrogen bonds : angle 4.57992 / 3.32 ( 1478) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 ASP cc_start: 0.8712 (m-30) cc_final: 0.8335 (p0) REVERT: A 465 MET cc_start: 0.8329 (ttp) cc_final: 0.8029 (tmm) REVERT: A 618 ASP cc_start: 0.8838 (t70) cc_final: 0.8329 (t0) REVERT: A 630 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8348 (pt0) REVERT: A 633 GLU cc_start: 0.8980 (tt0) cc_final: 0.8747 (tt0) REVERT: A 653 ARG cc_start: 0.7999 (mtt180) cc_final: 0.7765 (mtm-85) REVERT: A 654 ARG cc_start: 0.7464 (tpt170) cc_final: 0.6958 (ttm170) REVERT: A 762 GLU cc_start: 0.7838 (pp20) cc_final: 0.7157 (tm-30) REVERT: A 942 LYS cc_start: 0.8475 (mmmt) cc_final: 0.7561 (mtpt) REVERT: A 954 LYS cc_start: 0.8440 (mttt) cc_final: 0.8056 (ttmm) REVERT: A 1148 LYS cc_start: 0.8507 (mttt) cc_final: 0.7905 (mtpp) REVERT: A 1230 SER cc_start: 0.7740 (m) cc_final: 0.7513 (t) REVERT: A 1261 GLN cc_start: 0.8977 (mt0) cc_final: 0.8679 (mt0) REVERT: A 1326 TYR cc_start: 0.8363 (t80) cc_final: 0.8034 (t80) REVERT: A 1339 THR cc_start: 0.9257 (p) cc_final: 0.8966 (t) outliers start: 21 outliers final: 15 residues processed: 132 average time/residue: 0.0994 time to fit residues: 18.6494 Evaluate side-chains 103 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1268 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 75 optimal weight: 5.9990 chunk 67 optimal weight: 0.1980 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS A 511 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.167117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.109072 restraints weight = 19342.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.113014 restraints weight = 9008.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.115364 restraints weight = 6269.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.116727 restraints weight = 5238.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.117161 restraints weight = 4774.455| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 11986 Z= 0.170 Angle : 0.509 5.887 16831 Z= 0.303 Chirality : 0.039 0.234 1944 Planarity : 0.004 0.056 1601 Dihedral : 19.476 177.824 3143 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.07 % Favored : 96.83 % Rotamer: Outliers : 2.19 % Allowed : 8.43 % Favored : 89.38 % 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: 1.34 (0.26), residues: 1009 helix: 1.63 (0.23), residues: 516 sheet: 1.02 (0.50), residues: 102 loop : -0.07 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 71 TYR 0.026 0.001 TYR A 5 PHE 0.011 0.001 PHE A1258 TRP 0.006 0.001 TRP A1126 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (11986) covalent geometry : angle 0.50893 / 0.30 (16831) hydrogen bonds : bond 0.05509 / 3.54 ( 546) hydrogen bonds : angle 4.31813 / 3.15 ( 1478) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.7989 (m-30) cc_final: 0.7368 (m-30) REVERT: A 304 ASP cc_start: 0.8605 (m-30) cc_final: 0.8334 (p0) REVERT: A 465 MET cc_start: 0.8341 (ttp) cc_final: 0.8001 (tmm) REVERT: A 508 LEU cc_start: 0.8425 (mm) cc_final: 0.8120 (mp) REVERT: A 618 ASP cc_start: 0.8791 (t70) cc_final: 0.8264 (t0) REVERT: A 630 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8094 (pt0) REVERT: A 631 MET cc_start: 0.8321 (mmm) cc_final: 0.7722 (mmm) REVERT: A 653 ARG cc_start: 0.8037 (mtt180) cc_final: 0.7717 (mtm-85) REVERT: A 654 ARG cc_start: 0.7316 (tpt170) cc_final: 0.7010 (ttm170) REVERT: A 762 GLU cc_start: 0.7865 (pp20) cc_final: 0.7076 (tm-30) REVERT: A 954 LYS cc_start: 0.8391 (mttt) cc_final: 0.8025 (ttmm) REVERT: A 1148 LYS cc_start: 0.8485 (mttt) cc_final: 0.8058 (mtpp) REVERT: A 1261 GLN cc_start: 0.8948 (mt0) cc_final: 0.8659 (mt0) REVERT: A 1325 LYS cc_start: 0.8826 (tttt) cc_final: 0.8351 (ttmm) REVERT: A 1339 THR cc_start: 0.9241 (p) cc_final: 0.8963 (t) outliers start: 20 outliers final: 13 residues processed: 118 average time/residue: 0.0884 time to fit residues: 15.3533 Evaluate side-chains 102 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 517 TYR Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1268 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 52 optimal weight: 0.0050 chunk 106 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS A 511 HIS ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.164444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.112457 restraints weight = 19256.