Starting phenix.real_space_refine on Sat Jun 14 08:47:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wuu_37860/06_2025/8wuu_37860.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wuu_37860/06_2025/8wuu_37860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wuu_37860/06_2025/8wuu_37860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wuu_37860/06_2025/8wuu_37860.map" model { file = "/net/cci-nas-00/data/ceres_data/8wuu_37860/06_2025/8wuu_37860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wuu_37860/06_2025/8wuu_37860.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.006 sd= 0.169 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1607 atoms to isotropic. 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 181 5.49 5 S 21 5.16 5 C 8596 2.51 5 N 2569 2.21 5 O 3196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14563 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 10751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1313, 10751 Classifications: {'peptide': 1313} Link IDs: {'PTRANS': 35, 'TRANS': 1277} Chain breaks: 4 Chain: "C" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 777 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "D" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 313 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "B" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 2373 Classifications: {'RNA': 111} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 54, 'rna3p_pyr': 44} Link IDs: {'rna2p': 13, 'rna3p': 97} Chain breaks: 1 Chain: "F" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 349 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain breaks: 1 Time building chain proxies: 8.58, per 1000 atoms: 0.59 Number of scatterers: 14563 At special positions: 0 Unit cell: (90.783, 136.174, 145.253, 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 21 16.00 P 181 15.00 O 3196 8.00 N 2569 7.00 C 8596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 1.3 seconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2502 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 9 sheets defined 55.0% alpha, 9.4% beta 71 base pairs and 109 stacking pairs defined. Time for finding SS restraints: 5.27 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 5.242A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.609A 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 removed outlier: 3.844A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.707A pdb=" N PHE A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 282 Processing helix chain 'A' and resid 286 through 304 removed outlier: 4.049A 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 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 382 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.634A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.154A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 Processing helix chain 'A' and resid 436 through 446 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 526 removed outlier: 3.685A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 594 through 602 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.576A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 637 through 640 Processing helix chain 'A' and resid 644 through 654 Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 703 through 714 removed outlier: 3.619A pdb=" N SER A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 727 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 802 through 807 Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 872 through 889 removed outlier: 5.126A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 901 through 906 removed outlier: 3.753A pdb=" N ARG A 905 " --> pdb=" O THR A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 920 Processing helix chain 'A' and resid 925 through 940 Processing helix chain 'A' and resid 959 through 970 removed outlier: 4.226A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1001 Processing helix chain 'A' and resid 1004 through 1009 Processing helix chain 'A' and resid 1032 through 1041 removed outlier: 3.519A pdb=" N ASN A1041 " --> pdb=" O PHE A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1186 removed outlier: 3.607A pdb=" N GLY A1186 " --> pdb=" O LEU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 removed outlier: 3.648A pdb=" N GLN A1254 " --> pdb=" O GLU A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1280 removed outlier: 3.722A pdb=" N GLU A1268 " --> pdb=" O HIS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 4.031A pdb=" N HIS A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A1312 " --> pdb=" O ASN A1308 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.607A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 10.180A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA4, first strand: chain 'A' and resid 1049 through 1050 Processing sheet with id=AA5, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 3.568A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA7, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.520A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.520A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1324 through 1326 529 hydrogen bonds defined for protein. 