Starting phenix.real_space_refine on Sun Jul 21 09:44:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3y_41867/07_2024/8u3y_41867_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3y_41867/07_2024/8u3y_41867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3y_41867/07_2024/8u3y_41867.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3y_41867/07_2024/8u3y_41867.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3y_41867/07_2024/8u3y_41867_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3y_41867/07_2024/8u3y_41867_neut.cif" } resolution = 3.1 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 144 5.49 5 Mg 5 5.21 5 S 22 5.16 5 C 8375 2.51 5 N 2458 2.21 5 O 3008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 130": "OE1" <-> "OE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A GLU 579": "OE1" <-> "OE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A GLU 617": "OE1" <-> "OE2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A GLU 706": "OE1" <-> "OE2" Residue "A GLU 762": "OE1" <-> "OE2" Residue "A GLU 790": "OE1" <-> "OE2" Residue "A GLU 809": "OE1" <-> "OE2" Residue "A PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 923": "OE1" <-> "OE2" Residue "A GLU 952": "OE1" <-> "OE2" Residue "A GLU 1007": "OE1" <-> "OE2" Residue "A GLU 1049": "OE1" <-> "OE2" Residue "A GLU 1068": "OE1" <-> "OE2" Residue "A GLU 1071": "OE1" <-> "OE2" Residue "A GLU 1150": "OE1" <-> "OE2" Residue "A GLU 1170": "OE1" <-> "OE2" Residue "A GLU 1183": "OE1" <-> "OE2" Residue "A GLU 1205": "OE1" <-> "OE2" Residue "A GLU 1268": "OE1" <-> "OE2" Residue "A GLU 1275": "OE1" <-> "OE2" Residue "A GLU 1341": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14012 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 10962 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1336, 10951 Classifications: {'peptide': 1336} Link IDs: {'PTRANS': 35, 'TRANS': 1300} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 1336, 10951 Classifications: {'peptide': 1336} Link IDs: {'PTRANS': 35, 'TRANS': 1300} Chain breaks: 3 bond proxies already assigned to first conformer: 11134 Chain: "B" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2103 Classifications: {'RNA': 98} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 53, 'rna3p_pyr': 34} Link IDs: {'rna2p': 10, 'rna3p': 87} Chain: "C" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 325 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "c" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 341 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "D" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 271 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 783 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 783 " occ=0.50 Time building chain proxies: 14.49, per 1000 atoms: 1.03 Number of scatterers: 14012 At special positions: 0 Unit cell: (87.465, 128.282, 121.618, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 144 15.00 Mg 5 11.99 O 3008 8.00 N 2458 7.00 C 8375 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: 6.55 Conformation dependent library (CDL) restraints added in 3.6 seconds 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2548 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 10 sheets defined 55.6% alpha, 9.6% beta 48 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 5.53 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 5.086A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (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: 3.588A 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 175 through 179 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 184 through 196 Processing helix chain 'A' and resid 208 through 214 removed outlier: 4.086A pdb=" N ALA A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 240 through 246 Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 290 through 306 removed outlier: 4.142A pdb=" N LYS A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN A 295 " --> pdb=" O LEU A 291 " (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 383 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: 4.186A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.039A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.668A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) 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 