Starting phenix.real_space_refine on Fri Jul 3 10:51:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ed9_47941/07_2026/9ed9_47941.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ed9_47941/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ed9_47941/07_2026/9ed9_47941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ed9_47941/07_2026/9ed9_47941.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ed9_47941/07_2026/9ed9_47941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ed9_47941/07_2026/9ed9_47941.map" } 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-dev-6108/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: 3.25, per 1000 atoms: 0.24 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: 1.08 Conformation dependent library (CDL) restraints added in 640.3 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: 1.64 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: 3.61 Time building geometry restraints manager: 1.41 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: 19752 3.11 - 6.21: 206 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: 2265 0.117 - 0.234: 43 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: 17.790 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.280 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.190 ------------------------------------------------------------------------------- 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= 0.292 Angle : 0.882 15.532 20003 Z= 0.563 Chirality : 0.048 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 0.00458 / 0.29 (14338) covalent geometry : angle 0.88174 / 0.56 (20003) hydrogen bonds : bond 0.13248 / 13.19 ( 641) hydrogen bonds : angle 6.12496 / 7.55 ( 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 : 0.459 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: 0.5650 time to fit residues: 69.7094 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 : 0.479 ------------------------------------------------------------------------------- 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: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 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 854 ASN A 990 ASN A1364 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.124771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.081031 restraints weight = 24427.056| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.38 r_work: 0.2950 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14338 Z= 0.155 Angle : 0.575 11.264 20003 Z= 0.320 Chirality : 0.040 0.202 2310 Planarity : 0.004 0.046 2041 Dihedral : 19.330 85.551 3407 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.07 % Allowed : 19.67 % 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: -0.07 (0.22), residues: 1329 helix: 0.72 (0.20), residues: 658 sheet: -0.17 (0.47), residues: 131 loop : -0.88 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 664 TYR 0.013 0.001 TYR A 155 PHE 0.021 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 0.00323 / 0.16 (14338) covalent geometry : angle 0.57454 / 0.32 (20003) hydrogen bonds : bond 0.04426 / 4.52 ( 641) hydrogen bonds : angle 4.92411 / 6.25 ( 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 126 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7629 (mm) REVERT: A 218 LYS cc_start: 0.7586 (mtmt) cc_final: 0.7376 (mtmt) REVERT: A 500 LYS cc_start: 0.8110 (mmtt) cc_final: 0.7712 (mmtm) REVERT: A 648 MET cc_start: 0.7215 (ppp) cc_final: 0.6958 (tmm) REVERT: A 655 ARG cc_start: 0.7797 (mmm-85) cc_final: 0.7541 (mmm-85) REVERT: A 828 LEU cc_start: 0.6518 (pp) cc_final: 0.6116 (mm) REVERT: A 846 PHE cc_start: 0.8348 (m-10) cc_final: 0.7923 (m-10) REVERT: A 933 GLN cc_start: 0.8871 (tt0) cc_final: 0.8359 (tp40) REVERT: A 964 SER cc_start: 0.8727 (t) cc_final: 0.8346 (m) REVERT: A 1043 MET cc_start: 0.7892 (mmm) cc_final: 0.7655 (mmp) REVERT: A 1192 LYS cc_start: 0.8432 (tttt) cc_final: 0.7783 (tmtt) REVERT: A 1340 LYS cc_start: 0.8792 (tptt) cc_final: 0.8466 (mptt) outliers start: 24 outliers final: 9 residues processed: 116 average time/residue: 0.4921 time to fit residues: 63.2468 Evaluate side-chains 107 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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: 4.9990 chunk 122 optimal weight: 0.1980 chunk 100 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 94 optimal