Starting phenix.real_space_refine on Thu Feb 15 06:02:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n8o_3601/02_2024/5n8o_3601_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n8o_3601/02_2024/5n8o_3601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n8o_3601/02_2024/5n8o_3601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n8o_3601/02_2024/5n8o_3601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n8o_3601/02_2024/5n8o_3601_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n8o_3601/02_2024/5n8o_3601_neut.pdb" } resolution = 3.9 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= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 45 5.16 5 C 6975 2.51 5 N 2046 2.21 5 O 2278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 8": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A ARG 491": "NH1" <-> "NH2" Residue "A ARG 540": "NH1" <-> "NH2" Residue "A ARG 559": "NH1" <-> "NH2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 807": "NH1" <-> "NH2" Residue "A ARG 822": "NH1" <-> "NH2" Residue "A PHE 894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 934": "NH1" <-> "NH2" Residue "A ARG 1017": "NH1" <-> "NH2" Residue "A ARG 1118": "NH1" <-> "NH2" Residue "A ARG 1219": "NH1" <-> "NH2" Residue "A ARG 1238": "NH1" <-> "NH2" Residue "A ARG 1270": "NH1" <-> "NH2" Residue "A ARG 1296": "NH1" <-> "NH2" Residue "A ARG 1352": "NH1" <-> "NH2" Residue "A ARG 1381": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11362 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11002 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1432, 10991 Classifications: {'peptide': 1432} Link IDs: {'CIS': 7, 'PCIS': 1, 'PTRANS': 51, 'TRANS': 1372} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 1432, 10991 Classifications: {'peptide': 1432} Link IDs: {'CIS': 7, 'PCIS': 1, 'PTRANS': 51, 'TRANS': 1372} Chain breaks: 5 bond proxies already assigned to first conformer: 11141 Chain: "C" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 360 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Time building chain proxies: 11.23, per 1000 atoms: 0.99 Number of scatterers: 11362 At special positions: 0 Unit cell: (113.4, 131.25, 102.9, 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 45 16.00 P 18 15.00 O 2278 8.00 N 2046 7.00 C 6975 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: 4.59 Conformation dependent library (CDL) restraints added in 4.3 seconds 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2632 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 18 sheets defined 36.5% alpha, 8.5% beta 0 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 3.76 Creating SS restraints... Processing helix chain 'A' and resid 11 through 18 removed outlier: 4.223A pdb=" N THR A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 41 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 100 through 120 removed outlier: 4.209A pdb=" N AARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 192 through 212 Processing helix chain 'A' and resid 269 through 282 removed outlier: 3.853A pdb=" N ARG A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS A 282 " --> pdb=" O MET A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 304 removed outlier: 3.597A pdb=" N THR A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 336 through 347 removed outlier: 3.739A pdb=" N LEU A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 354 No H-bonds generated for 'chain 'A' and resid 353 through 354' Processing helix chain 'A' and resid 356 through 367 Processing helix chain 'A' and resid 383 through 402 removed outlier: 4.131A pdb=" N ARG A 397 " --> pdb=" O ARG A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 430 removed outlier: 3.929A pdb=" N ARG A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 460 removed outlier: 3.600A pdb=" N GLN A 459 " --> pdb=" O MET A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.520A pdb=" N LEU A 513 " --> pdb=" O GLY A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 527 removed outlier: 4.577A pdb=" N LEU A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 552 Processing helix chain 'A' and resid 576 through 593 Processing helix chain 'A' and resid 604 through 621 Processing helix chain 'A' and resid 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 763 through 767 removed outlier: 3.653A pdb=" N ALA A 767 " --> pdb=" O PRO A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 844 removed outlier: 3.844A pdb=" N GLN A 839 