removed outlier: 3.702A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 553 Processing helix chain 'A' and resid 560 through 568 removed outlier: 3.506A pdb=" N TYR A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 601 removed outlier: 3.526A pdb=" N ILE A 600 " --> pdb=" O ASP A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.611A 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 637 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 652 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 698 Processing helix chain 'A' and resid 703 through 711 Processing helix chain 'A' and resid 719 through 727 Processing helix chain 'A' and resid 731 through 751 removed outlier: 4.327A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 779 through 792 removed outlier: 3.617A pdb=" N GLY A 787 " --> pdb=" O AARG A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 804 through 807 Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 829 through 833 removed outlier: 3.854A pdb=" N LEU A 833 " --> pdb=" O ILE A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 866 Processing helix chain 'A' and resid 872 through 889 removed outlier: 5.419A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.454A 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 902 through 906 removed outlier: 3.736A pdb=" N GLY A 906 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 Processing helix chain 'A' and resid 917 through 940 removed outlier: 4.318A pdb=" N LEU A 921 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A 922 " --> pdb=" O LYS A 918 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 971 Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.339A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 3.799A pdb=" N PHE A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1043 removed outlier: 3.554A pdb=" N TYR A1039 " --> pdb=" O LYS A1035 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N MET A1043 " --> pdb=" O TYR A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1047 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 removed outlier: 3.585A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 Processing helix chain 'A' and resid 1191 through 1195 removed outlier: 3.707A pdb=" N ILE A1195 " --> pdb=" O LYS A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1240 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1310 Processing helix chain 'A' and resid 1311 through 1315 Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.609A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 959 removed outlier: 7.257A pdb=" N TYR A 5 " --> pdb=" O ASN A 758 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N VAL A 760 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLU A 762 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LEU A 9 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 10.079A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA4, first strand: chain 'A' and resid 837 through 840 Processing sheet with id=AA5, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA6, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 6.898A pdb=" N GLU A1064 " --> pdb=" O VAL A1073 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA8, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.613A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.613A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1324 through 1325 512 hydrogen bonds defined for protein. 1471 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 119 hydrogen bonds 234 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 8.02 Time building geometry restraints manager: 7.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2046 1.31 - 1.43: 4552 1.43 - 1.56: 7636 1.56 - 1.68: 284 1.68 - 1.81: 42 Bond restraints: 14560 Sorted by residual: bond pdb=" C PRO A1321 " pdb=" O PRO A1321 " ideal model delta sigma weight residual 1.233 1.183 0.050 1.34e-02 5.57e+03 1.42e+01 bond pdb=" O3' DG D 41 " pdb=" P DT D 42 " ideal model delta sigma weight residual 1.607 1.654 -0.047 1.50e-02 4.44e+03 9.78e+00 bond pdb=" CA ALA A1217 " pdb=" CB ALA A1217 " ideal model delta sigma weight residual 1.531 1.479 0.052 1.69e-02 3.50e+03 9.41e+00 bond pdb=" N PRO A1321 " pdb=" CA PRO A1321 " ideal model delta sigma weight residual 1.471 1.434 0.037 