weight: 0.1980 chunk 36 optimal weight: 0.0770 chunk 106 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 GLN A 281 GLN ** 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 = 0.3791 r_free = 0.3791 target = 0.125870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.082342 restraints weight = 24565.970| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.35 r_work: 0.2980 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14338 Z= 0.114 Angle : 0.511 10.381 20003 Z= 0.288 Chirality : 0.038 0.191 2310 Planarity : 0.004 0.047 2041 Dihedral : 19.192 86.103 3402 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.79 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: 0.35 (0.23), residues: 1329 helix: 1.18 (0.20), residues: 659 sheet: -0.30 (0.48), residues: 131 loop : -0.76 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 653 TYR 0.013 0.001 TYR A 656 PHE 0.017 0.001 PHE A 970 TRP 0.006 0.001 TRP A 476 HIS 0.003 0.001 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (14338) covalent geometry : angle 0.51136 / 0.29 (20003) hydrogen bonds : bond 0.03814 / 3.94 ( 641) hydrogen bonds : angle 4.61984 / 5.83 ( 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: 27 poor density : 111 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 500 LYS cc_start: 0.8140 (mmtt) cc_final: 0.7718 (mmtm) REVERT: A 599 LYS cc_start: 0.8613 (tppt) cc_final: 0.8282 (tptt) REVERT: A 648 MET cc_start: 0.7243 (ppp) cc_final: 0.6934 (tmm) REVERT: A 655 ARG cc_start: 0.7802 (mmm-85) cc_final: 0.7542 (mmm-85) REVERT: A 822 MET cc_start: 0.6373 (mmt) cc_final: 0.6072 (mmt) REVERT: A 828 LEU cc_start: 0.6534 (pp) cc_final: 0.6181 (mm) REVERT: A 846 PHE cc_start: 0.8415 (m-10) cc_final: 0.7988 (m-10) REVERT: A 933 GLN cc_start: 0.8899 (tt0) cc_final: 0.8375 (tp40) REVERT: A 964 SER cc_start: 0.8724 (t) cc_final: 0.8349 (m) REVERT: A 1043 MET cc_start: 0.7798 (mmm) cc_final: 0.7546 (mmp) REVERT: A 1251 ASP cc_start: 0.8450 (m-30) cc_final: 0.8222 (m-30) REVERT: A 1340 LYS cc_start: 0.8729 (tptt) cc_final: 0.8430 (mptt) outliers start: 27 outliers final: 9 residues processed: 124 average time/residue: 0.5356 time to fit residues: 73.3952 Evaluate side-chains 108 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 301 LEU 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 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: 3.9990 chunk 25 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 46 optimal weight: 0.0770 chunk 89 optimal weight: 1.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.124288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.080483 restraints weight = 24562.365| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.34 r_work: 0.2941 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14338 Z= 0.143 Angle : 0.516 12.521 20003 Z= 0.289 Chirality : 0.038 0.185 2310 Planarity : 0.004 0.047 2041 Dihedral : 19.160 86.668 3402 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.16 % Allowed : 18.03 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.49 (0.23), residues: 1329 helix: 1.30 (0.20), residues: 659 sheet: -0.38 (0.48), residues: 131 loop : -0.65 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 653 TYR 0.017 0.001 TYR A 529 PHE 0.015 0.001 PHE A 916 TRP 0.005 0.001 TRP A 883 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (14338) covalent geometry : angle 0.51573 / 0.29 (20003) hydrogen bonds : bond 0.03773 / 3.84 ( 641) hydrogen bonds : angle 4.54162 / 5.73 ( 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 135 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7769 (mmtm) REVERT: A 628 ASP cc_start: 0.7992 (t0) cc_final: 0.7498 (t0) REVERT: A 648 MET cc_start: 0.7237 (ppp) cc_final: 0.6879 (tmm) REVERT: A 655 ARG cc_start: 0.7891 (mmm-85) cc_final: 0.7631 (mmm-85) REVERT: A 709 GLN cc_start: 0.8175 (pp30) cc_final: 0.7630 (tp40) REVERT: A 828 LEU cc_start: 0.6663 (pp) cc_final: 0.6237 (mm) REVERT: A 846 PHE cc_start: 0.8465 (m-10) cc_final: 0.8038 (m-10) REVERT: A 879 MET cc_start: 0.1622 (OUTLIER) cc_final: 0.1308 (mmm) REVERT: A 933 GLN cc_start: 0.8931 (tt0) cc_final: 0.8395 (tp40) REVERT: A 964 SER cc_start: 0.8744 (t) cc_final: 0.8382 (m) REVERT: A 1340 LYS cc_start: 0.8746 (tptt) cc_final: 0.8453 (mptt) outliers start: 25 outliers final: 8 residues processed: 125 average time/residue: 0.5173 time to fit residues: 