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.110695 restraints weight = 10605.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112652 restraints weight = 9433.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112219 restraints weight = 7331.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112976 restraints weight = 6835.500| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11986 Z= 0.206 Angle : 0.551 9.641 16831 Z= 0.318 Chirality : 0.040 0.234 1944 Planarity : 0.004 0.055 1601 Dihedral : 19.559 177.777 3143 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.27 % Favored : 96.63 % Rotamer: Outliers : 2.52 % Allowed : 8.87 % Favored : 88.61 % 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: 1.12 (0.26), residues: 1009 helix: 1.54 (0.23), residues: 515 sheet: 0.41 (0.48), residues: 112 loop : -0.16 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1122 TYR 0.023 0.002 TYR A 5 PHE 0.014 0.002 PHE A 682 TRP 0.006 0.001 TRP A1126 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.21 (11986) covalent geometry : angle 0.55135 / 0.32 (16831) hydrogen bonds : bond 0.05833 / 3.77 ( 546) hydrogen bonds : angle 4.25276 / 3.10 ( 1478) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.8054 (m-30) cc_final: 0.7375 (m-30) REVERT: A 304 ASP cc_start: 0.8719 (m-30) cc_final: 0.8333 (p0) REVERT: A 441 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7978 (mt-10) REVERT: A 465 MET cc_start: 0.8406 (ttp) cc_final: 0.8045 (tmm) REVERT: A 618 ASP cc_start: 0.8828 (t70) cc_final: 0.8335 (t0) REVERT: A 630 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8420 (mt-10) REVERT: A 631 MET cc_start: 0.8499 (mmm) cc_final: 0.7782 (mmm) REVERT: A 648 MET cc_start: 0.8142 (mmt) cc_final: 0.7917 (mmt) REVERT: A 653 ARG cc_start: 0.8010 (mtt180) cc_final: 0.7696 (mtm-85) REVERT: A 654 ARG cc_start: 0.7322 (tpt170) cc_final: 0.7111 (ttm170) REVERT: A 762 GLU cc_start: 0.7883 (pp20) cc_final: 0.6927 (tm-30) REVERT: A 954 LYS cc_start: 0.8421 (mttt) cc_final: 0.8023 (ttmm) REVERT: A 1148 LYS cc_start: 0.8396 (mttt) cc_final: 0.7939 (mtpp) REVERT: A 1261 GLN cc_start: 0.8913 (mt0) cc_final: 0.8615 (mt0) REVERT: A 1325 LYS cc_start: 0.8811 (tttt) cc_final: 0.8315 (ttmm) REVERT: A 1339 THR cc_start: 0.9283 (p) cc_final: 0.8998 (t) outliers start: 23 outliers final: 17 residues processed: 108 average time/residue: 0.0860 time to fit residues: 13.6495 Evaluate side-chains 100 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 517 TYR Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1268 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 50 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 HIS ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 GLN ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.153851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.094552 restraints weight = 19127.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.098277 restraints weight = 9298.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.100502 restraints weight = 6526.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.101506 restraints weight = 5482.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.101798 restraints weight = 5048.782| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11986 Z= 0.285 Angle : 0.638 7.975 16831 Z= 0.362 Chirality : 0.044 0.231 1944 Planarity : 0.005 0.053 1601 Dihedral : 19.686 177.730 3143 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.57 % Favored : 96.33 % Rotamer: Outliers : 2.63 % Allowed : 10.95 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.26), residues: 1009 helix: 1.24 (0.23), residues: 515 sheet: 0.20 (0.48), residues: 112 loop : -0.41 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1333 TYR 0.023 0.002 TYR A 5 PHE 0.019 0.002 PHE A1258 TRP 0.007 0.002 TRP A1126 HIS 0.006 0.002 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.28 (11986) covalent geometry : angle 0.63791 / 0.36 (16831) hydrogen bonds : bond 0.06702 / 4.36 ( 546) hydrogen bonds : angle 4.41685 / 3.22 ( 