1.27e-02 6.20e+03 8.38e+00 bond pdb=" CA ALA A1322 " pdb=" CB ALA A1322 " ideal model delta sigma weight residual 1.531 1.491 0.040 1.48e-02 4.57e+03 7.27e+00 ... (remaining 14555 not shown) Histogram of bond angle deviations from ideal: 97.83 - 105.06: 751 105.06 - 112.28: 7597 112.28 - 119.51: 4858 119.51 - 126.73: 6573 126.73 - 133.96: 492 Bond angle restraints: 20271 Sorted by residual: angle pdb=" N TYR A1326 " pdb=" CA TYR A1326 " pdb=" C TYR A1326 " ideal model delta sigma weight residual 110.35 102.79 7.56 1.38e+00 5.25e-01 3.00e+01 angle pdb=" C THR A1339 " pdb=" CA THR A1339 " pdb=" CB THR A1339 " ideal model delta sigma weight residual 111.40 104.86 6.54 1.29e+00 6.01e-01 2.57e+01 angle pdb=" N LYS A1340 " pdb=" CA LYS A1340 " pdb=" C LYS A1340 " ideal model delta sigma weight residual 113.88 107.75 6.13 1.23e+00 6.61e-01 2.49e+01 angle pdb=" CA TYR A1336 " pdb=" C TYR A1336 " pdb=" O TYR A1336 " ideal model delta sigma weight residual 122.41 116.40 6.01 1.21e+00 6.83e-01 2.47e+01 angle pdb=" N PRO A1321 " pdb=" CA PRO A1321 " pdb=" CB PRO A1321 " ideal model delta sigma weight residual 103.17 98.83 4.34 8.90e-01 1.26e+00 2.38e+01 ... (remaining 20266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.24: 8351 34.24 - 68.47: 440 68.47 - 102.71: 40 102.71 - 136.94: 0 136.94 - 171.18: 5 Dihedral angle restraints: 8836 sinusoidal: 4901 harmonic: 3935 Sorted by residual: dihedral pdb=" O4' U B 59 " pdb=" C1' U B 59 " pdb=" N1 U B 59 " pdb=" C2 U B 59 " ideal model delta sinusoidal sigma weight residual 200.00 28.82 171.18 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' C B 70 " pdb=" C1' C B 70 " pdb=" N1 C B 70 " pdb=" C2 C B 70 " ideal model delta sinusoidal sigma weight residual 200.00 37.33 162.67 1 1.50e+01 4.44e-03 8.34e+01 dihedral pdb=" CA LYS A1153 " pdb=" C LYS A1153 " pdb=" N SER A1154 " pdb=" CA SER A1154 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 8833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2200 0.089 - 0.179: 113 0.179 - 0.268: 7 0.268 - 0.357: 1 0.357 - 0.447: 1 Chirality restraints: 2322 Sorted by residual: chirality pdb=" P DT c 23 " pdb=" OP1 DT c 23 " pdb=" OP2 DT c 23 " pdb=" O5' DT c 23 " both_signs ideal model delta sigma weight residual True 2.35 -2.79 -0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" CA TYR A1336 " pdb=" N TYR A1336 " pdb=" C TYR A1336 " pdb=" CB TYR A1336 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C3' A B 8 " pdb=" C4' A B 8 " pdb=" O3' A B 8 " pdb=" C2' A B 8 " both_signs ideal model delta sigma weight residual False -2.48 -2.26 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 2319 not shown) Planarity restraints: 2066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 730 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.48e+00 pdb=" N PRO A 731 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 731 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 731 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1228 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A1229 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A1229 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1229 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A1216 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C SER A1216 " 0.030 2.00e-02 2.50e+03 pdb=" O SER A1216 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA A1217 " -0.010 2.00e-02 2.50e+03 ... (remaining 2063 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 115 2.55 - 3.14: 10973 3.14 - 3.73: 22606 3.73 - 4.31: 32982 4.31 - 4.90: 52413 Nonbonded interactions: 119089 Sorted by model distance: nonbonded pdb=" OD1 ASP A 10 " pdb="MG MG A1401 " model vdw 1.963 2.170 nonbonded pdb=" OE2 GLU A 762 " pdb="MG MG A1401 " model vdw 2.080 2.170 nonbonded pdb=" ND1 HIS A 983 " pdb="MG MG A1402 " model vdw 2.093 2.250 nonbonded pdb=" OP2 A B 65 " pdb="MG MG B 101 " model vdw 2.106 2.170 nonbonded pdb=" OG1 THR A1167 " pdb=" OE1 GLU A1170 " model vdw 2.139 2.440 ... (remaining 119084 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: 9.