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 844 " --> pdb=" O ILE A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 858 removed outlier: 3.628A pdb=" N ALA A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 877 Proline residue: A 873 - end of helix Processing helix chain 'A' and resid 885 through 894 Processing helix chain 'A' and resid 901 through 914 removed outlier: 3.750A pdb=" N GLY A 905 " --> pdb=" O PHE A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 952 removed outlier: 3.545A pdb=" N GLU A 940 " --> pdb=" O SER A 936 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 942 " --> pdb=" O GLU A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 978 removed outlier: 4.011A pdb=" N THR A 977 " --> pdb=" O GLN A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1011 Processing helix chain 'A' and resid 1026 through 1036 Processing helix chain 'A' and resid 1043 through 1056 removed outlier: 3.671A pdb=" N LEU A1047 " --> pdb=" O LEU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1075 removed outlier: 3.886A pdb=" N VAL A1075 " --> pdb=" O SER A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1086 Processing helix chain 'A' and resid 1112 through 1117 Processing helix chain 'A' and resid 1133 through 1135 No H-bonds generated for 'chain 'A' and resid 1133 through 1135' Processing helix chain 'A' and resid 1136 through 1146 Processing helix chain 'A' and resid 1147 through 1155 Processing helix chain 'A' and resid 1156 through 1158 No H-bonds generated for 'chain 'A' and resid 1156 through 1158' Processing helix chain 'A' and resid 1183 through 1195 Processing helix chain 'A' and resid 1209 through 1217 removed outlier: 4.124A pdb=" N VAL A1213 " --> pdb=" O TYR A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1224 Processing helix chain 'A' and resid 1235 through 1251 Processing helix chain 'A' and resid 1271 through 1275 removed outlier: 4.524A pdb=" N LEU A1274 " --> pdb=" O ASP A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1281 removed outlier: 3.908A pdb=" N TRP A1280 " --> pdb=" O ARG A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1392 Processing helix chain 'A' and resid 1428 through 1436 removed outlier: 3.835A pdb=" N ALA A1432 " --> pdb=" O GLY A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1451 through 1459 Processing helix chain 'A' and resid 1465 through 1469 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 34 removed outlier: 3.561A pdb=" N ARG A 32 " --> pdb=" O LEU A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 127 Processing sheet with id=AA5, first strand: chain 'A' and resid 505 through 506 removed outlier: 7.096A pdb=" N VAL A 505 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR A 535 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA A 434 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASP A 536 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL A 436 " --> pdb=" O ASP A 536 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 569 through 570 removed outlier: 6.207A pdb=" N THR A 569 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL A 788 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N GLU A 776 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA A 599 " --> pdb=" O GLU A 776 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 629 through 631 Processing sheet with id=AA8, first strand: chain 'A' and resid 655 through 660 removed outlier: 3.772A pdb=" N SER A 665 " --> pdb=" O ASN A 660 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 674 through 675 removed outlier: 3.502A pdb=" N THR A 675 " --> pdb=" O SER A 680 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 733 through 735 removed outlier: 3.800A pdb=" N ASP A 733 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 720 " --> pdb=" O ASP A 733 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 718 " --> pdb=" O LEU A 735 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 745 through 746 Processing sheet with id=AB3, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.687A pdb=" N THR A 988 " --> pdb=" O ALA A1096 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1040 through 1041 removed outlier: 6.287A pdb=" N GLY A1022 " --> pdb=" O GLN A1041 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1399 through 1401 removed outlier: 7.005A pdb=" N ALA A1413 " --> pdb=" O GLN A1444 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1260 through 1266 Processing sheet with id=AB7, first strand: chain 'A' and resid 1296 through 1301 removed outlier: 6.949A pdb=" N THR A1308 " --> pdb=" O ALA A1298 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE A1300 " --> pdb=" O LEU A1306 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU A1306 " --> pdb=" O ILE A1300 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1361 through 1363 Processing sheet with id=AB9, first strand: chain 'A' and resid 1372 through 1374 removed outlier: 3.752A pdb=" N ARG A1381 " --> pdb=" O LEU A1374 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 4.44 Time building geometry restraints manager: 5.