71.8516 Evaluate side-chains 111 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 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 530 VAL Chi-restraints excluded: chain A residue 549 VAL 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: 0.8980 chunk 82 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 128 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 ASN ** A 695 GLN ** 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 = 0.3758 r_free = 0.3758 target = 0.123551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.079683 restraints weight = 24652.676| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.32 r_work: 0.2929 rms_B_bonded: 3.02 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: 0.8704 moved from start: 0.1614 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= 0.147 Angle : 0.520 11.375 20003 Z= 0.286 Chirality : 0.038 0.214 2310 Planarity : 0.003 0.046 2041 Dihedral : 19.111 87.464 3400 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.67 % Allowed : 17.77 % 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: 0.56 (0.23), residues: 1329 helix: 1.41 (0.20), residues: 661 sheet: -0.38 (0.49), residues: 126 loop : -0.69 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 653 TYR 0.013 0.001 TYR A 155 PHE 0.011 0.001 PHE A 446 TRP 0.005 0.001 TRP A 476 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (14338) covalent geometry : angle 0.51963 / 0.29 (20003) hydrogen bonds : bond 0.03759 / 3.84 ( 641) hydrogen bonds : angle 4.47011 / 5.66 ( 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 136 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 TRP cc_start: 0.8600 (p90) cc_final: 0.8386 (p90) REVERT: A 500 LYS cc_start: 0.8326 (mmtt) cc_final: 0.7860 (mmtm) REVERT: A 628 ASP cc_start: 0.8045 (t0) cc_final: 0.7556 (t70) REVERT: A 645 ASP cc_start: 0.7788 (p0) cc_final: 0.7547 (p0) REVERT: A 648 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6757 (tmm) REVERT: A 655 ARG cc_start: 0.7784 (mmm-85) cc_final: 0.7464 (mmm-85) REVERT: A 709 GLN cc_start: 0.8246 (pp30) cc_final: 0.7631 (tp40) REVERT: A 746 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8534 (tt0) REVERT: A 822 MET cc_start: 0.6047 (mmt) cc_final: 0.5592 (mmt) REVERT: A 828 LEU cc_start: 0.6797 (pp) cc_final: 0.6319 (mm) REVERT: A 846 PHE cc_start: 0.8507 (m-10) cc_final: 0.8100 (m-10) REVERT: A 879 MET cc_start: 0.1658 (OUTLIER) cc_final: 0.1066 (mmm) REVERT: A 933 GLN cc_start: 0.8934 (tt0) cc_final: 0.8395 (tp40) REVERT: A 1192 LYS cc_start: 0.8449 (tttt) cc_final: 0.7830 (tmtt) REVERT: A 1340 LYS cc_start: 0.8745 (tptt) cc_final: 0.8449 (mptt) outliers start: 31 outliers final: 13 residues processed: 123 average time/residue: 0.5859 time to fit residues: 79.5144 Evaluate side-chains 116 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 461 ARG 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 648 MET Chi-restraints excluded: chain A residue 662 LEU 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 908 LEU 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: 0.6980 chunk 44 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 GLN ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 ASN A1224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.123227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.079285 restraints weight = 24416.463| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.31 r_work: 0.2923 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14338 Z= 0.146 Angle : 0.510 11.604 20003 Z= 0.283 Chirality : 0.038 0.172 2310 Planarity : 0.003 0.046 2041 Dihedral : 19.043 87.896 3400 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.33 % Allowed : 18.46 % Favored : 79.21 % 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: 1.51 (0.21), residues: 661 sheet: -0.44 (0.48), residues: 126 loop : -0.67 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 653 TYR 0.013 0.001 TYR A 155 PHE 0.013 0.001 PHE A 185 TRP 0.006 0.001 TRP A 476 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (14338) covalent geometry : angle 0.51048 / 0.28 (20003) hydrogen bonds : bond 0.03715 / 3.78 ( 641) hydrogen bonds : angle 4.40365 / 5.60 ( 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 132 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 LYS cc_start: 0.8343 (mmtt) cc_final: 0.7892 (mmtm) REVERT: A 628 ASP cc_start: 