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 56.050 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.080 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 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 0.058 14560 Z= 0.406 Angle : 0.718 11.053 20271 Z= 0.431 Chirality : 0.045 0.447 2322 Planarity : 0.003 0.047 2066 Dihedral : 18.578 171.176 6288 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.25 % Allowed : 0.50 % Favored : 99.25 % 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: -0.24 (0.23), residues: 1331 helix: 0.41 (0.20), residues: 652 sheet: -0.39 (0.49), residues: 115 loop : -0.66 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 18 HIS 0.006 0.001 HIS A 412 PHE 0.024 0.002 PHE A1324 TYR 0.020 0.002 TYR A 362 ARG 0.014 0.001 ARG A 832 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 1.281 Fit side-chains REVERT: A 534 MET cc_start: 0.7192 (mmm) cc_final: 0.6989 (mmm) REVERT: A 1256 GLN cc_start: 0.7433 (mt0) cc_final: 0.7180 (tt0) outliers start: 3 outliers final: 0 residues processed: 78 average time/residue: 0.3398 time to fit residues: 37.7919 Evaluate side-chains 62 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 37 optimal weight: 0.0570 chunk 74 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A1364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14560 Z= 0.184 Angle : 0.564 11.944 20271 Z= 0.298 Chirality : 0.039 0.191 2322 Planarity : 0.003 0.043 2066 Dihedral : 19.519 170.897 3430 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.08 % Allowed : 3.82 % Favored : 96.10 % 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: 0.25 (0.23), residues: 1331 helix: 0.81 (0.20), residues: 650 sheet: 0.24 (0.59), residues: 84 loop : -0.46 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 464 HIS 0.009 0.001 HIS A 41 PHE 0.012 0.001 PHE A 970 TYR 0.017 0.001 TYR A1242 ARG 0.006 0.000 ARG A 832 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 1.343 Fit side-chains REVERT: A 781 MET cc_start: 0.8011 (tpt) cc_final: 0.7637 (tpt) REVERT: A 943 TYR cc_start: 0.8215 (m-80) cc_final: 0.8003 (m-80) REVERT: A 1256 GLN cc_start: 0.7596 (mt0) cc_final: 0.7271 (tt0) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.2726 time to fit residues: 31.1042 Evaluate side-chains 62 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A1364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14560 Z= 0.245 Angle : 0.544 8.337 20271 Z= 0.288 Chirality : 0.039 0.196 2322 Planarity : 0.003 0.043 2066 Dihedral : 19.465 169.862 3430 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.17 % Allowed : 5.32 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.42 (0.23), residues: 1331 helix: 1.00 (0.20), residues: 650 sheet: -0.57 (0.52), residues: 113 loop : -0.28 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.009 0.001 HIS A 41 PHE 0.012 0.001 PHE A 970 TYR 0.016 0.001 TYR A1242 ARG 0.005 0.000 ARG A 832 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 1.413 Fit side-chains REVERT: A 781 MET cc_start: 0.8133 (tpt) cc_final: 0.7780 (tpt) REVERT: A 1256 GLN cc_start: 0.7619 (mt0) cc_final: 0.7232 (tt0) outliers start: 2 outliers final: 1 residues processed: 68 average time/residue: 0.3030 time to fit residues: 30.5577 Evaluate side-chains 65 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1158 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14560 Z= 0.180 Angle : 0.504 10.355 20271 Z= 0.266 Chirality : 0.037 0.178 2322 Planarity : 0.003 0.041 2066 Dihedral : 19.349 169.430 3430 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.33 % Allowed : 6.06 % Favored : 93.60 % 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: 0.68 (0.23), residues: 1331 helix: 1.26 (0.21), residues: 650 sheet: -0.48 (0.52), residues: 115 loop : -0.20 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 476 HIS 0.003 0.001 HIS A 723 PHE 0.011 0.001 PHE A 970 TYR 0.017 0.001 TYR A1242 ARG 0.004 0.000 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 1.483 Fit side-chains REVERT: A 781 MET cc_start: 0.8091 (tpt) cc_final: 0.7782 (tpt) REVERT: A 786 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: A 1256 GLN cc_start: 0.7607 (mt0) cc_final: 0.7287 (tt0) outliers start: 4 outliers final: 1 residues processed: 72 average time/residue: 0.2606 time to fit residues: 28.6745 Evaluate side-chains 66 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 786 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.8475 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 14560 Z= 0.554 Angle : 0.679 13.027 20271 Z= 0.353 Chirality : 0.047 0.238 2322 