Starting phenix.real_space_refine on Tue Aug 6 09:06:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuu_37860/08_2024/8wuu_37860.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuu_37860/08_2024/8wuu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuu_37860/08_2024/8wuu_37860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuu_37860/08_2024/8wuu_37860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuu_37860/08_2024/8wuu_37860.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuu_37860/08_2024/8wuu_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 Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 384": "OD1" <-> "OD2" Residue "A PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 8.13, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 6.74 Conformation dependent library (CDL) restraints added in 1.8 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: 5.91 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: 8.74 Time building geometry restraints manager: 7.32 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: 98.66 - 105.74: 1020 105.74 - 112.81: 8466 112.81 - 119.89: 5201 119.89 - 126.96: 6106 126.96 - 134.04: 517 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: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 48.100 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.150 ------------------------------------------------------------------------------- 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= 0.394 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.361 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: 0.4870 time to fit residues: 39.5730 Evaluate side-chains 31 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 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= 0.241 Angle : 0.487 6.147 21310 Z= 0.265 Chirality : 0.035 0.144 2454 Planarity : 0.003 0.050 2062 Dihedral : 19.639 131.942 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 *********************** 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 fitting. rotamer outliers: 20 poor density : 31 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LEU cc_start: 0.9180 (mp) cc_final: 0.8748 (tp) REVERT: A 235 ASN cc_start: 0.8560 (m-40) cc_final: 0.8090 (t0) REVERT: A 534 MET cc_start: 0.3349 (mtp) cc_final: 0.0909 (ptm) REVERT: A 1242 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.6772 (m-80) outliers start: 20 outliers final: 6 residues processed: 50 average time/residue: 0.2867 time to fit residues: 22.0113 Evaluate side-chains 34 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 799 HIS Chi-restraints excluded: chain A residue 1037 PHE 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 74 optimal weight: 30.0000 chunk 41 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN A 990 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15208 Z= 0.175 Angle : 0.431 6.279 21310 Z= 0.236 Chirality : 0.034 0.155 2454 Planarity : 0.003 0.047 2062 Dihedral : 19.487 119.708 3920 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.69 % Allowed : 19.07 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 678 sheet: 0.45 (0.58), residues: 85 loop : -0.26 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 883 HIS 0.004 0.001 HIS A 328 PHE 0.011 0.001 PHE A 518 TYR 0.009 0.001 TYR A 155 ARG 0.003 0.000 ARG A 778 *********************** 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 49 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 29 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8585 (m-40) cc_final: 0.8075 (t0) REVERT: A 534 MET cc_start: 0.2844 (mtp) cc_final: 0.0442 (ptm) REVERT: A 879 MET cc_start: 0.1400 (mpp) cc_final: 0.0702 (mpp) REVERT: A 1242 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6756 (m-80) outliers start: 20 outliers final: 9 residues processed: 49 average time/residue: 0.3144 time to fit residues: 23.3165 Evaluate side-chains 37 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 27 time to evaluate : 1.928 ------------------------------------------------------------------------------- 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 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 69 optimal weight: 50.0000 chunk 14 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 127 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 826 GLN A 854 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.2317 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= 0.332 Angle : 0.536 6.693 21310 Z= 0.286 Chirality : 0.037 0.156 2454 Planarity : 0.004 0.049 2062 Dihedral : 19.718 103.705 3920 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.12 % Allowed : 20.08 % 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: 1.32 (0.24), residues: 1303 helix: 1.93 (0.21), residues: 690 sheet: -0.31 (0.47), residues: 126 loop : -0.26 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 883 HIS 0.007 0.001 HIS A 595 PHE 0.020 0.002 PHE A1235 TYR 0.013 0.002 TYR A 136 ARG 0.003 0.001 ARG A1279 *********************** 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 52 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 27 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.3612 (mtp) cc_final: 0.1234 (ptm) REVERT: A 879 MET cc_start: 0.2468 (mpp) cc_final: 0.1523 (mpp) REVERT: A 1089 MET cc_start: 0.9259 (mtm) cc_final: 0.8906 (mtm) REVERT: A 1242 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.6693 (m-80) outliers start: 25 outliers final: 12 residues processed: 52 average time/residue: 0.2736 time to fit residues: 22.3418 Evaluate side-chains 38 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 25 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE 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 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1274 SER 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 118 optimal weight: 9.9990 chunk 80 optimal weight: 30.0000 chunk 2 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15208 