0.8069 (t0) cc_final: 0.7504 (t70) REVERT: A 648 MET cc_start: 0.7439 (ppp) cc_final: 0.6916 (tmm) REVERT: A 655 ARG cc_start: 0.7764 (mmm-85) cc_final: 0.7392 (mmm-85) REVERT: A 709 GLN cc_start: 0.8313 (pp30) cc_final: 0.7680 (tp40) REVERT: A 746 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8541 (tt0) REVERT: A 828 LEU cc_start: 0.6790 (pp) cc_final: 0.6342 (mm) REVERT: A 846 PHE cc_start: 0.8566 (m-10) cc_final: 0.8228 (m-10) REVERT: A 879 MET cc_start: 0.1841 (OUTLIER) cc_final: 0.1419 (mmm) REVERT: A 933 GLN cc_start: 0.8938 (tt0) cc_final: 0.8399 (tp40) REVERT: A 1049 GLU cc_start: 0.8092 (pm20) cc_final: 0.6998 (pp20) REVERT: A 1192 LYS cc_start: 0.8456 (tttt) cc_final: 0.7840 (tmtt) REVERT: A 1340 LYS cc_start: 0.8739 (tptt) cc_final: 0.8436 (mptt) outliers start: 27 outliers final: 11 residues processed: 124 average time/residue: 0.5331 time to fit residues: 73.5986 Evaluate side-chains 112 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 662 LEU 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 Chi-restraints excluded: chain A residue 1224 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 91 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 0.1980 chunk 61 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 74 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 116 optimal weight: 0.0770 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1224 ASN A1364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.123752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.079941 restraints weight = 24475.583| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.31 r_work: 0.2935 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14338 Z= 0.124 Angle : 0.522 12.769 20003 Z= 0.285 Chirality : 0.037 0.188 2310 Planarity : 0.003 0.044 2041 Dihedral : 19.011 88.135 3400 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.16 % Allowed : 19.07 % 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: 0.72 (0.23), residues: 1329 helix: 1.60 (0.21), residues: 661 sheet: -0.57 (0.47), residues: 131 loop : -0.61 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 653 TYR 0.013 0.001 TYR A 812 PHE 0.011 0.001 PHE A 446 TRP 0.005 0.001 TRP A 476 HIS 0.003 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (14338) covalent geometry : angle 0.52225 / 0.28 (20003) hydrogen bonds : bond 0.03588 / 3.68 ( 641) hydrogen bonds : angle 4.40980 / 5.60 ( 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 134 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 500 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7742 (mmtm) REVERT: A 558 LYS cc_start: 0.8568 (mmmt) cc_final: 0.8277 (mmmm) REVERT: A 628 ASP cc_start: 0.7995 (t0) cc_final: 0.7513 (t70) REVERT: A 648 MET cc_start: 0.7278 (ppp) cc_final: 0.6817 (tmm) REVERT: A 709 GLN cc_start: 0.8340 (pp30) cc_final: 0.7727 (tp40) REVERT: A 746 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: A 822 MET cc_start: 0.5941 (mmt) cc_final: 0.5565 (mmt) REVERT: A 828 LEU cc_start: 0.6749 (pp) cc_final: 0.6340 (mm) REVERT: A 846 PHE cc_start: 0.8647 (m-10) cc_final: 0.8193 (m-10) REVERT: A 879 MET cc_start: 0.1395 (OUTLIER) cc_final: 0.0932 (mmm) REVERT: A 920 GLN cc_start: 0.8930 (mp10) cc_final: 0.8114 (mp10) REVERT: A 933 GLN cc_start: 0.8931 (tt0) cc_final: 0.8390 (tp40) REVERT: A 959 LYS cc_start: 0.8245 (ttpp) cc_final: 0.7784 (ptmt) REVERT: A 1340 LYS cc_start: 0.8724 (tptt) cc_final: 0.8429 (mptt) outliers start: 25 outliers final: 12 residues processed: 125 average time/residue: 0.5353 time to fit residues: 73.8339 Evaluate side-chains 116 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 461 ARG 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 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 916 PHE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1224 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 131 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 49 optimal weight: 0.0570 chunk 85 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 14 optimal weight: 0.5980 chunk 72 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.123759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.079912 restraints weight = 24416.697| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.31 r_work: 0.2933 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14338 Z= 0.125 Angle : 0.521 