Starting phenix.real_space_refine on Thu Aug 6 05:34:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ed9_47941/08_2026/9ed9_47941.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ed9_47941/08_2026/9ed9_47941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ed9_47941/08_2026/9ed9_47941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ed9_47941/08_2026/9ed9_47941.map" model { file = "/net/cci-nas-00/data/ceres_data/9ed9_47941/08_2026/9ed9_47941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ed9_47941/08_2026/9ed9_47941.cif" } resolution = 2.95 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= -0.000 sd= 0.012 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 143 5.49 5 S 22 5.16 5 C 8244 2.51 5 N 2400 2.21 5 O 2976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13785 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 2038 Classifications: {'RNA': 95} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 51, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 83} Chain: "C" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 302 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "D" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "c" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 10767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10767 Classifications: {'peptide': 1337} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 35, 'TRANS': 1301} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 8, 'ASP:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 87 Time building chain proxies: 2.86, per 1000 atoms: 0.21 Number of scatterers: 13785 At special positions: 0 Unit cell: (89.9856, 137.478, 122.48, 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 22 16.00 P 143 15.00 O 2976 8.00 N 2400 7.00 C 8244 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: 0.93 Conformation dependent library (CDL) restraints added in 398.5 milliseconds 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2546 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 9 sheets defined 54.7% alpha, 7.6% beta 50 base pairs and 96 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.890A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (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: 3.772A 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 180 through 196 Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.551A pdb=" N PHE A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 286 through 304 removed outlier: 3.930A pdb=" N ASP A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 347 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 387 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.837A pdb=" N ASN A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.229A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 4.045A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 445 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 512 through 527 removed outlier: 3.689A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 557 removed outlier: 4.300A pdb=" N LYS A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.516A pdb=" N LEU A 616 " --> pdb=" O ASN A 612 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 639 through 643 removed outlier: 3.562A pdb=" N LEU A 642 " --> pdb=" O TYR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 654 Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 703 through 714 Processing helix chain 'A' and resid 719 through 727 removed outlier: 3.720A pdb=" N LEU A 727 " --> pdb=" O HIS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 751 Processing helix chain 'A' and resid 776 through 792 Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 803 through 807 Processing helix chain 'A' and resid 808 through 817 removed outlier: 3.598A pdb=" N GLN A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 865 removed outlier: 3.789A pdb=" N ASN A 863 " --> pdb=" O SER A 860 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A 865 " --> pdb=" O LYS A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 888 removed outlier: 5.657A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 902 Processing helix chain 'A' and resid 909 through 919 Processing