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2304 1.32 - 1.44: 2620 1.44 - 1.57: 6509 1.57 - 1.69: 37 1.69 - 1.81: 90 Bond restraints: 11560 Sorted by residual: bond pdb=" C GLU A1471 " pdb=" N PRO A1472 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.96e+00 bond pdb=" C VAL A 413 " pdb=" N PRO A 414 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.64e+00 bond pdb=" CB THR A 541 " pdb=" CG2 THR A 541 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.83e+00 bond pdb=" CG LEU A1416 " pdb=" CD2 LEU A1416 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.54e+00 bond pdb=" C LEU A 872 " pdb=" N PRO A 873 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.54e+00 ... (remaining 11555 not shown) Histogram of bond angle deviations from ideal: 97.44 - 105.05: 283 105.05 - 112.66: 5982 112.66 - 120.27: 4850 120.27 - 127.88: 4491 127.88 - 135.50: 102 Bond angle restraints: 15708 Sorted by residual: angle pdb=" CA LEU A 818 " pdb=" CB LEU A 818 " pdb=" CG LEU A 818 " ideal model delta sigma weight residual 116.30 135.50 -19.20 3.50e+00 8.16e-02 3.01e+01 angle pdb=" C VAL A 782 " pdb=" N SER A 783 " pdb=" CA SER A 783 " ideal model delta sigma weight residual 121.54 111.24 10.30 1.91e+00 2.74e-01 2.91e+01 angle pdb=" N GLU A1471 " pdb=" CA GLU A1471 " pdb=" C GLU A1471 " ideal model delta sigma weight residual 109.81 121.55 -11.74 2.21e+00 2.05e-01 2.82e+01 angle pdb=" C ASP A1291 " pdb=" N ASN A1292 " pdb=" CA ASN A1292 " ideal model delta sigma weight residual 121.70 131.16 -9.46 1.80e+00 3.09e-01 2.76e+01 angle pdb=" C PHE A 380 " pdb=" N THR A 381 " pdb=" CA THR A 381 " ideal model delta sigma weight residual 121.54 131.04 -9.50 1.91e+00 2.74e-01 2.47e+01 ... (remaining 15703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 6619 17.32 - 34.64: 284 34.64 - 51.96: 67 51.96 - 69.28: 21 69.28 - 86.59: 14 Dihedral angle restraints: 7005 sinusoidal: 2914 harmonic: 4091 Sorted by residual: dihedral pdb=" CA GLU A 376 " pdb=" C GLU A 376 " pdb=" N LYS A 377 " pdb=" CA LYS A 377 " ideal model delta harmonic sigma weight residual -180.00 -150.93 -29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ILE A 571 " pdb=" C ILE A 571 " pdb=" N SER A 572 " pdb=" CA SER A 572 " ideal model delta harmonic sigma weight residual -180.00 -151.05 -28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ASP A 819 " pdb=" C ASP A 819 " pdb=" N GLU A 820 " pdb=" CA GLU A 820 " ideal model delta harmonic sigma weight residual -180.00 -151.93 -28.07 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 7002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1286 0.065 - 0.129: 410 0.129 - 0.194: 76 0.194 - 0.258: 14 0.258 - 0.322: 4 Chirality restraints: 1790 Sorted by residual: chirality pdb=" CB ILE A 487 " pdb=" CA ILE A 487 " pdb=" CG1 ILE A 487 " pdb=" CG2 ILE A 487 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB THR A1308 " pdb=" CA THR A1308 " pdb=" OG1 THR A1308 " pdb=" CG2 THR A1308 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CG LEU A1287 " pdb=" CB LEU A1287 " pdb=" CD1 LEU A1287 " pdb=" CD2 LEU A1287 " both_signs ideal model delta sigma weight residual False -2.59 -2.86 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1787 not shown) Planarity restraints: 2015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A1283 " 0.044 5.00e-02 4.00e+02 6.82e-02 7.43e+00 pdb=" N PRO A1284 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A1284 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1284 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 576 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C ARG A 576 " -0.041 2.00e-02 2.50e+03 pdb=" O ARG A 576 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A 577 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 335 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.04e+00 pdb=" C THR A 335 " 0.039 2.00e-02 2.50e+03 pdb=" O THR A 335 