Z= 0.266 Angle : 0.483 6.823 21310 Z= 0.260 Chirality : 0.035 0.148 2454 Planarity : 0.003 0.050 2062 Dihedral : 19.621 98.537 3920 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.86 % Allowed : 20.08 % Favored : 78.05 % 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: 1.39 (0.24), residues: 1303 helix: 2.02 (0.21), residues: 690 sheet: -0.30 (0.50), residues: 112 loop : -0.31 (0.27), residues: 501 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 0.012 0.001 PHE A1235 TYR 0.010 0.001 TYR A 568 ARG 0.002 0.000 ARG A 557 *********************** 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 48 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 26 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8553 (ptm160) REVERT: A 534 MET cc_start: 0.3494 (mtp) cc_final: 0.1497 (ptm) REVERT: A 879 MET cc_start: 0.2475 (mpp) cc_final: 0.1442 (mpp) REVERT: A 1242 TYR cc_start: 0.7608 (OUTLIER) cc_final: 0.6845 (m-80) REVERT: A 1364 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8045 (mt0) REVERT: A 1365 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8151 (pp) outliers start: 22 outliers final: 12 residues processed: 46 average time/residue: 0.3371 time to fit residues: 23.3421 Evaluate side-chains 40 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 24 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE 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 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 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 Chi-restraints excluded: chain A residue 1365 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 chunk 28 optimal weight: 30.0000 chunk 83 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 142 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 65 optimal weight: 40.0000 chunk 11 optimal weight: 7.9990 chunk 74 optimal weight: 30.0000 chunk 137 optimal weight: 10.0000 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6160 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 15208 Z= 0.351 Angle : 0.542 7.203 21310 Z= 0.289 Chirality : 0.037 0.148 2454 Planarity : 0.004 0.052 2062 Dihedral : 19.746 97.607 3920 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.95 % Allowed : 19.75 % Favored : 78.31 % 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: 1.19 (0.24), residues: 1303 helix: 1.88 (0.20), residues: 690 sheet: -0.52 (0.47), residues: 122 loop : -0.37 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 18 HIS 0.004 0.001 HIS A 595 PHE 0.018 0.001 PHE A1235 TYR 0.011 0.002 TYR A 136 ARG 0.006 0.000 ARG A 215 *********************** 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 fitting. rotamer outliers: 23 poor density : 26 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8587 (ptm160) REVERT: A 534 MET cc_start: 0.3275 (mtp) cc_final: 0.1318 (ptm) REVERT: A 879 MET cc_start: 0.3030 (mpp) cc_final: 0.2041 (mpp) REVERT: A 1242 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.6931 (m-80) REVERT: A 1364 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7926 (mp10) outliers start: 23 outliers final: 13 residues processed: 48 average time/residue: 0.2838 time to fit residues: 21.3552 Evaluate side-chains 40 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 24 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE 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 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 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1274 SER Chi-restraints excluded: chain A residue 1364 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 80 optimal weight: 50.0000 chunk 119 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 141 optimal weight: 20.0000 chunk 88 optimal weight: 30.0000 chunk 86 optimal weight: 50.0000 chunk 65 optimal weight: 30.0000 chunk 87 optimal weight: 10.0000 overall best weight: 11.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 HIS A 799 HIS ** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 15208 Z= 0.448 Angle : 0.623 8.308 21310 Z= 0.330 Chirality : 0.040 0.166 2454 Planarity : 0.004 0.053 2062 Dihedral : 20.083 96.466 3920 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.95 % Allowed : 20.42 % Favored : 77.63 % 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: 0.73 (0.24), residues: 1303 helix: 1.47 (0.20), residues: 691 sheet: -0.83 (0.46), residues: 122 loop : -0.50 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 18 HIS 0.007 0.001 HIS A 116 PHE 0.021 0.002 PHE A1235 TYR 0.014 0.002 TYR A 521 ARG 0.005 0.001 ARG A 307 *********************** 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 46 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 23 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8634 (ptm160) REVERT: A 1242 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.7229 (m-80) REVERT: A 1364 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8092 (mt0) REVERT: A 1365 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8076 (pp) outliers start: 23 outliers final: 14 residues processed: 45 average time/residue: 0.2989 time to fit residues: 20.8065 Evaluate side-chains 41 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 23 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE 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 761 ILE 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 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1330 THR Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1365 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 30.0000 chunk 84 optimal weight: 30.0000 chunk 42 optimal weight: 0.8980 chunk 27 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 135 optimal weight: 30.