1478) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.7999 (m-30) cc_final: 0.7351 (m-30) REVERT: A 304 ASP cc_start: 0.8650 (m-30) cc_final: 0.8356 (p0) REVERT: A 321 MET cc_start: 0.9024 (mmt) cc_final: 0.8734 (mmt) REVERT: A 465 MET cc_start: 0.8367 (ttp) cc_final: 0.8142 (tmm) REVERT: A 618 ASP cc_start: 0.8838 (t70) cc_final: 0.8350 (t0) REVERT: A 630 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8398 (mt-10) REVERT: A 631 MET cc_start: 0.8401 (mmm) cc_final: 0.7585 (mmm) REVERT: A 648 MET cc_start: 0.8109 (mmt) cc_final: 0.7894 (mmt) REVERT: A 653 ARG cc_start: 0.8084 (mtt180) cc_final: 0.7721 (mtm-85) REVERT: A 654 ARG cc_start: 0.7306 (tpt170) cc_final: 0.7032 (ttm170) REVERT: A 951 ARG cc_start: 0.6918 (mtt-85) cc_final: 0.6707 (mtt-85) REVERT: A 954 LYS cc_start: 0.8480 (mttt) cc_final: 0.8110 (ttmm) REVERT: A 1148 LYS cc_start: 0.8493 (mttt) cc_final: 0.8229 (mtpp) REVERT: A 1261 GLN cc_start: 0.8927 (mt0) cc_final: 0.8649 (mt0) REVERT: A 1303 ARG cc_start: 0.7728 (ptm-80) cc_final: 0.7479 (ptm-80) REVERT: A 1325 LYS cc_start: 0.8856 (tttt) cc_final: 0.8377 (ttmm) REVERT: A 1339 THR cc_start: 0.9297 (p) cc_final: 0.8993 (t) outliers start: 24 outliers final: 18 residues processed: 107 average time/residue: 0.0908 time to fit residues: 14.2348 Evaluate side-chains 98 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 517 TYR Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1240 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 112 optimal weight: 30.0000 chunk 89 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.157696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.099282 restraints weight = 18991.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.103180 restraints weight = 8850.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.105588 restraints weight = 6094.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.106904 restraints weight = 5047.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.107643 restraints weight = 4589.937| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11986 Z= 0.123 Angle : 0.496 9.110 16831 Z= 0.295 Chirality : 0.038 0.232 1944 Planarity : 0.004 0.049 1601 Dihedral : 19.574 176.228 3143 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.78 % Favored : 97.13 % Rotamer: Outliers : 1.64 % Allowed : 11.39 % Favored : 86.97 % 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 (0.26), residues: 1009 helix: 1.45 (0.23), residues: 515 sheet: 0.38 (0.49), residues: 112 loop : -0.34 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 951 TYR 0.024 0.001 TYR A 5 PHE 0.012 0.001 PHE A 164 TRP 0.005 0.001 TRP A 464 HIS 0.008 0.001 HIS A1264 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 (11986) covalent geometry : angle 0.49568 / 0.29 (16831) hydrogen bonds : bond 0.05208 / 3.30 ( 546) hydrogen bonds : angle 4.11271 / 3.03 ( 1478) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.7954 (m-30) cc_final: 0.7245 (m-30) REVERT: A 304 ASP cc_start: 0.8492 (m-30) cc_final: 0.8282 (p0) REVERT: A 321 MET cc_start: 0.9030 (mmt) cc_final: 0.8697 (mmt) REVERT: A 465 MET cc_start: 0.8291 (ttp) cc_final: 0.8045 (tmm) REVERT: A 618 ASP cc_start: 0.8842 (t70) cc_final: 0.8334 (t0) REVERT: A 630 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8240 (pt0) REVERT: A 631 MET cc_start: 0.8347 (mmm) cc_final: 0.7651 (mmm) REVERT: A 653 ARG cc_start: 0.8033 (mtt180) cc_final: 0.7671 (mtm-85) REVERT: A 654 ARG cc_start: 0.7308 (tpt170) cc_final: 0.7052 (ttm170) REVERT: A 762 GLU cc_start: 0.7809 (pp20) cc_final: 0.7179 (tp30) REVERT: A 954 LYS cc_start: 0.8431 (mttt) cc_final: 0.8060 (ttmm) REVERT: A 1089 MET cc_start: 0.8535 (mtt) cc_final: 0.7752 (mtm) REVERT: A 1261 GLN cc_start: 0.8923 (mt0) cc_final: 0.8660 (mt0) REVERT: A 1303 ARG cc_start: 0.7568 (ptm-80) cc_final: 0.7325 (ptm-80) REVERT: A 1325 LYS cc_start: 0.8820 (tttt) cc_final: 0.8441 (ttmm) REVERT: A 1327 PHE cc_start: 0.8047 (m-80) cc_final: 0.7790 (m-80) REVERT: A 1339 THR cc_start: 0.9243 (p) cc_final: 0.8942 (t) outliers start: 15 outliers final: 11 residues processed: 105 average time/residue: 0.0972 time to fit residues: 15.0505 Evaluate side-chains 95 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1109 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 69 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 81 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.156149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.097054 restraints weight = 19082.