12.323 20003 Z= 0.284 Chirality : 0.037 0.187 2310 Planarity : 0.003 0.044 2041 Dihedral : 18.984 88.355 3400 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.42 % Allowed : 19.07 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.77 (0.23), residues: 1329 helix: 1.64 (0.20), residues: 661 sheet: -0.56 (0.47), residues: 127 loop : -0.60 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 653 TYR 0.014 0.001 TYR A 529 PHE 0.034 0.001 PHE A 682 TRP 0.005 0.001 TRP A 476 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (14338) covalent geometry : angle 0.52056 / 0.28 (20003) hydrogen bonds : bond 0.03543 / 3.62 ( 641) hydrogen bonds : angle 4.38280 / 5.56 ( 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 130 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 LYS cc_start: 0.8162 (mmtt) cc_final: 0.7720 (mmtm) REVERT: A 628 ASP cc_start: 0.8019 (t0) cc_final: 0.7495 (t70) REVERT: A 648 MET cc_start: 0.7296 (ppp) cc_final: 0.6854 (tmm) REVERT: A 709 GLN cc_start: 0.8432 (pp30) cc_final: 0.7764 (tp40) REVERT: A 746 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8506 (tt0) REVERT: A 822 MET cc_start: 0.5980 (mmt) cc_final: 0.5559 (mmt) REVERT: A 846 PHE cc_start: 0.8606 (m-10) cc_final: 0.8096 (m-10) REVERT: A 879 MET cc_start: 0.1323 (OUTLIER) cc_final: 0.0913 (mmm) REVERT: A 920 GLN cc_start: 0.8952 (mp10) cc_final: 0.8392 (mp10) REVERT: A 933 GLN cc_start: 0.8931 (tt0) cc_final: 0.8388 (tp40) REVERT: A 1340 LYS cc_start: 0.8718 (tptt) cc_final: 0.8428 (mptt) outliers start: 28 outliers final: 9 residues processed: 121 average time/residue: 0.5620 time to fit residues: 75.2656 Evaluate side-chains 111 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 549 VAL 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 916 PHE 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: 0.7980 chunk 78 optimal weight: 0.0970 chunk 84 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 49 optimal weight: 0.0870 chunk 104 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 72 optimal weight: 0.0570 chunk 46 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.3474 ------------------------------------------------------------------------------- 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** A1224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.124784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.081838 restraints weight = 24524.363| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.15 r_work: 0.2953 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14338 Z= 0.112 Angle : 0.515 12.343 20003 Z= 0.282 Chirality : 0.037 0.172 2310 Planarity : 0.003 0.044 2041 Dihedral : 18.942 88.730 3400 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.64 % Allowed : 19.93 % 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: 0.91 (0.23), residues: 1329 helix: 1.73 (0.20), residues: 667 sheet: -0.43 (0.48), residues: 126 loop : -0.54 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 653 TYR 0.011 0.001 TYR A 812 PHE 0.023 0.001 PHE A 682 TRP 0.005 0.001 TRP A 476 HIS 0.003 0.001 HIS A 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (14338) covalent geometry : angle 0.51505 / 0.28 (20003) hydrogen bonds : bond 0.03401 / 3.49 ( 641) hydrogen bonds : angle 4.30714 / 5.47 ( 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 123 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7687 (mmtm) REVERT: A 534 MET cc_start: 0.5125 (mtm) cc_final: 0.4704 (tpt) REVERT: A 628 ASP cc_start: 0.7949 (t0) cc_final: 0.7473 (t70) REVERT: A 648 MET cc_start: 0.7310 (ppp) cc_final: 0.6881 (tmm) REVERT: A 653 ARG cc_start: 0.7628 (mtp-110) cc_final: 0.7371 (ttm-80) REVERT: A 709 GLN cc_start: 0.8470 (pp30) cc_final: 0.7789 (tp40) REVERT: A 815 TYR cc_start: 0.9047 (m-10) cc_final: 0.8813 (m-10) REVERT: A 822 MET cc_start: 0.6182 (mmt) cc_final: 0.5947 (mmt) REVERT: A 846 PHE cc_start: 0.8654 (m-10) cc_final: 0.8082 (m-10) REVERT: A 879 MET cc_start: 0.1326 (OUTLIER) cc_final: 0.0969 (mmm) REVERT: A 916 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8598 (m-10) REVERT: A 920 GLN cc_start: 0.8958 (mp10) cc_final: 0.8294 (mp10) REVERT: A 933 GLN cc_start: 0.8979 (tt0) cc_final: 0.8443 (tp40) REVERT: A 964 SER cc_start: 0.8840 (t) cc_final: 0.8490 (m) REVERT: A 1340 LYS cc_start: 0.8742 (tptt) cc_final: 0.8531 (mptt) outliers start: 19 outliers final: 9 