Starting phenix.real_space_refine on Sun Jul 21 22:37:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuu_37860/07_2024/8wuu_37860.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuu_37860/07_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_37860/07_2024/8wuu_37860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuu_37860/07_2024/8wuu_37860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuu_37860/07_2024/8wuu_37860.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wuu_37860/07_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 7.98, per 1000 atoms: 0.55 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: 6.40 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: 6.62 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: 8.73 Time building geometry restraints manager: 6.94 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 2.440 nonbonded pdb=" OE1 GLU A 977 " pdb=" OH TYR A1242 " model vdw 2.219 2.440 nonbonded pdb=" O2' C B 3 " pdb=" O5' C B 4 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR A 5 " pdb=" O HIS A 754 " model vdw 2.236 2.440 nonbonded pdb=" OE2 GLU A1162 " pdb=" OH TYR A1187 " model vdw 2.242 2.440 ... (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 ========== 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: 0.140 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: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 49.160 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.230 ------------------------------------------------------------------------------- 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 : 1.429 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: 0.4785 time to fit residues: 39.4124 Evaluate side-chains 31 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 1.422 ------------------------------------------------------------------------------- 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: 0.1980 chunk 61 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 75 optimal weight: 40.0000 chunk 59 optimal weight: 4.9990 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: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN A1066 ASN A1221 GLN A1262 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.1319 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= 0.213 Angle : 0.466 6.499 21310 Z= 0.254 Chirality : 0.034 0.145 2454 Planarity : 0.003 0.047 2062 Dihedral : 19.601 128.561 3920 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.44 % Allowed : 20.17 % Favored : 78.39 % 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: 1.51 (0.24), residues: 1303 helix: 2.13 (0.21), residues: 678 sheet: 0.17 (0.52), residues: 101 loop : -0.31 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 18 HIS 0.006 0.001 HIS A 328 PHE 0.012 0.001 PHE A1235 TYR 0.011 0.001 TYR A 815 ARG 0.004 0.000 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 48 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 31 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8520 (m-40) cc_final: 0.8076 (t0) REVERT: A 534 MET cc_start: 0.3013 (mtp) cc_final: 0.0685 (ptm) REVERT: A 1242 TYR cc_start: 0.7205 (OUTLIER) cc_final: 0.6525 (m-80) outliers start: 17 outliers final: 6 residues processed: 47 average time/residue: 0.2933 time to fit residues: 21.6126 Evaluate side-chains 33 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 26 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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: 20.0000 chunk 41 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 119 optimal weight: 0.0070 chunk 132 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 overall best weight: 7.0008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A 826 GLN A1297 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.1914 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= 0.273 Angle : 0.484 6.095 21310 Z= 0.263 Chirality : 0.035 0.136 2454 Planarity : 0.003 0.047 2062 Dihedral : 19.601 112.138 3920 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.37 % Allowed : 20.00 % 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: 1.38 (0.24), residues: 1303 helix: 2.02 (0.21), residues: 684 sheet: -0.33 (0.46), residues: 133 loop : -0.26 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 883 HIS 0.005 0.001 HIS A 595 PHE 0.017 0.001 PHE A1235 TYR 0.012 0.001 TYR A 521 ARG 0.003 0.000 ARG A 75 *********************** 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 57 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 29 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASN cc_start: 0.8661 (m-40) cc_final: 0.8087 (t0) REVERT: A 534 MET cc_start: 0.3515 (mtp) cc_final: 0.1193 (ptm) REVERT: A 763 MET cc_start: 0.8588 (mtp) cc_final: 0.8316 (mtp) REVERT: A 879 MET cc_start: 0.0945 (mpp) cc_final: 0.0245 (mpp) REVERT: A 1089 MET cc_start: 0.9266 (mtm) cc_final: 0.8899 (mtm) REVERT: A 1242 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.6679 (m-80) outliers start: 28 outliers final: 10 residues processed: 57 average time/residue: 0.2781 time to fit residues: 24.2849 Evaluate side-chains 37 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 26 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 313 THR 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: 40.0000 chunk 14 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 127 optimal weight: 0.0000 chunk 38 optimal weight: 10.