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.100918 restraints weight = 9080.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.103285 restraints weight = 6318.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.104591 restraints weight = 5273.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.104895 restraints weight = 4813.949| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11986 Z= 0.179 Angle : 0.530 9.932 16831 Z= 0.307 Chirality : 0.040 0.231 1944 Planarity : 0.004 0.048 1601 Dihedral : 19.544 177.019 3143 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.57 % Favored : 96.33 % Rotamer: Outliers : 2.19 % Allowed : 11.94 % Favored : 85.87 % 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: 0.88 (0.26), residues: 1009 helix: 1.42 (0.23), residues: 515 sheet: 0.30 (0.49), residues: 112 loop : -0.40 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 951 TYR 0.025 0.001 TYR A 5 PHE 0.010 0.001 PHE A1258 TRP 0.004 0.001 TRP A1126 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (11986) covalent geometry : angle 0.53011 / 0.31 (16831) hydrogen bonds : bond 0.05592 / 3.58 ( 546) hydrogen bonds : angle 4.10399 / 3.02 ( 1478) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.7986 (m-30) cc_final: 0.7276 (m-30) REVERT: A 321 MET cc_start: 0.9017 (mmt) cc_final: 0.8799 (mmt) REVERT: A 465 MET cc_start: 0.8291 (ttp) cc_final: 0.8081 (tmm) REVERT: A 618 ASP cc_start: 0.8855 (t70) cc_final: 0.8357 (t0) REVERT: A 630 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8252 (pt0) REVERT: A 631 MET cc_start: 0.8376 (mmm) cc_final: 0.7664 (mmm) REVERT: A 653 ARG cc_start: 0.8019 (mtt180) cc_final: 0.7673 (mtm-85) REVERT: A 654 ARG cc_start: 0.7350 (tpt170) cc_final: 0.7124 (ttm170) REVERT: A 762 GLU cc_start: 0.7851 (pp20) cc_final: 0.7227 (tp30) REVERT: A 954 LYS cc_start: 0.8443 (mttt) cc_final: 0.8086 (ttmm) REVERT: A 956 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8091 (tt) REVERT: A 1261 GLN cc_start: 0.8966 (mt0) cc_final: 0.8694 (mt0) REVERT: A 1303 ARG cc_start: 0.7644 (ptm-80) cc_final: 0.7395 (ptm-80) REVERT: A 1325 LYS cc_start: 0.8850 (tttt) cc_final: 0.8460 (ttmm) REVERT: A 1339 THR cc_start: 0.9284 (p) cc_final: 0.8976 (t) outliers start: 20 outliers final: 18 residues processed: 104 average time/residue: 0.0971 time to fit residues: 14.7169 Evaluate side-chains 102 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 517 TYR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1240 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 72 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.164566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.106230 restraints weight = 19214.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110043 restraints weight = 9139.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.112323 restraints weight = 6373.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.113598 restraints weight = 5339.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.114135 restraints weight = 4878.846| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 11986 Z= 0.171 Angle : 0.519 9.337 16831 Z= 0.302 Chirality : 0.039 0.229 1944 Planarity : 0.004 0.047 1601 Dihedral : 19.541 176.428 3143 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.53 % Rotamer: Outliers : 2.30 % Allowed : 12.16 % Favored : 85.54 % 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: 0.85 (0.26), residues: 1009 helix: 1.40 (0.23), residues: 515 sheet: 0.34 (0.50), residues: 112 loop : -0.45 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 951 TYR 0.043 0.001 TYR A 5 PHE 0.011 0.001 PHE A1080 TRP 0.004 0.001 TRP A1126 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (11986) covalent geometry : angle 0.51851 / 0.30 (16831) hydrogen bonds : bond 0.05372 / 3.42 ( 546) hydrogen bonds : angle 4.05342 / 2.98 ( 1478) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.7967 (m-30) cc_final: 0.7256 (m-30) REVERT: A 178 