helix chain 'A' and resid 925 through 940 Processing helix chain 'A' and resid 959 through 969 removed outlier: 4.228A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.312A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 Processing helix chain 'A' and resid 1032 through 1041 Processing helix chain 'A' and resid 1078 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 4.530A pdb=" N SER A1172 " --> pdb=" O ILE A1168 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N SER A1173 " --> pdb=" O MET A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1263 through 1281 removed outlier: 4.311A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 Processing helix chain 'A' and resid 1340 through 1344 Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 955 through 957 removed outlier: 6.187A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 9.705A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 509 removed outlier: 5.330A pdb=" N LEU A 508 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA5, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA6, first strand: chain 'A' and resid 1049 through 1050 Processing sheet with id=AA7, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 3.978A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1156 through 1167 Processing sheet with id=AA9, first strand: chain 'A' and resid 1324 through 1326 520 hydrogen bonds defined for protein. 1503 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 238 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 96 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2478 1.33 - 1.45: 4237 1.45 - 1.57: 7298 1.57 - 1.70: 283 1.70 - 1.82: 42 Bond restraints: 14338 Sorted by residual: bond pdb=" C3' DG D 1 " pdb=" C2' DG D 1 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.22e+00 bond pdb=" C3' DG C 18 " pdb=" C2' DG C 18 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.96e+00 bond pdb=" C3' DG c 3 " pdb=" C2' DG c 3 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.21e+00 bond pdb=" C3' DC c 2 " pdb=" C2' DC c 2 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.16e+00 bond pdb=" C3' DC c -4 " pdb=" C2' DC c -4 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.15e+00 ... (remaining 14333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 19751 3.11 - 6.21: 207 6.21 - 9.32: 27 9.32 - 12.43: 16 12.43 - 15.53: 2 Bond angle restraints: 20003 Sorted by residual: angle pdb=" CG ARG A 664 " pdb=" CD ARG A 664 " pdb=" NE ARG A 664 " ideal model delta sigma weight residual 112.00 123.52 -11.52 2.20e+00 2.07e-01 2.74e+01 angle pdb=" CA LYS A 558 " pdb=" CB LYS A 558 " pdb=" CG LYS A 558 " ideal model delta sigma weight residual 114.10 123.72 -9.62 2.00e+00 2.50e-01 2.31e+01 angle pdb=" O4' DC C 7 " pdb=" C4' DC C 7 " pdb=" C3' DC C 7 " ideal model delta sigma weight residual 106.00 103.16 2.84 6.00e-01 2.78e+00 2.23e+01 angle pdb=" CA LYS A 382 " pdb=" CB LYS A 382 " pdb=" CG LYS A 382 " ideal model delta sigma weight residual 114.10 123.39 -9.29 2.00e+00 2.50e-01 2.16e+01 angle pdb=" C1' C B 18 " pdb=" N1 C B 18 " pdb=" C2 C B 18 " ideal model delta sigma weight residual 118.80 123.85 -5.05 1.10e+00 8.26e-01 2.11e+01 ... (remaining 19998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7254 17.97 - 35.93: 854 35.93 - 53.90: 336 53.90 - 71.86: 168 71.86 - 89.83: 32 Dihedral angle restraints: 8644 sinusoidal: 4710 harmonic: 3934 Sorted by residual: dihedral pdb=" CA ASP A 969 " pdb=" C ASP A 969 " pdb=" N PHE A 970 " pdb=" CA PHE A 970 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA THR A 555 " pdb=" C THR A 555 " pdb=" N ASN A 556 " pdb=" CA ASN A 556 " ideal model delta harmonic sigma weight residual -180.00 -156.36 -23.64 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ASN A 692 " pdb=" C ASN A 692 " pdb=" N PHE A 693 " pdb=" CA PHE A 693 " ideal model delta harmonic sigma weight residual -180.00 -158.48 -21.52 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 8641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2183 0.117 - 0.234: 125 0.234 - 0.351: 0 0.351 - 0.469: 1 0.469 - 0.586: 1 Chirality restraints: 2310 Sorted by residual: chirality pdb=" CG LEU A 636 " pdb=" CB LEU A 636 " pdb=" CD1 LEU A 636 " pdb=" CD2 LEU A 636 " both_signs ideal model delta sigma weight residual False -2.59 -2.00 -0.59 2.00e-01 2.50e+01 8.58e+00 chirality pdb=" P DT C 4 " pdb=" OP1 DT C 4 " pdb=" OP2 DT C 4 " pdb=" O5' DT C 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.75 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CG LEU A 540 " pdb=" CB LEU A 540 " pdb=" CD1 LEU A 540 " pdb=" CD2 LEU A 540 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 2307 not shown) Planarity restraints: 2041 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 549 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C VAL A 549 " -0.066 2.00e-02 2.50e+03 pdb=" O VAL A 549 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP A 550 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 565 " -0.015 2.00e-02 2.50e+03 3.11e-02 9.64e+00 pdb=" C LYS A 565 " 0.054 2.00e-02 2.50e+03 pdb=" O LYS A 565 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A 566 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 382 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.86e+00 pdb=" C LYS A 382 " -0.048 2.00e-02 2.50e+03 pdb=" O LYS A 382 " 0.019 2.00e-02 2.50e+03 pdb=" N MET A 383 " 0.015 2.00e-02 2.50e+03 ... (remaining 2038 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3007 2.79 - 3.31: 12191 3.31 - 3.84: 24853 3.84 - 4.37: 29097 4.37 - 4.90: 45443 Nonbonded interactions: 114591 Sorted by model distance: nonbonded pdb=" O2' U B 22 " pdb=" O ILE A1110 " model vdw 2.258 3.040 nonbonded pdb=" O2' A B 47 " pdb=" O LEU A 101 " model vdw 2.267 3.040 nonbonded pdb=" OG1 THR A 249 " pdb=" OE1 GLN A 265 " model vdw 2.271 3.040 nonbonded pdb=" NE2 GLN A 817 " pdb=" O ARG A 820 " model vdw 2.309 3.120 nonbonded pdb=" O LYS A 209 " pdb=" OG SER A 213 " model vdw 2.310 3.040 ... (remaining 114586 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.640 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.250 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14338 Z= 0.297 Angle : 0.925 15.532 20003 Z= 0.605 Chirality : 0.054 0.586 2310 Planarity : 0.006 0.063 2041 Dihedral : 19.236 89.831 6098 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.52 % Allowed : 21.23 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.21), residues: 1329 helix: -0.24 (0.18), residues: 648 sheet: -0.01 (0.47), residues: 133 loop : -1.04 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 653 TYR 0.038 0.002 TYR A 594 PHE 0.047 0.003 PHE A 970 TRP 0.026 0.003 TRP A 883 HIS 0.009 0.001 HIS A 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.30 (14338) covalent geometry : angle 0.92477 / 0.60 (20003) hydrogen bonds : bond 0.13248 / 15.00 ( 641) hydrogen bonds : angle 6.12496 / 7.84 ( 1741) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.9437 (tm) cc_final: 0.9229 (tm) REVERT: A 500 LYS cc_start: 0.8190 (mmtt) cc_final: 0.7836 (mmtm) REVERT: A 648 MET cc_start: 0.7319 (ppp) cc_final: 0.7094 (tmm) REVERT: A 828 LEU cc_start: 0.6784 (pp) cc_final: 0.6344 (mm) REVERT: A 846 PHE cc_start: 0.8416 (m-10) cc_final: 0.7953 (m-10) REVERT: A 933 GLN cc_start: 0.9001 (tt0) cc_final: 0.8676 (tp40) REVERT: A 964 SER cc_start: 0.9118 (t) cc_final: 0.8735 (m) REVERT: A 1043 MET cc_start: 0.7997 (mmm) cc_final: 0.7731 (mmp) REVERT: A 1192 LYS cc_start: 0.8373 (tttt) cc_final: 0.8007 (tmtt) outliers start: 6 outliers final: 3 residues processed: 112 average time/residue: 0.5359 time to fit residues: 65.9804 Evaluate side-chains 101 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 762 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 854 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.125025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.081345 restraints weight = 24376.009| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.36 r_work: 0.2957 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14338 Z= 0.146 Angle : 0.577 11.032 20003 Z= 0.320 Chirality : 0.040 0.197 2310 Planarity : 0.004 0.047 2041 Dihedral : 19.291 83.239 3407 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.07 % Allowed : 19.50 % Favored : 78.43 % 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: -0.08 (0.22), residues: 1329 helix: 0.71 (0.20), residues: 658 sheet: -0.17 (0.47), residues: 131 loop : -0.89 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 653 TYR 0.012 0.001 TYR A 155 PHE 0.020 0.002 PHE A 970 TRP 0.015 0.001 TRP A 883 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 (14338) covalent geometry : angle 0.57712 / 0.32 (20003) hydrogen bonds : bond 0.04428 / 4.93 ( 641) hydrogen bonds : angle 4.91937 / 6.43 ( 1741) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7621 (mm) REVERT: A 296 LEU cc_start: 0.9290 (tm) cc_final: 0.9037 (tm) REVERT: A 500 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7697 (mmtm) REVERT: A 628 ASP cc_start: 0.7899 (t0) cc_final: 0.7543 (t0) REVERT: A 648 MET cc_start: 0.7208 (ppp) cc_final: 0.6954 (tmm) REVERT: A 655 ARG cc_start: 0.7796 (mmm-85) cc_final: 0.7545 (mmm-85) REVERT: A 828 LEU cc_start: 0.6514 (pp) cc_final: 0.6115 (mm) REVERT: A 846 PHE cc_start: 0.8348 (m-10) cc_final: 0.7926 (m-10) REVERT: A 933 GLN cc_start: 0.8871 (tt0) cc_final: 0.8358 (tp40) REVERT: A 964 SER cc_start: 0.8722 (t) cc_final: 0.8340 (m) REVERT: A 1192 LYS cc_start: 0.8426 (tttt) cc_final: 0.7825 (tmtt) REVERT: A 1340 LYS cc_start: 0.8789 (tptt) cc_final: 0.8463 (mptt) outliers start: 24 outliers final: 9 residues processed: 117 average time/residue: 0.4745 time to fit residues: 61.3598 Evaluate side-chains 106 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1072 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN A 501 ASN ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN A1364 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.123583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.079690 restraints weight = 24588.833| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.35 r_work: 0.2927 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14338 Z= 0.156 Angle : 0.543 10.470 20003 Z= 0.303 Chirality : 0.040 0.196 2310 Planarity : 0.004 0.049 2041 Dihedral : 19.180 84.074 3402 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.42 % Allowed : 18.03 % Favored : 79.55 % 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: 0.33 (0.23), residues: 1329 helix: 1.12 (0.20), residues: 659 sheet: -0.34 (0.47), residues: 131 loop : -0.70 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 653 TYR 0.019 0.001 TYR A 812 PHE 0.022 0.002 PHE A 970 TRP 0.008 0.001 TRP A 883 HIS 0.006 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (14338) covalent geometry : angle 0.54319 / 0.30 (20003) hydrogen bonds : bond 0.04182 / 4.63 ( 641) hydrogen bonds : angle 4.69356 / 6.10 ( 1741) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.9126 (OUTLIER) cc_final: 0.8892 (p) REVERT: A 500 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7790 (mmtm) REVERT: A 648 MET cc_start: 0.7311 (ppp) cc_final: 0.6968 (tmm) REVERT: A 828 LEU cc_start: 0.6490 (pp) cc_final: 0.6119 (mm) REVERT: A 846 PHE cc_start: 0.8426 (m-10) cc_final: 0.7994 (m-10) REVERT: A 933 GLN cc_start: 0.8908 (tt0) cc_final: 0.8394 (tp40) REVERT: A 1192 LYS cc_start: 0.8477 (tttt) cc_final: 0.7868 (tmtt) REVERT: A 1340 LYS cc_start: 0.8770 (tptt) cc_final: 0.8446 (mptt) outliers start: 28 outliers final: 10 residues processed: 125 average time/residue: 0.4860 time to fit residues: 66.8223 Evaluate side-chains 110 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1072 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 104 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 114 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 61 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.123655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.079697 restraints weight = 24568.364| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.33 r_work: 0.2930 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14338 Z= 0.139 Angle : 0.523 11.123 20003 Z= 0.292 Chirality : 0.038 0.186 2310 Planarity : 0.004 0.047 2041 Dihedral : 19.166 84.120 3402 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.50 % Allowed : 17.86 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.23), residues: 1329 helix: 1.29 (0.20), residues: 659 sheet: -0.44 (0.47), residues: 131 loop : -0.66 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 467 TYR 0.016 0.001 TYR A 529 PHE 0.020 0.001 PHE A 916 TRP 0.008 0.001 TRP A 464 