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 ASN A 888 ASN A 990 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.2387 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= 0.266 Angle : 0.485 5.898 21310 Z= 0.260 Chirality : 0.035 0.136 2454 Planarity : 0.003 0.049 2062 Dihedral : 19.557 97.988 3920 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.80 % Allowed : 20.08 % Favored : 77.12 % 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: 1.38 (0.24), residues: 1303 helix: 2.03 (0.21), residues: 684 sheet: -0.29 (0.49), residues: 116 loop : -0.31 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 883 HIS 0.004 0.001 HIS A 595 PHE 0.013 0.001 PHE A1235 TYR 0.012 0.001 TYR A 521 ARG 0.003 0.000 ARG A1303 *********************** 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 60 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 27 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8533 (ptm160) REVERT: A 534 MET cc_start: 0.3495 (mtp) cc_final: 0.1061 (ptm) REVERT: A 763 MET cc_start: 0.8430 (mtp) cc_final: 0.8208 (mtp) REVERT: A 879 MET cc_start: 0.2061 (mpp) cc_final: 0.1140 (mpp) REVERT: A 1242 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.6765 (m-80) REVERT: A 1364 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8019 (mt0) outliers start: 33 outliers final: 14 residues processed: 58 average time/residue: 0.3019 time to fit residues: 26.4288 Evaluate side-chains 42 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 25 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 504 ASN 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 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: 10.0000 chunk 80 optimal weight: 50.0000 chunk 2 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 58 optimal weight: 30.0000 chunk 121 optimal weight: 5.9990 chunk 98 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN A 692 ASN A 854 ASN A1305 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15208 Z= 0.292 Angle : 0.504 6.704 21310 Z= 0.270 Chirality : 0.036 0.138 2454 Planarity : 0.003 0.050 2062 Dihedral : 19.591 94.039 3920 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.46 % Allowed : 20.00 % 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: 1.30 (0.24), residues: 1303 helix: 1.96 (0.21), residues: 690 sheet: -0.31 (0.47), residues: 122 loop : -0.37 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 18 HIS 0.005 0.001 HIS A 595 PHE 0.015 0.001 PHE A1235 TYR 0.011 0.001 TYR A 521 ARG 0.004 0.000 ARG A 215 *********************** 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 56 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 27 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8668 (ptt180) REVERT: A 288 ASP cc_start: 0.9476 (OUTLIER) cc_final: 0.9168 (p0) REVERT: A 461 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8550 (ptm160) REVERT: A 534 MET cc_start: 0.3070 (mtp) cc_final: 0.1030 (ptm) REVERT: A 635 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8746 (mmm-85) REVERT: A 879 MET cc_start: 0.2722 (mpp) cc_final: 0.1751 (mpp) REVERT: A 1242 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.6752 (m-80) REVERT: A 1364 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7997 (mt0) REVERT: A 1365 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8153 (pp) outliers start: 29 outliers final: 16 residues processed: 56 average time/residue: 0.3061 time to fit residues: 25.5006 Evaluate side-chains 48 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 25 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 635 ARG 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 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 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: 6.9990 chunk 127 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 30.0000 chunk 35 optimal weight: 9.9990 chunk 142 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 74 optimal weight: 30.0000 chunk 137 optimal weight: 10.