ASN cc_start: 0.5396 (m-40) cc_final: 0.5129 (m110) REVERT: A 321 MET cc_start: 0.9024 (mmt) cc_final: 0.8693 (mmt) REVERT: A 465 MET cc_start: 0.8348 (ttp) cc_final: 0.8104 (tmm) REVERT: A 618 ASP cc_start: 0.8898 (t70) cc_final: 0.8385 (t0) REVERT: A 630 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8263 (pt0) REVERT: A 631 MET cc_start: 0.8373 (mmm) cc_final: 0.7638 (mmm) REVERT: A 653 ARG cc_start: 0.8034 (mtt180) cc_final: 0.7665 (mtm-85) REVERT: A 654 ARG cc_start: 0.7333 (tpt170) cc_final: 0.7070 (ttm170) REVERT: A 762 GLU cc_start: 0.7915 (pp20) cc_final: 0.7197 (tp30) REVERT: A 939 MET cc_start: 0.8398 (mmm) cc_final: 0.8065 (mmm) REVERT: A 954 LYS cc_start: 0.8439 (mttt) cc_final: 0.8088 (ttmm) REVERT: A 956 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8065 (tt) REVERT: A 1261 GLN cc_start: 0.8944 (mt0) cc_final: 0.8666 (mt0) REVERT: A 1325 LYS cc_start: 0.8852 (tttt) cc_final: 0.8468 (ttmm) REVERT: A 1339 THR cc_start: 0.9277 (p) cc_final: 0.8966 (t) outliers start: 21 outliers final: 16 residues processed: 105 average time/residue: 0.0906 time to fit residues: 14.0564 Evaluate side-chains 99 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 517 TYR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 956 ILE Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 9.9990 chunk 84 optimal weight: 0.0770 chunk 5 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 33 optimal weight: 0.0030 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 overall best weight: 0.9952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.158557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.099961 restraints weight = 18847.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.103907 restraints weight = 8891.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.106321 restraints weight = 6160.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.107687 restraints weight = 5123.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.108218 restraints weight = 4662.926| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11986 Z= 0.116 Angle : 0.495 12.457 16831 Z= 0.285 Chirality : 0.037 0.230 1944 Planarity : 0.003 0.045 1601 Dihedral : 19.484 175.957 3143 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.78 % Favored : 97.13 % Rotamer: Outliers : 1.31 % Allowed : 13.25 % Favored : 85.43 % 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: 0.97 (0.26), residues: 1009 helix: 1.51 (0.24), residues: 514 sheet: 0.48 (0.49), residues: 110 loop : -0.44 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 951 TYR 0.012 0.001 TYR A 5 PHE 0.011 0.001 PHE A 164 TRP 0.005 0.001 TRP A 464 HIS 0.003 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.12 (11986) covalent geometry : angle 0.49514 / 0.28 (16831) hydrogen bonds : bond 0.04773 / 3.01 ( 546) hydrogen bonds : angle 3.95346 / 2.92 ( 1478) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 124 ASP cc_start: 0.7944 (m-30) cc_final: 0.7211 (m-30) REVERT: A 178 ASN cc_start: 0.5572 (m-40) cc_final: 0.5363 (m110) REVERT: A 618 ASP cc_start: 0.8884 (t70) cc_final: 0.8358 (t0) REVERT: A 630 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8262 (pt0) REVERT: A 631 MET cc_start: 0.8306 (mmm) cc_final: 0.7594 (mmm) REVERT: A 653 ARG cc_start: 0.7989 (mtt180) cc_final: 0.7559 (mtm-85) REVERT: A 654 ARG cc_start: 0.7314 (tpt170) cc_final: 0.7006 (ttp-170) REVERT: A 762 GLU cc_start: 0.7892 (pp20) cc_final: 0.7171 (tp30) REVERT: A 939 MET cc_start: 0.8375 (mmm) cc_final: 0.8065 (mmm) REVERT: A 954 LYS cc_start: 0.8398 (mttt) cc_final: 0.8062 (ttmm) REVERT: A 956 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8081 (tt) REVERT: A 979 ASN cc_start: 0.8736 (p0) cc_final: 0.8504 (p0) REVERT: A 1261 GLN cc_start: 0.8940 (mt0) cc_final: 0.8639 (mt0) REVERT: A 1317 ASN cc_start: 0.8296 (t0) cc_final: 0.8018 (t0) REVERT: A 1325 LYS cc_start: 0.8816 (tttt) cc_final: 0.8433 (ttmm) REVERT: A 1327 PHE cc_start: 0.7982 (m-80) cc_final: 0.7749 (m-80) REVERT: A 1339 THR cc_start: 0.9293 (p) cc_final: 0.8947 (t) outliers start: 12 outliers final: 8 residues processed: 97 average time/residue: 0.1109 time to fit residues: 15.5793 Evaluate side-chains 94 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 956 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 36 optimal weight: 0.0170 chunk 56 optimal weight: 9.9990 chunk 112 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.164180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.114110 restraints weight = 19396.