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (14338) covalent geometry : angle 0.52277 / 0.29 (20003) hydrogen bonds : bond 0.03828 / 4.25 ( 641) hydrogen bonds : angle 4.56043 / 5.95 ( 1741) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8923 (p) REVERT: A 218 LYS cc_start: 0.7985 (mtmt) cc_final: 0.7677 (mtmt) REVERT: A 500 LYS cc_start: 0.8320 (mmtt) cc_final: 0.7858 (mmtm) REVERT: A 628 ASP cc_start: 0.8047 (t0) cc_final: 0.7484 (t0) REVERT: A 648 MET cc_start: 0.7334 (ppp) cc_final: 0.6943 (tmm) REVERT: A 655 ARG cc_start: 0.7558 (tpt-90) cc_final: 0.7081 (tpt90) REVERT: A 709 GLN cc_start: 0.8204 (pp30) cc_final: 0.7637 (tp40) REVERT: A 822 MET cc_start: 0.6418 (mmt) cc_final: 0.6100 (mmt) REVERT: A 828 LEU cc_start: 0.6643 (pp) cc_final: 0.6205 (mm) REVERT: A 846 PHE cc_start: 0.8466 (m-10) cc_final: 0.8038 (m-10) REVERT: A 879 MET cc_start: 0.1594 (OUTLIER) cc_final: 0.1296 (mmm) REVERT: A 933 GLN cc_start: 0.8929 (tt0) cc_final: 0.8395 (tp40) REVERT: A 1080 PHE cc_start: 0.7288 (m-10) cc_final: 0.7003 (m-10) REVERT: A 1192 LYS cc_start: 0.8492 (tttt) cc_final: 0.7878 (tmtt) REVERT: A 1340 LYS cc_start: 0.8747 (tptt) cc_final: 0.8433 (mptt) outliers start: 29 outliers final: 11 residues processed: 120 average time/residue: 0.4946 time to fit residues: 65.7439 Evaluate side-chains 111 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1072 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 33 optimal weight: 0.0870 chunk 82 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 133 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN A1364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.124145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.080343 restraints weight = 24673.009| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.34 r_work: 0.2942 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14338 Z= 0.122 Angle : 0.493 10.395 20003 Z= 0.275 Chirality : 0.037 0.155 2310 Planarity : 0.003 0.045 2041 Dihedral : 19.052 84.476 3402 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.07 % Allowed : 18.29 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.23), residues: 1329 helix: 1.48 (0.20), residues: 660 sheet: -0.38 (0.48), residues: 126 loop : -0.65 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1359 TYR 0.011 0.001 TYR A 812 PHE 0.011 0.001 PHE A 446 TRP 0.008 0.001 TRP A 464 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (14338) covalent geometry : angle 0.49256 / 0.27 (20003) hydrogen bonds : bond 0.03608 / 3.99 ( 641) hydrogen bonds : angle 4.43313 / 5.80 ( 1741) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LYS cc_start: 0.7950 (mtmt) cc_final: 0.7679 (mtmt) REVERT: A 500 LYS cc_start: 0.8307 (mmtt) cc_final: 0.7827 (mmtm) REVERT: A 628 ASP cc_start: 0.7879 (t0) cc_final: 0.7291 (t70) REVERT: A 645 ASP cc_start: 0.7765 (p0) cc_final: 0.7531 (p0) REVERT: A 648 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6962 (tmm) REVERT: A 655 ARG cc_start: 0.7578 (tpt-90) cc_final: 0.7276 (tpt-90) REVERT: A 709 GLN cc_start: 0.8290 (pp30) cc_final: 0.7639 (tp40) REVERT: A 746 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8519 (tt0) REVERT: A 815 TYR cc_start: 0.9009 (m-10) cc_final: 0.8784 (m-10) REVERT: A 828 LEU cc_start: 0.6780 (pp) cc_final: 0.6330 (mm) REVERT: A 846 PHE cc_start: 0.8530 (m-10) cc_final: 0.8183 (m-10) REVERT: A 879 MET cc_start: 0.1758 (OUTLIER) cc_final: 0.1385 (mmm) REVERT: A 933 GLN cc_start: 0.8945 (tt0) cc_final: 0.8398 (tp40) REVERT: A 1049 GLU cc_start: 0.7908 (pm20) cc_final: 0.6808 (pp20) REVERT: A 1340 LYS cc_start: 0.8728 (tptt) cc_final: 0.8434 (mptt) outliers start: 24 outliers final: 10 residues processed: 119 average time/residue: 0.4554 time to fit residues: 60.2494 Evaluate side-chains 111 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1072 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 72 optimal weight: 0.0060 chunk 44 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.124028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.080334 restraints weight = 24393.438| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.31 r_work: 0.2941 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14338 Z= 0.121 Angle : 0.508 13.163 20003 