1536 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 179 hydrogen bonds 354 hydrogen bond angles 0 basepair planarities 71 basepair parallelities 109 stacking parallelities Total time for adding SS restraints: 7.61 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2614 1.33 - 1.45: 4470 1.45 - 1.57: 7727 1.57 - 1.68: 356 1.68 - 1.80: 41 Bond restraints: 15208 Sorted by residual: bond pdb=" C1' DT C 1 " pdb=" N1 DT C 1 " ideal model delta sigma weight residual 1.490 1.453 0.037 3.00e-02 1.11e+03 1.52e+00 bond pdb=" O4' DG D 1 " pdb=" C1' DG D 1 " ideal model delta sigma weight residual 1.414 1.390 0.024 2.00e-02 2.50e+03 1.38e+00 bond pdb=" N1 DT C 1 " pdb=" C2 DT C 1 " ideal model delta sigma weight residual 1.379 1.356 0.023 2.00e-02 2.50e+03 1.34e+00 bond pdb=" CB ARG A 400 " pdb=" CG ARG A 400 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.27e+00 bond pdb=" CB ARG A 324 " pdb=" CG ARG A 324 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.22e+00 ... (remaining 15203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 19978 1.11 - 2.22: 1118 2.22 - 3.33: 180 3.33 - 4.44: 26 4.44 - 5.55: 8 Bond angle restraints: 21310 Sorted by residual: angle pdb=" N LYS A 929 " pdb=" CA LYS A 929 " pdb=" C LYS A 929 " ideal model delta sigma weight residual 110.97 107.98 2.99 1.09e+00 8.42e-01 7.54e+00 angle pdb=" N ILE A 600 " pdb=" CA ILE A 600 " pdb=" C ILE A 600 " ideal model delta sigma weight residual 111.67 109.07 2.60 9.50e-01 1.11e+00 7.48e+00 angle pdb=" C LEU A 997 " pdb=" N ILE A 998 " pdb=" CA ILE A 998 " ideal model delta sigma weight residual 120.64 116.79 3.85 1.66e+00 3.63e-01 5.38e+00 angle pdb=" CA TYR A 155 " pdb=" CB TYR A 155 " pdb=" CG TYR A 155 " ideal model delta sigma weight residual 113.90 110.05 3.85 1.80e+00 3.09e-01 4.57e+00 angle pdb=" C2' DA C 22 " pdb=" C1' DA C 22 " pdb=" N9 DA C 22 " ideal model delta sigma weight residual 113.50 110.45 3.05 1.50e+00 4.44e-01 4.14e+00 ... (remaining 21305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.60: 8174 27.60 - 55.19: 835 55.19 - 82.79: 209 82.79 - 110.39: 6 110.39 - 137.98: 1 Dihedral angle restraints: 9225 sinusoidal: 5362 harmonic: 3863 Sorted by residual: dihedral pdb=" CA PHE A 86 " pdb=" C PHE A 86 " pdb=" N SER A 87 " pdb=" CA SER A 87 " ideal model delta harmonic sigma weight residual -180.00 -161.27 -18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ASP A 605 " pdb=" CB ASP A 605 " pdb=" CG ASP A 605 " pdb=" OD1 ASP A 605 " ideal model delta sinusoidal sigma weight residual -30.00 -89.05 59.05 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASN A1066 " pdb=" CB ASN A1066 " pdb=" CG ASN A1066 " pdb=" OD1 ASN A1066 " ideal model delta sinusoidal sigma weight residual 120.00 -168.62 -71.38 2 2.00e+01 2.50e-03 1.08e+01 ... (remaining 9222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1574 0.035 - 0.069: 636 0.069 - 0.104: 171 0.104 - 0.138: 66 0.138 - 0.173: 7 Chirality restraints: 2454 Sorted by residual: chirality pdb=" CA ILE A 48 " pdb=" N ILE A 48 " pdb=" C ILE A 48 " pdb=" CB ILE A 48 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CA PRO A 117 " pdb=" N PRO A 117 " pdb=" C PRO A 117 " pdb=" CB PRO A 117 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" C1' U B 22 " pdb=" O4' U B 22 " pdb=" C2' U B 22 " pdb=" N1 U B 22 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.16 2.00e-01 2.50e+01 6.77e-01 ... (remaining 2451 not shown) Planarity restraints: 2062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 46 " -0.022 2.00e-02 2.50e+03 1.33e-02 4.90e+00 pdb=" N9 A B 46 " 0.036 2.00e-02 2.50e+03 pdb=" C8 A B 46 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A B 46 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A B 46 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A B 46 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B 46 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A B 46 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A B 46 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A B 46 " 0.001 2.00e-02 2.50e+03 pdb=" C4 A B 46 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 870 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 871 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 871 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 871 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 693 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C PHE A 693 " 0.032 2.00e-02 2.50e+03 pdb=" O PHE A 693 " -0.012 2.00e-02 2.50e+03 pdb=" N MET A 694 " -0.011 2.00e-02 2.50e+03 ... (remaining 2059 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 558 2.70 - 3.25: 13515 3.25 - 3.80: 25377 3.80 - 4.35: 32906 4.35 - 4.90: 50111 Nonbonded interactions: 122467 Sorted by model distance: nonbonded pdb=" OG SER A 512 " pdb=" OE1 GLU A 617 " model vdw 2.145 3.040 nonbonded pdb=" OE1 GLU A 977 " pdb=" OH TYR A1242 " model vdw 2.219 3.040 nonbonded pdb=" O2' C B 3 " pdb=" O5' C B 4 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR A 5 " pdb=" O HIS A 754 " model vdw 2.236 3.040 nonbonded pdb=" OE2 GLU A1162 " pdb=" OH TYR A1187 " model vdw 2.242 3.040 ... (remaining 122462 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.150 Process input model: 39.430 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6051 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 15208 Z= 0.274 Angle : 0.581 5.554 21310 Z= 0.320 Chirality : 0.042 0.173 2454 Planarity : 0.004 0.049 2062 Dihedral : 20.532 137.981 6723 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 20.42 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.24), residues: 1303 helix: 1.87 (0.21), residues: 689 sheet: -0.26 (0.51), residues: 114 loop : -0.42 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 18 HIS 0.006 0.002 HIS A1311 PHE 0.027 0.002 PHE A1235 TYR 0.018 0.002 TYR A 136 ARG 0.007 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.11500 ( 697) hydrogen bonds : angle 4.97462 ( 1890) covalent geometry : bond 0.00618 (15208) covalent geometry : angle 0.58142 (21310) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8409 (m-40) cc_final: 0.8048 (t0) REVERT: A 534 MET cc_start: 0.3165 (mtp) cc_final: 0.0839 (ptm) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.4831 time to fit residues: 39.1131 Evaluate side-chains 31 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 75 optimal weight: 40.0000 chunk 59 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 85 optimal weight: 30.0000 chunk 133 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN A 758 ASN A1066 ASN A1221 GLN A1262 HIS A1297 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.058606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.037299 restraints weight = 84620.120| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.42 r_work: 0.2781 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15208 Z= 0.178 Angle : 0.487 6.147 21310 Z= 0.265 Chirality : 0.035 0.144 2454 Planarity : 0.003 0.050 2062 Dihedral : 19.639 131.943 3920 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.69 % Allowed : 18.98 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.24), residues: 1303 helix: 2.04 (0.21), residues: 683 sheet: 0.14 (0.51), residues: 101 loop : -0.33 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 18 HIS 0.006 0.001 HIS A 328 PHE 0.014 0.001 PHE A1235 TYR 0.012 0.001 TYR A 815 ARG 0.008 0.001 ARG A 778 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 697) hydrogen bonds : angle 4.06762 ( 1890) covalent geometry : bond 0.00381 (15208) covalent geometry : angle 0.48722 (21310) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 31 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LEU cc_start: 0.9119 (mp) cc_final: 0.8679 (tp) REVERT: A 235 ASN cc_start: 0.8869 (m-40) cc_final: 0.8244 (t0) REVERT: A 534 MET cc_start: 0.5956 (mtp) cc_final: 0.4093 (ptm) REVERT: A 762 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7864 (pp20) REVERT: A 1069 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.9022 (p) REVERT: A 1242 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.6876 (m-80) outliers start: 20 outliers final: 6 residues processed: 50 average time/residue: 0.3041 time to fit residues: 23.4254 Evaluate side-chains 36 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 22 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 69 optimal weight: 50.0000 chunk 109 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 82 optimal weight: 30.0000 chunk 10 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN A 826 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.057347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.036208 restraints weight = 86284.119| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.43 r_work: 0.2738 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 15208 Z= 0.241 Angle : 0.525 6.247 21310 Z= 0.282 Chirality : 0.037 0.159 2454 Planarity : 0.004 0.049 2062 Dihedral : 19.735 117.193 3920 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.03 % Allowed : 20.00 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.24), residues: 1303 helix: 1.90 (0.21), residues: 691 sheet: -0.38 (0.46), residues: 133 loop : -0.27 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 883 HIS 0.004 0.001 HIS A 116 PHE 0.019 0.002 PHE A1235 TYR 0.013 0.002 TYR A 136 ARG 0.004 0.001 ARG A1279 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 697) hydrogen bonds : angle 4.16946 ( 1890) covalent geometry : bond 0.00520 (15208) covalent geometry : angle 0.52503 (21310) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 27 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.6264 (mtp) cc_final: 0.4478 (ptm) REVERT: A 879 MET cc_start: 0.0688 (mpp) cc_final: 0.0333 (mpp) REVERT: A 1069 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.9060 (p) REVERT: A 1242 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.6867 (m-80) REVERT: A 1260 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8729 (tm-30) REVERT: A 1341 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8832 (pm20) REVERT: A 1364 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8177 (mp10) outliers start: 24 outliers final: 9 residues processed: 51 average time/residue: 0.2961 time to fit residues: 23.0495 Evaluate side-chains 38 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 24 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1341 GLU Chi-restraints excluded: chain A residue 1364 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 130 optimal weight: 7.9990 chunk 74 optimal weight: 30.0000 chunk 139 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 135 optimal weight: 30.0000 chunk 68 optimal weight: 30.0000 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 0.3980 chunk 119 optimal weight: 2.