Planarity : 0.004 0.048 2066 Dihedral : 19.460 170.703 3430 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.91 % Allowed : 6.73 % Favored : 92.36 % 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: 0.10 (0.23), residues: 1331 helix: 0.73 (0.20), residues: 659 sheet: -0.56 (0.49), residues: 118 loop : -0.48 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 18 HIS 0.006 0.002 HIS A 167 PHE 0.015 0.002 PHE A 491 TYR 0.023 0.002 TYR A 362 ARG 0.006 0.001 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 1.382 Fit side-chains REVERT: A 786 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: A 1256 GLN cc_start: 0.7666 (mt0) cc_final: 0.7417 (tt0) REVERT: A 1260 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7899 (mt-10) outliers start: 11 outliers final: 6 residues processed: 68 average time/residue: 0.2764 time to fit residues: 28.6415 Evaluate side-chains 65 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1158 LYS Chi-restraints excluded: chain A residue 1260 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 0.0270 chunk 73 optimal weight: 0.5980 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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: 0.8378 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14560 Z= 0.172 Angle : 0.501 7.566 20271 Z= 0.267 Chirality : 0.037 0.186 2322 Planarity : 0.003 0.041 2066 Dihedral : 19.380 169.565 3430 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.50 % Allowed : 7.14 % Favored : 92.36 % 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: 0.60 (0.23), residues: 1331 helix: 1.19 (0.21), residues: 650 sheet: 0.60 (0.63), residues: 75 loop : -0.44 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 476 HIS 0.002 0.001 HIS A 412 PHE 0.019 0.001 PHE A 575 TYR 0.012 0.001 TYR A1242 ARG 0.007 0.000 ARG A 832 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 1.424 Fit side-chains REVERT: A 707 ASP cc_start: 0.7827 (m-30) cc_final: 0.7562 (m-30) REVERT: A 781 MET cc_start: 0.8110 (tpt) cc_final: 0.7799 (tpt) REVERT: A 786 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: A 1260 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7873 (mt-10) outliers start: 6 outliers final: 4 residues processed: 74 average time/residue: 0.2900 time to fit residues: 33.3190 Evaluate side-chains 72 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1158 LYS Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1270 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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: 0.8429 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14560 Z= 0.315 Angle : 0.568 14.242 20271 Z= 0.296 Chirality : 0.040 0.205 2322 Planarity : 0.004 0.042 2066 Dihedral : 19.357 169.825 3430 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.75 % Allowed : 7.23 % Favored : 92.03 % 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: 0.50 (0.23), residues: 1331 helix: 1.10 (0.20), residues: 650 sheet: 0.39 (0.60), residues: 81 loop : -0.47 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 18 HIS 0.004 0.001 HIS A 167 PHE 0.018 0.001 PHE A 575 TYR 0.017 0.001 TYR A 362 ARG 0.008 0.000 ARG A 832 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 1.230 Fit side-chains REVERT: A 781 MET cc_start: 0.8215 (tpt) cc_final: 0.7829 (tpt) REVERT: A 786 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: A 1170 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7583 (pm20) outliers start: 9 outliers final: 4 residues processed: 71 average time/residue: 0.2668 time to fit residues: 29.0120 Evaluate side-chains 70 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1125 ASP Chi-restraints excluded: chain A residue 1158 LYS Chi-restraints excluded: chain A residue 1170 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 27 optimal weight: 0.0070 chunk 88 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14560 Z= 0.194 Angle : 0.508 8.286 20271 Z= 0.268 Chirality : 0.037 0.183 2322 Planarity : 0.003 0.041 2066 Dihedral : 19.311 169.259 3430 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.33 % Allowed : 7.56 % Favored : 92.11 % 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: 0.68 (0.23), residues: 1331 helix: 1.28 (0.21), residues: 650 sheet: 0.60 (0.61), residues: 80 loop : -0.43 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 