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- 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: 0.6134 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15208 Z= 0.248 Angle : 0.472 7.059 21310 Z= 0.255 Chirality : 0.035 0.133 2454 Planarity : 0.003 0.050 2062 Dihedral : 19.514 93.891 3920 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.37 % Allowed : 20.34 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.03 (0.20), residues: 684 sheet: -0.44 (0.47), residues: 122 loop : -0.38 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 18 HIS 0.004 0.001 HIS A 328 PHE 0.010 0.001 PHE A1235 TYR 0.010 0.001 TYR A 521 ARG 0.003 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 54 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 26 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 ASP cc_start: 0.9464 (OUTLIER) cc_final: 0.9149 (p0) REVERT: A 461 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8515 (ptm160) REVERT: A 534 MET cc_start: 0.3040 (mtp) cc_final: 0.0981 (ptm) REVERT: A 781 MET cc_start: 0.9029 (mtp) cc_final: 0.8479 (mtm) REVERT: A 1242 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.6765 (m-80) REVERT: A 1365 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8159 (pp) outliers start: 28 outliers final: 19 residues processed: 53 average time/residue: 0.2671 time to fit residues: 22.5977 Evaluate side-chains 49 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 26 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 688 PHE Chi-restraints excluded: chain A residue 719 SER 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 1145 VAL Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1365 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 7.9990 chunk 81 optimal weight: 0.4980 chunk 103 optimal weight: 0.0670 chunk 80 optimal weight: 50.0000 chunk 119 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 86 optimal weight: 30.0000 chunk 65 optimal weight: 0.8980 chunk 87 optimal weight: 0.4980 overall best weight: 1.7920 ------------------------------------------------------------------------------- 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: 0.6089 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15208 Z= 0.120 Angle : 0.409 8.521 21310 Z= 0.222 Chirality : 0.032 0.142 2454 Planarity : 0.003 0.048 2062 Dihedral : 19.233 94.112 3920 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.10 % Allowed : 21.78 % Favored : 77.12 % 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: 1.60 (0.24), residues: 1303 helix: 2.25 (0.21), residues: 686 sheet: -0.27 (0.50), residues: 110 loop : -0.26 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 476 HIS 0.004 0.001 HIS A 328 PHE 0.008 0.001 PHE A 518 TYR 0.008 0.001 TYR A 359 ARG 0.004 0.000 ARG A 215 *********************** 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 39 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 26 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 ASP cc_start: 0.9440 (OUTLIER) cc_final: 0.9139 (p0) REVERT: A 534 MET cc_start: 0.2846 (mtp) cc_final: 0.0903 (ptm) REVERT: A 781 MET cc_start: 0.9132 (mtp) cc_final: 0.8641 (mtm) REVERT: A 879 MET cc_start: 0.3212 (mpp) cc_final: 0.2413 (mpp) REVERT: A 1242 TYR cc_start: 0.7303 (OUTLIER) cc_final: 0.6594 (m-80) REVERT: A 1365 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8047 (pp) outliers start: 13 outliers final: 6 residues processed: 38 average time/residue: 0.2614 time to fit residues: 16.3727 Evaluate side-chains 34 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1242 TYR 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: 2.9990 chunk 84 optimal weight: 40.0000 chunk 42 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 135 optimal weight: 30.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 15208 Z= 0.307 Angle : 0.505 10.868 21310 Z= 0.270 Chirality : 0.036 0.134 2454 Planarity : 0.003 0.050 2062 Dihedral : 19.515 94.809 3920 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.86 % Allowed : 21.36 % Favored : 76.78 % 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: 1.38 (0.24), residues: 1303 helix: 2.04 (0.21), residues: 685 sheet: -0.36 (0.47), residues: 122 loop : -0.31 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.005 0.001 HIS A 595 PHE 0.015 0.001 PHE A1235 TYR 0.012 0.001 TYR A 136 ARG 0.003 0.000 ARG A 557 *********************** 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 48 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 26 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 ASP cc_start: 0.9434 (OUTLIER) cc_final: 0.9099 (p0) REVERT: A 461 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8542 (ptm160) REVERT: A 534 MET cc_start: 0.2902 (mtp) cc_final: 0.0966 (ptm) REVERT: A 1242 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.6786 (m-80) outliers start: 22 outliers final: 14 residues processed: 47 average time/residue: 0.3203 time to fit residues: 22.7999 Evaluate side-chains 43 