Z= 0.277 Chirality : 0.037 0.182 2310 Planarity : 0.003 0.045 2041 Dihedral : 18.968 84.948 3400 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.33 % Allowed : 18.38 % Favored : 79.29 % 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: 0.74 (0.23), residues: 1329 helix: 1.58 (0.20), residues: 660 sheet: -0.42 (0.48), residues: 126 loop : -0.59 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 653 TYR 0.012 0.001 TYR A 155 PHE 0.017 0.001 PHE A 970 TRP 0.008 0.001 TRP A 464 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (14338) covalent geometry : angle 0.50824 / 0.28 (20003) hydrogen bonds : bond 0.03572 / 3.95 ( 641) hydrogen bonds : angle 4.37390 / 5.71 ( 1741) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LYS cc_start: 0.7909 (mtmt) cc_final: 0.7683 (mtmt) REVERT: A 500 LYS cc_start: 0.8317 (mmtt) cc_final: 0.7738 (mmtm) REVERT: A 628 ASP cc_start: 0.7891 (t0) cc_final: 0.7421 (t70) REVERT: A 631 MET cc_start: 0.8445 (mmp) cc_final: 0.8245 (mmp) REVERT: A 648 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6955 (tmm) REVERT: A 709 GLN cc_start: 0.8329 (pp30) cc_final: 0.7705 (tp40) REVERT: A 746 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8509 (tt0) REVERT: A 822 MET cc_start: 0.6005 (mmt) cc_final: 0.5623 (mmt) REVERT: A 846 PHE cc_start: 0.8623 (m-10) cc_final: 0.8153 (m-10) REVERT: A 879 MET cc_start: 0.1529 (OUTLIER) cc_final: 0.1062 (mmm) REVERT: A 933 GLN cc_start: 0.8926 (tt0) cc_final: 0.8382 (tp40) REVERT: A 959 LYS cc_start: 0.8305 (ttmt) cc_final: 0.8093 (mtpt) REVERT: A 1340 LYS cc_start: 0.8725 (tptt) cc_final: 0.8438 (mptt) outliers start: 27 outliers final: 12 residues processed: 121 average time/residue: 0.5209 time to fit residues: 69.8863 Evaluate side-chains 111 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1072 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 91 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 61 optimal weight: 0.0670 chunk 108 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.122548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.078580 restraints weight = 24481.278| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.30 r_work: 0.2909 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14338 Z= 0.159 Angle : 0.532 12.084 20003 Z= 0.289 Chirality : 0.038 0.184 2310 Planarity : 0.003 0.045 2041 Dihedral : 18.958 85.791 3400 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.67 % Allowed : 18.55 % Favored : 78.77 % 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: 0.75 (0.23), residues: 1329 helix: 1.59 (0.20), residues: 660 sheet: -0.45 (0.48), residues: 126 loop : -0.59 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 653 TYR 0.015 0.001 TYR A 155 PHE 0.011 0.001 PHE A 446 TRP 0.008 0.001 TRP A 464 HIS 0.006 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (14338) covalent geometry : angle 0.53176 / 0.29 (20003) hydrogen bonds : bond 0.03826 / 4.19 ( 641) hydrogen bonds : angle 4.40623 / 5.77 ( 1741) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LYS cc_start: 0.7879 (mtmt) cc_final: 0.7640 (mtmt) REVERT: A 500 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7726 (mmtm) REVERT: A 628 ASP cc_start: 0.8047 (t0) cc_final: 0.7572 (t70) REVERT: A 648 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.7030 (tmm) REVERT: A 709 GLN cc_start: 0.8465 (pp30) cc_final: 0.7798 (tp40) REVERT: A 746 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8548 (tt0) REVERT: A 815 TYR cc_start: 0.9077 (m-10) cc_final: 0.8833 (m-10) REVERT: A 822 MET cc_start: 0.6020 (mmt) cc_final: 0.5786 (mmt) REVERT: A 828 LEU cc_start: 0.6720 (pp) cc_final: 0.6208 (mm) REVERT: A 846 PHE cc_start: 0.8622 (m-10) cc_final: 0.8166 (m-10) REVERT: A 879 MET cc_start: 0.1483 (OUTLIER) cc_final: 0.1115 (mmm) REVERT: A 920 GLN cc_start: 0.8948 (mp10) cc_final: 0.8432 (mp10) REVERT: A 933 GLN cc_start: 0.8957 (tt0) cc_final: 0.8398 (tp40) REVERT: A 1340 LYS cc_start: 0.8744 (tptt) cc_final: 0.8437 (mptt) outliers start: 31 outliers final: 11 residues processed: 126 average time/residue: 0.5903 time to fit residues: 81.8859 Evaluate side-chains 111 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1089 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 