476 HIS 0.003 0.001 HIS A1262 PHE 0.018 0.001 PHE A 575 TYR 0.012 0.001 TYR A1242 ARG 0.008 0.000 ARG A 832 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 1.355 Fit side-chains REVERT: A 43 ILE cc_start: 0.8962 (mm) cc_final: 0.8740 (mm) REVERT: A 707 ASP cc_start: 0.7817 (m-30) cc_final: 0.7581 (m-30) REVERT: A 781 MET cc_start: 0.8137 (tpt) cc_final: 0.7834 (tpt) REVERT: A 786 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7243 (mp0) outliers start: 4 outliers final: 3 residues processed: 69 average time/residue: 0.2628 time to fit residues: 27.8639 Evaluate side-chains 68 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1158 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8401 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14560 Z= 0.231 Angle : 0.531 15.699 20271 Z= 0.277 Chirality : 0.038 0.188 2322 Planarity : 0.003 0.043 2066 Dihedral : 19.279 169.176 3430 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.42 % Allowed : 7.72 % Favored : 91.86 % 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: 0.67 (0.23), residues: 1331 helix: 1.28 (0.21), residues: 650 sheet: 0.55 (0.61), residues: 80 loop : -0.44 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 18 HIS 0.003 0.001 HIS A 167 PHE 0.020 0.001 PHE A 575 TYR 0.014 0.001 TYR A1242 ARG 0.009 0.000 ARG A 832 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 707 ASP cc_start: 0.7801 (m-30) cc_final: 0.7559 (m-30) REVERT: A 781 MET cc_start: 0.8169 (tpt) cc_final: 0.7828 (tpt) REVERT: A 786 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7302 (mp0) outliers start: 5 outliers final: 4 residues processed: 69 average time/residue: 0.2889 time to fit residues: 30.4570 Evaluate side-chains 70 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1158 LYS Chi-restraints excluded: chain A residue 1170 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 0.0020 chunk 95 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 132 optimal weight: 0.0870 chunk 115 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.4766 ------------------------------------------------------------------------------- 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: 0.8378 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14560 Z= 0.161 Angle : 0.513 15.656 20271 Z= 0.268 Chirality : 0.037 0.178 2322 Planarity : 0.003 0.045 2066 Dihedral : 19.283 168.831 3430 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.50 % Allowed : 7.81 % Favored : 91.69 % 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: 0.77 (0.23), residues: 1331 helix: 1.35 (0.21), residues: 650 sheet: 0.67 (0.62), residues: 80 loop : -0.40 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 476 HIS 0.003 0.001 HIS A 116 PHE 0.023 0.001 PHE A 575 TYR 0.012 0.001 TYR A1242 ARG 0.010 0.000 ARG A 832 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 707 ASP cc_start: 0.7791 (m-30) cc_final: 0.7566 (m-30) REVERT: A 781 MET cc_start: 0.8140 (tpt) cc_final: 0.7805 (tpt) REVERT: A 786 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7291 (mp0) outliers start: 6 outliers final: 5 residues processed: 70 average time/residue: 0.2628 time to fit residues: 28.3682 Evaluate side-chains 71 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1158 LYS Chi-restraints excluded: chain A residue 1170 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 101 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.125132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.087483 restraints weight = 42385.148| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.29 r_work: 0.2907 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14560 Z= 0.161 Angle : 0.506 15.850 20271 Z= 0.264 Chirality : 0.037 0.175 2322 Planarity : 0.003 0.042 2066 Dihedral : 19.224 168.502 3430 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.42 % Allowed : 7.97 % Favored : 91.61 % 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: 0.86 (0.23), residues: 1331 helix: 1.44 (0.21), residues: 650 sheet: 0.77 (0.63), residues: 80 loop : -0.37 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 476 HIS 0.003 0.001 HIS A 116 PHE 0.022 0.001 PHE A 575 TYR 0.010 0.001 TYR A1242 ARG 0.009 0.000 ARG A 832 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2900.88 seconds wall clock time: 54 minutes 27.44 seconds (3267.44 seconds total)