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.057920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.036533 restraints weight = 88288.335| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.59 r_work: 0.2738 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 15208 Z= 0.143 Angle : 0.442 6.339 21310 Z= 0.240 Chirality : 0.034 0.152 2454 Planarity : 0.003 0.050 2062 Dihedral : 19.530 104.156 3920 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.03 % Allowed : 19.75 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.24), residues: 1303 helix: 2.13 (0.21), residues: 690 sheet: -0.28 (0.47), residues: 126 loop : -0.23 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 883 HIS 0.004 0.001 HIS A 116 PHE 0.010 0.001 PHE A 518 TYR 0.009 0.001 TYR A 521 ARG 0.002 0.000 ARG A 654 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 697) hydrogen bonds : angle 3.90643 ( 1890) covalent geometry : bond 0.00306 (15208) covalent geometry : angle 0.44158 (21310) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 27 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASN cc_start: 0.9000 (m-40) cc_final: 0.8274 (t0) REVERT: A 534 MET cc_start: 0.6366 (mtp) cc_final: 0.4638 (ptm) REVERT: A 762 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7916 (pp20) REVERT: A 879 MET cc_start: 0.0827 (mpp) cc_final: 0.0132 (mpp) REVERT: A 1069 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8927 (p) REVERT: A 1242 TYR cc_start: 0.7875 (OUTLIER) cc_final: 0.7032 (m-80) REVERT: A 1364 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8219 (mt0) outliers start: 24 outliers final: 10 residues processed: 51 average time/residue: 0.2891 time to fit residues: 23.1898 Evaluate side-chains 41 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 27 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1364 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 117 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 20 optimal weight: 0.0170 chunk 144 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 overall best weight: 6.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 HIS A 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.057324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.035566 restraints weight = 89065.498| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.50 r_work: 0.2725 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 15208 Z= 0.185 Angle : 0.477 6.113 21310 Z= 0.256 Chirality : 0.035 0.148 2454 Planarity : 0.003 0.050 2062 Dihedral : 19.579 98.362 3920 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.12 % Allowed : 19.66 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.24), residues: 1303 helix: 2.06 (0.21), residues: 689 sheet: -0.18 (0.50), residues: 112 loop : -0.27 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 883 HIS 0.004 0.001 HIS A 328 PHE 0.014 0.001 PHE A1235 TYR 0.010 0.001 TYR A 155 ARG 0.002 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 697) hydrogen bonds : angle 3.98726 ( 1890) covalent geometry : bond 0.00399 (15208) covalent geometry : angle 0.47697 (21310) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 27 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ARG cc_start: 0.9274 (OUTLIER) cc_final: 0.8730 (ptm160) REVERT: A 534 MET cc_start: 0.5961 (mtp) cc_final: 0.4270 (ptm) REVERT: A 762 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7892 (pp20) REVERT: A 879 MET cc_start: 0.1040 (mpp) cc_final: 0.0311 (mpp) REVERT: A 1069 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.8901 (p) REVERT: A 1242 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.6813 (m-80) REVERT: A 1260 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8733 (tm-30) REVERT: A 1341 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8713 (pm20) REVERT: A 1364 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8229 (mt0) outliers start: 25 outliers final: 13 residues processed: 51 average time/residue: 0.3190 time to fit residues: 24.8512 Evaluate side-chains 45 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 25 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1274 SER Chi-restraints excluded: chain A residue 1341 GLU Chi-restraints excluded: chain A residue 1364 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 93 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 80 optimal weight: 30.0000 chunk 49 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 34 optimal weight: 0.2980 overall best weight: 6.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 854 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.057341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.035957 restraints weight = 88814.931| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.53 r_work: 0.2722 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15208 Z= 0.174 Angle : 0.467 7.436 21310 Z= 0.251 Chirality : 0.035 0.146 2454 Planarity : 0.003 0.050 2062 Dihedral : 19.521 98.236 3920 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.95 % Allowed : 19.83 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1303 helix: 2.09 (0.21), residues: 685 sheet: -0.28 (0.50), residues: 110 loop : -0.23 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 18 HIS 0.004 0.001 HIS A 116 PHE 0.010 0.001 PHE A1235 TYR 0.010 0.001 TYR A 521 ARG 0.003 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 697) hydrogen bonds : angle 3.94150 ( 1890) covalent