131 optimal weight: 0.6980 chunk 34 optimal weight: 0.0020 chunk 49 optimal weight: 0.0770 chunk 85 optimal weight: 0.6980 chunk 101 optimal weight: 8.9990 chunk 14 optimal weight: 0.2980 chunk 72 optimal weight: 0.9990 chunk 63 optimal weight: 0.0270 chunk 124 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.2204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.124544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.080938 restraints weight = 24255.241| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.32 r_work: 0.2944 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 14338 Z= 0.110 Angle : 0.529 13.066 20003 Z= 0.285 Chirality : 0.037 0.181 2310 Planarity : 0.003 0.044 2041 Dihedral : 18.937 85.716 3400 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.81 % Allowed : 20.02 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.87 (0.23), residues: 1329 helix: 1.68 (0.20), residues: 667 sheet: -0.42 (0.48), residues: 122 loop : -0.54 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 653 TYR 0.012 0.001 TYR A 812 PHE 0.031 0.001 PHE A 682 TRP 0.006 0.001 TRP A 464 HIS 0.003 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (14338) covalent geometry : angle 0.52893 / 0.28 (20003) hydrogen bonds : bond 0.03488 / 3.88 ( 641) hydrogen bonds : angle 4.36897 / 5.69 ( 1741) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LYS cc_start: 0.7875 (mtmt) cc_final: 0.7625 (mtmt) REVERT: A 500 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7639 (mmtm) REVERT: A 628 ASP cc_start: 0.8009 (t0) cc_final: 0.7447 (t70) REVERT: A 648 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.7022 (tmm) REVERT: A 709 GLN cc_start: 0.8453 (pp30) cc_final: 0.7756 (tp40) REVERT: A 815 TYR cc_start: 0.9048 (m-10) cc_final: 0.8832 (m-10) REVERT: A 822 MET cc_start: 0.6127 (mmt) cc_final: 0.5871 (mmt) REVERT: A 846 PHE cc_start: 0.8625 (m-10) cc_final: 0.8131 (m-10) REVERT: A 879 MET cc_start: 0.1389 (OUTLIER) cc_final: 0.1029 (mmm) REVERT: A 920 GLN cc_start: 0.8938 (mp10) cc_final: 0.7991 (mp10) REVERT: A 933 GLN cc_start: 0.8900 (tt0) cc_final: 0.8348 (tp40) REVERT: A 959 LYS cc_start: 0.8216 (ttpp) cc_final: 0.7816 (ptmt) REVERT: A 964 SER cc_start: 0.8723 (t) cc_final: 0.8357 (m) REVERT: A 1049 GLU cc_start: 0.7730 (pm20) cc_final: 0.6707 (pp20) REVERT: A 1340 LYS cc_start: 0.8691 (tptt) cc_final: 0.8424 (mptt) outliers start: 21 outliers final: 11 residues processed: 115 average time/residue: 0.5560 time to fit residues: 70.6379 Evaluate side-chains 111 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1072 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 109 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 49 optimal weight: 0.0970 chunk 104 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 121 optimal weight: 0.2980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.124130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.081094 restraints weight = 24477.576| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.16 r_work: 0.2940 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14338 Z= 0.121 Angle : 0.530 12.514 20003 Z= 0.285 Chirality : 0.037 0.222 2310 Planarity : 0.003 0.044 2041 Dihedral : 18.905 86.175 3400 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.38 % Allowed : 20.62 % Favored : 78.00 % 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 (0.23), residues: 1329 helix: 1.75 (0.20), residues: 667 sheet: -0.38 (0.47), residues: 126 loop : -0.51 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 653 TYR 0.014 0.001 TYR A 529 PHE 0.024 0.001 PHE A 682 TRP 0.007 0.001 TRP A 464 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (14338) covalent geometry : angle 0.53032 / 0.29 (20003) hydrogen bonds : bond 0.03458 / 3.78 ( 641) hydrogen bonds : angle 4.30907 / 5.63 ( 1741) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LYS cc_start: 0.7882 (mtmt) cc_final: 0.7624 (mtmt) REVERT: A 500 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7717 (mmtm) REVERT: A 558 LYS cc_start: 0.8645 (mmtp) cc_final: 0.8364 (mmmm) REVERT: A 628 ASP cc_start: 0.7985 (t0) cc_final: 0.7489 (t70) REVERT: A 648 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7103 (tmm) REVERT: A 846 