residues processed: 116 average time/residue: 0.5719 time to fit residues: 73.2551 Evaluate side-chains 108 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 461 ARG 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 670 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 941 THR 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: 0.9980 chunk 84 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 129 optimal weight: 0.0970 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.123559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.080497 restraints weight = 24486.638| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.14 r_work: 0.2933 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14338 Z= 0.141 Angle : 0.540 13.156 20003 Z= 0.291 Chirality : 0.038 0.218 2310 Planarity : 0.003 0.045 2041 Dihedral : 18.937 89.266 3400 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.21 % Allowed : 20.71 % Favored : 78.08 % 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: 0.91 (0.23), residues: 1329 helix: 1.74 (0.20), residues: 667 sheet: -0.44 (0.48), residues: 122 loop : -0.54 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 653 TYR 0.013 0.001 TYR A 529 PHE 0.020 0.001 PHE A 970 TRP 0.005 0.001 TRP A 464 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (14338) covalent geometry : angle 0.54026 / 0.29 (20003) hydrogen bonds : bond 0.03552 / 3.61 ( 641) hydrogen bonds : angle 4.32626 / 5.48 ( 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 114 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7716 (mmtm) REVERT: A 534 MET cc_start: 0.5136 (mtm) cc_final: 0.4821 (tpt) REVERT: A 558 LYS cc_start: 0.8595 (mmmt) cc_final: 0.8231 (mmmm) REVERT: A 628 ASP cc_start: 0.7943 (t0) cc_final: 0.7477 (t70) REVERT: A 648 MET cc_start: 0.7355 (ppp) cc_final: 0.6921 (tmm) REVERT: A 653 ARG cc_start: 0.7618 (mtp-110) cc_final: 0.7372 (ttm-80) REVERT: A 709 GLN cc_start: 0.8497 (pp30) cc_final: 0.7800 (tp40) REVERT: A 822 MET cc_start: 0.6215 (mmt) cc_final: 0.5954 (mmt) REVERT: A 846 PHE cc_start: 0.8712 (m-10) cc_final: 0.8238 (m-10) REVERT: A 879 MET cc_start: 0.1577 (OUTLIER) cc_final: 0.1129 (mmm) REVERT: A 916 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.8424 (m-10) REVERT: A 920 GLN cc_start: 0.8868 (mp10) cc_final: 0.8237 (mp10) REVERT: A 933 GLN cc_start: 0.8984 (tt0) cc_final: 0.8455 (tp40) REVERT: A 964 SER cc_start: 0.8855 (t) cc_final: 0.8496 (m) REVERT: A 1340 LYS cc_start: 0.8768 (tptt) cc_final: 0.8547 (mptt) outliers start: 14 outliers final: 8 residues processed: 108 average time/residue: 0.5857 time to fit residues: 70.0800 Evaluate side-chains 110 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 670 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain A residue 916 PHE Chi-restraints excluded: chain A residue 941 THR 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: 0.0980 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 0.0060 chunk 69 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 128 optimal weight: 0.5980 chunk 140 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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** A1224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.124440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.081429 restraints weight = 24594.590| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.15 r_work: 0.2955 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2276 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= 0.118 Angle : 0.527 13.163 20003 Z= 0.286 Chirality : 0.037 0.190 2310 Planarity : 0.003 0.051 2041 Dihedral : 18.933 89.573 3400 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.21 % Allowed : 20.88 % 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: 0.96 (0.23), residues: 1329 helix: 1.80 (0.20), residues: 668 sheet: -0.46 (0.48), residues: 122 loop : -0.55 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 307 TYR 0.010 0.001 TYR A 155 PHE 0.025 0.001 PHE A 970 TRP 0.005 0.001 TRP A 476 HIS 0.003 0.001 HIS A 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (14338) covalent geometry : angle 0.52703 / 0.29 (20003) hydrogen bonds : bond 0.03411 / 3.48 ( 641) hydrogen bonds : angle 4.27619 / 5.44 ( 1741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4765.32 seconds wall clock time: 82 minutes 7.31 seconds (4927.31 seconds total)