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 26 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 288 ASP 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 798 GLU Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 830 ILE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 135 optimal weight: 30.0000 chunk 79 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 119 optimal weight: 30.0000 chunk 124 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6162 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 15208 Z= 0.349 Angle : 0.542 10.804 21310 Z= 0.288 Chirality : 0.037 0.133 2454 Planarity : 0.004 0.050 2062 Dihedral : 19.809 94.918 3920 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.03 % Allowed : 21.19 % Favored : 76.78 % 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: 1.08 (0.24), residues: 1303 helix: 1.75 (0.20), residues: 689 sheet: -0.51 (0.47), residues: 122 loop : -0.40 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 18 HIS 0.005 0.001 HIS A 116 PHE 0.016 0.002 PHE A1235 TYR 0.012 0.002 TYR A 271 ARG 0.004 0.001 ARG A1114 *********************** 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 49 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 25 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8828 (ptt180) REVERT: A 288 ASP cc_start: 0.9471 (OUTLIER) cc_final: 0.9176 (p0) REVERT: A 461 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8542 (ptm160) REVERT: A 534 MET cc_start: 0.2948 (mtp) cc_final: 0.1083 (ptm) REVERT: A 781 MET cc_start: 0.9032 (mtp) cc_final: 0.8445 (mtm) REVERT: A 1242 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.7013 (m-80) outliers start: 24 outliers final: 19 residues processed: 48 average time/residue: 0.2975 time to fit residues: 22.1369 Evaluate side-chains 48 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 25 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 761 ILE 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 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 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: 30.0000 chunk 66 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 146 optimal weight: 50.0000 chunk 134 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- 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: 0.6160 moved from start: 0.3707 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= 0.326 Angle : 0.524 11.472 21310 Z= 0.278 Chirality : 0.036 0.135 2454 Planarity : 0.003 0.050 2062 Dihedral : 19.759 94.537 3920 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.03 % Allowed : 20.93 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.10 (0.24), residues: 1303 helix: 1.77 (0.20), residues: 689 sheet: -0.66 (0.46), residues: 129 loop : -0.31 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 18 HIS 0.005 0.001 HIS A 595 PHE 0.017 0.001 PHE A1235 TYR 0.011 0.001 TYR A 271 ARG 0.003 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 48 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 24 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8687 (ptt180) REVERT: A 288 ASP cc_start: 0.9435 (OUTLIER) cc_final: 0.9122 (p0) REVERT: A 534 MET cc_start: 0.3157 (mtp) cc_final: 0.1013 (ptm) REVERT: A 781 MET cc_start: 0.9097 (mtp) cc_final: 0.8566 (mtm) REVERT: A 1242 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.7016 (m-80) outliers start: 24 outliers final: 18 residues processed: 47 average time/residue: 0.2773 time to fit residues: 21.1926 Evaluate side-chains 45 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 24 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 761 ILE 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 17 optimal weight: 30.0000 chunk 32 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 30.0000 chunk 102 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.057295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.036200 restraints weight = 88405.111| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.55 r_work: 0.2737 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15208 Z= 0.162 Angle : 0.441 11.328 21310 Z= 0.236 Chirality : 0.033 0.135 2454 Planarity : 0.003 0.050 2062 Dihedral : 19.506 94.667 3920 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.27 % Allowed : 21.78 % Favored : 76.95 % 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: 1.40 (0.24), residues: 1303 helix: 2.07 (0.21), residues: 685 sheet: -0.44 (0.47), residues: 122 loop : -0.30 (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 328 PHE 0.010 0.001 PHE A 626 TYR 0.009 0.001 TYR A 521 ARG 0.003 0.000 ARG A 215 =============================================================================== Job complete usr+sys time: 2338.21 seconds wall clock time: 43 minutes 22.62 seconds (2602.62 seconds total)