PHE cc_start: 0.8695 (m-10) cc_final: 0.8143 (m-10) REVERT: A 879 MET cc_start: 0.1437 (OUTLIER) cc_final: 0.1064 (mmm) REVERT: A 920 GLN cc_start: 0.8997 (mp10) cc_final: 0.8379 (mp10) REVERT: A 933 GLN cc_start: 0.8978 (tt0) cc_final: 0.8439 (tp40) REVERT: A 964 SER cc_start: 0.8851 (t) cc_final: 0.8498 (m) REVERT: A 1049 GLU cc_start: 0.7874 (pm20) cc_final: 0.6861 (pp20) REVERT: A 1340 LYS cc_start: 0.8751 (tptt) cc_final: 0.8526 (mptt) outliers start: 16 outliers final: 11 residues processed: 109 average time/residue: 0.5378 time to fit residues: 65.4310 Evaluate side-chains 107 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1072 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 67 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 68 optimal weight: 0.0870 chunk 129 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.123855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.080663 restraints weight = 24406.599| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.15 r_work: 0.2929 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14338 Z= 0.133 Angle : 0.549 13.209 20003 Z= 0.291 Chirality : 0.038 0.201 2310 Planarity : 0.003 0.044 2041 Dihedral : 18.905 86.667 3400 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.29 % Allowed : 20.79 % Favored : 77.91 % 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: 0.98 (0.23), residues: 1329 helix: 1.76 (0.20), residues: 667 sheet: -0.38 (0.47), residues: 126 loop : -0.48 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 653 TYR 0.012 0.001 TYR A 155 PHE 0.024 0.001 PHE A 970 TRP 0.007 0.001 TRP A 464 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (14338) covalent geometry : angle 0.54888 / 0.29 (20003) hydrogen bonds : bond 0.03556 / 3.92 ( 641) hydrogen bonds : angle 4.33367 / 5.63 ( 1741) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LYS cc_start: 0.7880 (mtmt) cc_final: 0.7618 (mtmt) REVERT: A 558 LYS cc_start: 0.8623 (mmtp) cc_final: 0.8346 (mmmm) REVERT: A 628 ASP cc_start: 0.7970 (t0) cc_final: 0.7429 (t70) REVERT: A 648 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7123 (tmm) REVERT: A 822 MET cc_start: 0.6109 (mmt) cc_final: 0.4292 (mpt) REVERT: A 828 LEU cc_start: 0.6524 (pp) cc_final: 0.5849 (mm) REVERT: A 846 PHE cc_start: 0.8703 (m-10) cc_final: 0.8228 (m-10) REVERT: A 920 GLN cc_start: 0.8984 (mp10) cc_final: 0.8298 (mp10) REVERT: A 933 GLN cc_start: 0.8981 (tt0) cc_final: 0.8448 (tp40) REVERT: A 964 SER cc_start: 0.8865 (t) cc_final: 0.8504 (m) REVERT: A 1049 GLU cc_start: 0.7918 (pm20) cc_final: 0.6917 (pp20) REVERT: A 1340 LYS cc_start: 0.8752 (tptt) cc_final: 0.8526 (mptt) outliers start: 15 outliers final: 9 residues processed: 104 average time/residue: 0.5675 time to fit residues: 65.4506 Evaluate side-chains 104 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1072 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 52 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 135 optimal weight: 0.6980 chunk 129 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 140 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 ASN ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.123785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.080617 restraints weight = 24496.406| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.15 r_work: 0.2929 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14338 Z= 0.131 Angle : 0.536 13.227 20003 Z= 0.287 Chirality : 0.037 0.187 2310 Planarity : 0.003 0.045 2041 Dihedral : 18.902 86.985 3400 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.12 % Allowed : 21.23 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.23), residues: 1329 helix: 1.79 (0.20), residues: 667 sheet: -0.40 (0.47), residues: 122 loop : -0.49 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 653 TYR 0.014 0.001 TYR A 529 PHE 0.028 0.001 PHE A 970 TRP 0.007 0.001 TRP A 464 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (14338) covalent geometry : angle 0.53556 / 0.29 (20003) hydrogen bonds : bond 0.03529 / 3.85 ( 641) hydrogen bonds : angle 4.30887 / 5.62 ( 1741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4646.59 seconds wall clock time: 79 minutes 56.10 seconds (4796.10 seconds total)