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15208 Z= 0.206 Angle : 0.482 8.871 21310 Z= 0.258 Chirality : 0.035 0.142 2454 Planarity : 0.003 0.051 2062 Dihedral : 19.755 98.837 3920 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: 1.14 (0.24), residues: 1303 helix: 1.88 (0.21), residues: 689 sheet: -0.70 (0.49), residues: 110 loop : -0.43 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.016 0.001 HIS A 799 PHE 0.009 0.001 PHE A1045 TYR 0.010 0.001 TYR A 521 ARG 0.002 0.000 ARG A 215 *********************** 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 fitting. rotamer outliers: 18 poor density : 25 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8558 (ptm160) REVERT: A 534 MET cc_start: 0.3518 (ttm) cc_final: 0.2482 (ptm) REVERT: A 1242 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.7057 (m-80) REVERT: A 1364 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.8056 (mt0) REVERT: A 1365 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8089 (pp) outliers start: 18 outliers final: 11 residues processed: 43 average time/residue: 0.3165 time to fit residues: 20.9589 Evaluate side-chains 39 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 24 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 188 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 761 ILE 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 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 Chi-restraints excluded: chain A residue 1365 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 135 optimal weight: 30.0000 chunk 79 optimal weight: 30.0000 chunk 57 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 40 optimal weight: 0.0270 chunk 119 optimal weight: 30.0000 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 86 optimal weight: 50.0000 overall best weight: 5.8048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15208 Z= 0.234 Angle : 0.490 12.174 21310 Z= 0.260 Chirality : 0.035 0.140 2454 Planarity : 0.003 0.052 2062 Dihedral : 19.635 97.485 3920 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.44 % Allowed : 21.10 % Favored : 77.46 % 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: 1.23 (0.24), residues: 1303 helix: 1.96 (0.21), residues: 685 sheet: -0.65 (0.49), residues: 110 loop : -0.38 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 883 HIS 0.004 0.001 HIS A 799 PHE 0.011 0.001 PHE A1045 TYR 0.010 0.001 TYR A 155 ARG 0.002 0.000 ARG A 557 *********************** 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 41 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 24 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8520 (ptm160) REVERT: A 534 MET cc_start: 0.3499 (ttm) cc_final: 0.2409 (ptm) REVERT: A 1242 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.7003 (m-80) REVERT: A 1364 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8071 (mt0) REVERT: A 1365 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8089 (pp) outliers start: 17 outliers final: 13 residues processed: 40 average time/residue: 0.2797 time to fit residues: 17.7774 Evaluate side-chains 40 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 23 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 188 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 761 ILE 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 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1365 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 97 optimal weight: 4.9990 chunk 146 optimal weight: 50.0000 chunk 134 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 15208 Z= 0.309 Angle : 0.527 11.324 21310 Z= 0.278 Chirality : 0.036 0.143 2454 Planarity : 0.003 0.052 2062 Dihedral : 19.787 96.864 3920 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.44 % Allowed : 21.36 % Favored : 77.20 % 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: 1.06 (0.24), residues: 1303 helix: 1.78 (0.20), residues: 691 sheet: -0.71 (0.47), residues: 122 loop : -0.41 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 883 HIS 0.004 0.001 HIS A 328 PHE 0.012 0.001 PHE A1235 TYR 0.011 0.001 TYR A 521 ARG 0.002 0.000 ARG A 557 ********************** 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 40 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 23 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8562 (ptm160) REVERT: A 534 MET cc_start: 0.3594 (ttm) cc_final: 0.2422 (ptm) REVERT: A 1242 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.7129 (m-80) REVERT: A 1364 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8083 (mt0) REVERT: A 1365 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8112 (pp) outliers start: 17 outliers final: 12 residues processed: 39 average time/residue: 0.3027 time to fit residues: 18.9916 Evaluate side-chains 39 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 23 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 188 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 761 ILE 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 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1364 GLN Chi-restraints excluded: chain A residue 1365 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 30.0000 chunk 102 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.056341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.035297 restraints weight = 87522.572| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.45 r_work: 0.2705 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 15208 Z= 0.286 Angle : 0.513 11.501 21310 Z= 0.271 Chirality : 0.036 0.142 2454 Planarity : 0.003 0.052 2062 Dihedral : 19.747 97.443 3920 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.53 % Allowed : 21.27 % Favored : 77.20 % 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: 1.11 (0.24), residues: 1303 helix: 1.84 (0.21), residues: 690 sheet: -0.71 (0.49), residues: 110 loop : -0.44 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 883 HIS 0.005 0.001 HIS A 116 PHE 0.011 0.001 PHE A1235 TYR 0.010 0.001 TYR A 521 ARG 0.002 0.000 ARG A 69 =============================================================================== Job complete usr+sys time: 2421.92 seconds wall clock time: 44 minutes 42.33 seconds (2682.33 seconds total)