geometry : bond 0.00374 (15208) covalent geometry : angle 0.46673 (21310) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 26 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ARG cc_start: 0.9269 (OUTLIER) cc_final: 0.8723 (ptm160) REVERT: A 534 MET cc_start: 0.5897 (mtp) cc_final: 0.4272 (ptm) REVERT: A 762 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7864 (pp20) REVERT: A 879 MET cc_start: 0.1519 (mpp) cc_final: 0.0919 (mpp) REVERT: A 1069 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8934 (p) REVERT: A 1242 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.6928 (m-80) REVERT: A 1260 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8758 (tm-30) REVERT: A 1341 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8686 (pm20) outliers start: 23 outliers final: 12 residues processed: 49 average time/residue: 0.3012 time to fit residues: 23.2043 Evaluate side-chains 42 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 24 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1341 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 83 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 21 optimal weight: 30.0000 chunk 66 optimal weight: 30.0000 chunk 51 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 82 optimal weight: 40.0000 chunk 20 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.057071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.035439 restraints weight = 89326.365| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.56 r_work: 0.2710 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15208 Z= 0.199 Angle : 0.495 8.623 21310 Z= 0.264 Chirality : 0.035 0.150 2454 Planarity : 0.003 0.052 2062 Dihedral : 19.562 97.387 3920 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.12 % Allowed : 20.00 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.24), residues: 1303 helix: 2.03 (0.20), residues: 690 sheet: -0.37 (0.50), residues: 110 loop : -0.25 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 18 HIS 0.004 0.001 HIS A 116 PHE 0.014 0.001 PHE A1235 TYR 0.010 0.001 TYR A 155 ARG 0.008 0.000 ARG A 215 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 697) hydrogen bonds : angle 4.01986 ( 1890) covalent geometry : bond 0.00428 (15208) covalent geometry : angle 0.49548 (21310) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 26 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.8732 (ptm160) REVERT: A 534 MET cc_start: 0.5974 (mtp) cc_final: 0.4345 (ptm) REVERT: A 762 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7893 (pp20) REVERT: A 1069 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8937 (p) REVERT: A 1242 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.7027 (m-80) REVERT: A 1260 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8707 (tm-30) REVERT: A 1341 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8679 (pm20) outliers start: 25 outliers final: 14 residues processed: 50 average time/residue: 0.3338 time to fit residues: 25.4682 Evaluate side-chains 45 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 25 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1341 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 5.9990 chunk 142 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.057469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.035847 restraints weight = 89019.436| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.56 r_work: 0.2732 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15208 Z= 0.146 Angle : 0.454 10.584 21310 Z= 0.244 Chirality : 0.034 0.169 2454 Planarity : 0.003 0.052 2062 Dihedral : 19.458 97.781 3920 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.53 % Allowed : 20.93 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.24), residues: 1303 helix: 2.17 (0.21), residues: 685 sheet: -0.30 (0.47), residues: 122 loop : -0.17 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.004 0.001 HIS A 116 PHE 0.008 0.001 PHE A1235 TYR 0.009 0.001 TYR A 155 ARG 0.004 0.000 ARG A 215 Details of bonding type rmsd hydrogen bonds : bond 0.03420 ( 697) hydrogen bonds : angle 3.88162 ( 1890) covalent geometry : bond 0.00316 (15208) covalent geometry : angle 0.45449 (21310) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 25 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.8705 (ptm160) REVERT: A 534 MET cc_start: 0.5986 (mtp) cc_final: 0.4407 (ptm) REVERT: A 762 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7872 (pp20) REVERT: A 879 MET cc_start: 0.1721 (mpp) cc_final: 0.1482 (mpp) REVERT: A 1069 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.8945 (p) REVERT: A 1242 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7042 (m-80) REVERT: A 1260 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8695 (tm-30) REVERT: A 1341 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8708 (pm20) outliers start: 18 outliers final: 12 residues processed: 43 average time/residue: 0.3376 time to fit residues: 23.0059 Evaluate side-chains 43 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 25 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1341 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 46 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 30 optimal weight: 20.0000 chunk 133 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.057457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.035911 