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.114409 restraints weight = 10814.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.114189 restraints weight = 9329.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114500 restraints weight = 6790.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.116561 restraints weight = 6313.934| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11986 Z= 0.196 Angle : 0.551 9.068 16831 Z= 0.313 Chirality : 0.040 0.229 1944 Planarity : 0.004 0.047 1601 Dihedral : 19.531 176.761 3143 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.47 % Favored : 96.43 % Rotamer: Outliers : 1.42 % Allowed : 13.25 % Favored : 85.32 % 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: 0.83 (0.26), residues: 1009 helix: 1.44 (0.24), residues: 513 sheet: 0.24 (0.49), residues: 113 loop : -0.51 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 951 TYR 0.011 0.001 TYR A 450 PHE 0.012 0.001 PHE A1080 TRP 0.004 0.001 TRP A 659 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 (11986) covalent geometry : angle 0.55136 / 0.31 (16831) hydrogen bonds : bond 0.05557 / 3.56 ( 546) hydrogen bonds : angle 4.04417 / 2.98 ( 1478) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 ASN cc_start: 0.5807 (m-40) cc_final: 0.5601 (m110) REVERT: A 618 ASP cc_start: 0.8779 (t70) cc_final: 0.8280 (t0) REVERT: A 630 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8228 (pt0) REVERT: A 631 MET cc_start: 0.8188 (mmm) cc_final: 0.7458 (mmm) REVERT: A 653 ARG cc_start: 0.7888 (mtt180) cc_final: 0.7506 (ttm-80) REVERT: A 954 LYS cc_start: 0.8489 (mttt) cc_final: 0.8167 (ttmm) REVERT: A 1261 GLN cc_start: 0.8943 (mt0) cc_final: 0.8667 (mt0) REVERT: A 1303 ARG cc_start: 0.7670 (ptm-80) cc_final: 0.7441 (ptm-80) REVERT: A 1325 LYS cc_start: 0.8831 (tttt) cc_final: 0.8445 (ttmm) REVERT: A 1339 THR cc_start: 0.9245 (p) cc_final: 0.8926 (t) outliers start: 13 outliers final: 12 residues processed: 97 average time/residue: 0.1106 time to fit residues: 15.5586 Evaluate side-chains 91 residues out of total 913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 517 TYR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 992 VAL Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 72 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 95 optimal weight: 10.0000 chunk 105 optimal weight: 50.0000 chunk 63 optimal weight: 0.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1308 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.155377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.096661 restraints weight = 18925.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.100443 restraints weight = 9053.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.102689 restraints weight = 6311.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.103961 restraints weight = 5283.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.104536 restraints weight = 4825.735| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11986 Z= 0.197 Angle : 0.545 8.318 16831 Z= 0.313 Chirality : 0.040 0.227 1944 Planarity : 0.004 0.047 1601 Dihedral : 19.578 176.352 3143 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.67 % Favored : 96.23 % Rotamer: Outliers : 1.10 % Allowed : 14.02 % Favored : 84.88 % 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: 0.70 (0.26), residues: 1009 helix: 1.33 (0.23), residues: 513 sheet: 0.18 (0.50), residues: 113 loop : -0.56 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 951 TYR 0.015 0.001 TYR A 5 PHE 0.011 0.001 PHE A1080 TRP 0.003 0.001 TRP A 476 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 (11986) covalent geometry : angle 0.54543 / 0.31 (16831) hydrogen bonds : bond 0.05533 / 3.52 ( 546) hydrogen bonds : angle 4.10796 / 3.01 ( 1478) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1883.01 seconds wall clock time: 33 minutes 10.91 seconds (1990.91 seconds total)