restraints weight = 88608.992| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.58 r_work: 0.2734 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15208 Z= 0.142 Angle : 0.447 11.060 21310 Z= 0.239 Chirality : 0.034 0.138 2454 Planarity : 0.003 0.051 2062 Dihedral : 19.404 96.997 3920 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.61 % Allowed : 20.59 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.24), residues: 1303 helix: 2.20 (0.21), residues: 686 sheet: -0.25 (0.49), residues: 110 loop : -0.21 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 883 HIS 0.005 0.001 HIS A 328 PHE 0.009 0.001 PHE A1045 TYR 0.009 0.001 TYR A 155 ARG 0.003 0.000 ARG A 215 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 697) hydrogen bonds : angle 3.82597 ( 1890) covalent geometry : bond 0.00305 (15208) covalent geometry : angle 0.44704 (21310) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 25 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ARG cc_start: 0.9255 (OUTLIER) cc_final: 0.8696 (ptm160) REVERT: A 534 MET cc_start: 0.6053 (mtp) cc_final: 0.4450 (ptm) REVERT: A 762 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7883 (pp20) REVERT: A 1069 THR cc_start: 0.9289 (OUTLIER) cc_final: 0.9015 (p) REVERT: A 1242 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7039 (m-80) REVERT: A 1260 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8690 (tm-30) REVERT: A 1341 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8689 (pm20) outliers start: 19 outliers final: 11 residues processed: 44 average time/residue: 0.3039 time to fit residues: 20.9076 Evaluate side-chains 42 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 25 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1341 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 42 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 66 optimal weight: 40.0000 chunk 26 optimal weight: 0.0570 chunk 50 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 21 optimal weight: 40.0000 chunk 10 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 overall best weight: 4.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.057527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.035779 restraints weight = 88947.164| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.56 r_work: 0.2733 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15208 Z= 0.129 Angle : 0.438 11.176 21310 Z= 0.235 Chirality : 0.033 0.137 2454 Planarity : 0.003 0.051 2062 Dihedral : 19.346 96.747 3920 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.53 % Allowed : 20.59 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.24), residues: 1303 helix: 2.21 (0.21), residues: 686 sheet: -0.22 (0.49), residues: 110 loop : -0.18 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 883 HIS 0.004 0.001 HIS A 328 PHE 0.009 0.001 PHE A1045 TYR 0.009 0.001 TYR A 155 ARG 0.003 0.000 ARG A 215 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 697) hydrogen bonds : angle 3.77535 ( 1890) covalent geometry : bond 0.00277 (15208) covalent geometry : angle 0.43788 (21310) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 26 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.8669 (ptm160) REVERT: A 534 MET cc_start: 0.5544 (mtp) cc_final: 0.3610 (ptm) REVERT: A 762 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7828 (pp20) REVERT: A 879 MET cc_start: 0.2293 (mpp) cc_final: 0.2083 (mpp) REVERT: A 1069 THR cc_start: 0.9298 (OUTLIER) cc_final: 0.9030 (p) REVERT: A 1242 TYR cc_start: 0.7936 (OUTLIER) cc_final: 0.7014 (m-80) REVERT: A 1260 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8704 (tm-30) REVERT: A 1341 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8648 (pm20) outliers start: 18 outliers final: 11 residues processed: 44 average time/residue: 0.3043 time to fit residues: 21.2967 Evaluate side-chains 43 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 26 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1341 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 99 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 chunk 74 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 chunk 11 optimal weight: 0.5980 chunk 45 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.057397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.036163 restraints weight = 88733.161| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.52 r_work: 0.2729 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15208 Z= 0.136 Angle : 0.443 11.240 21310 Z= 0.236 Chirality : 0.033 0.138 2454 Planarity : 0.003 0.051 2062 Dihedral : 19.350 95.867 3920 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.53 % Allowed : 20.51 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1303 helix: 2.20 (0.21), residues: 686 sheet: -0.25 (0.47), residues: 122 loop : -0.14 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 883 HIS 0.003 0.001 HIS A 328 PHE 0.008 0.001 PHE A1045 TYR 0.009 0.001 TYR A 155 ARG 0.002 0.000 ARG A 215 Details of bonding type rmsd hydrogen bonds : bond 0.03315 ( 697) hydrogen bonds : angle 3.79097 ( 1890) covalent geometry : bond 0.00293 (15208) covalent geometry : angle 0.44296 (21310) =============================================================================== Job complete usr+sys time: 9610.96 seconds wall clock time: 169 minutes 49.80 seconds (10189.80 seconds total)