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR A 336 " -0.013 2.00e-02 2.50e+03 ... (remaining 2012 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 71 2.48 - 3.09: 7690 3.09 - 3.69: 16792 3.69 - 4.30: 23982 4.30 - 4.90: 38556 Nonbonded interactions: 87091 Sorted by model distance: nonbonded pdb=" OG SER A1350 " pdb=" O TYR A1356 " model vdw 1.878 2.440 nonbonded pdb=" O GLY A1355 " pdb=" NH2 ARG A1381 " model vdw 2.033 2.520 nonbonded pdb=" OD2 ASP A1215 " pdb=" OH TYR A1446 " model vdw 2.093 2.440 nonbonded pdb=" ND2 ASN A1265 " pdb=" OD2 ASP A1335 " model vdw 2.119 2.520 nonbonded pdb=" OE2 GLU A 376 " pdb=" ND1 HIS A 869 " model vdw 2.123 2.520 ... (remaining 87086 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.560 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: 0.000 Extract box with map and model: 2.260 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 43.890 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 : 0.008 0.068 11560 Z= 0.500 Angle : 1.259 19.196 15708 Z= 0.660 Chirality : 0.065 0.322 1790 Planarity : 0.007 0.068 2015 Dihedral : 11.993 86.593 4373 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 15.00 % Favored : 84.79 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -5.69 (0.16), residues: 1423 helix: -3.62 (0.13), residues: 506 sheet: -3.26 (0.30), residues: 213 loop : -4.11 (0.18), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP A1280 HIS 0.012 0.002 HIS A 528 PHE 0.037 0.005 PHE A1412 TYR 0.021 0.003 TYR A 190 ARG 0.017 0.001 ARG A 934 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8587 (mtt90) cc_final: 0.8027 (ttm-80) REVERT: A 104 ASP cc_start: 0.8900 (m-30) cc_final: 0.8646 (m-30) REVERT: A 118 GLU cc_start: 0.8552 (tt0) cc_final: 0.7918 (tm-30) REVERT: A 141 MET cc_start: 0.7229 (mtm) cc_final: 0.7019 (ttm) REVERT: A 183 THR cc_start: 0.5402 (p) cc_final: 0.4842 (p) REVERT: A 202 GLU cc_start: 0.8612 (tp30) cc_final: 0.8234 (mm-30) REVERT: A 398 ASP cc_start: 0.7994 (m-30) cc_final: 0.7736 (t0) REVERT: A 402 GLN cc_start: 0.8519 (mp-120) cc_final: 0.8028 (mp10) REVERT: A 486 LEU cc_start: 0.6250 (pp) cc_final: 0.5753 (tp) REVERT: A 536 ASP cc_start: 0.7444 (t70) cc_final: 0.7233 (t0) REVERT: A 631 MET cc_start: 0.8343 (ttp) cc_final: 0.8078 (ttt) REVERT: A 667 ASP cc_start: 0.8105 (m-30) cc_final: 0.7881 (p0) REVERT: A 795 MET cc_start: 0.7755 (mtp) cc_final: 0.7420 (mtp) REVERT: A 819 ASP cc_start: 0.7300 (m-30) cc_final: 0.6964 (p0) REVERT: A 937 TYR cc_start: 0.7954 (t80) cc_final: 0.7719 (t80) REVERT: A 974 ARG cc_start: 0.7639 (ptm160) cc_final: 0.7232 (ptm160) REVERT: A 1011 MET cc_start: 0.8917 (ttt) cc_final: 0.8443 (tmm) REVERT: A 1032 GLU cc_start: 0.8418 (tt0) cc_final: 0.7841 (tm-30) REVERT: A 1070 ASP cc_start: 0.8284 (p0) cc_final: 0.6705 (p0) REVERT: A 1195 MET cc_start: 0.8017 (mmm) cc_final: 0.7475 (mmt) REVERT: A 1226 GLN cc_start: 0.6255 (tp-100) cc_final: 0.5699 (tt0) REVERT: A 1273 GLU cc_start: 0.8101 (tt0) cc_final: 0.7778 (tt0) REVERT: A 1400 ILE cc_start: 0.8072 (mp) cc_final: 0.7814 (mm) REVERT: A 1425 LEU cc_start: 0.7944 (pp) cc_final: 0.7643 (mt) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.3149 time to fit residues: 123.4165 Evaluate side-chains 172 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 37 optimal weight: 0.0030 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 overall best weight: 2.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 GLN ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN A 445 GLN ** A 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN ** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11560 Z= 0.255 Angle : 0.850 17.147 15708 Z= 0.434 Chirality : 0.047 0.293 1790 Planarity : 0.006 0.071 2015 Dihedral : 12.997 87.732 1749 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.24 % Favored : 86.55 % Rotamer: Outliers : 2.22 % Allowed : 9.32 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -4.37 (0.19), residues: 1423 helix: -1.82 (0.20), residues: 528 sheet: -2.85 (0.31), residues: 230 loop : -3.88 (0.19), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 560 HIS 0.009 0.001 HIS A 76 PHE 0.022 0.002 PHE A 894 TYR 0.029 0.002 TYR A1141 ARG 0.009 0.001 ARG A1093 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 197 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8574 (mtt90) cc_final: 0.7905 (ttm-80) REVERT: A 60 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8450 (tp) REVERT: A 69 MET cc_start: 0.5900 (mmm) cc_final: 0.5698 (tmm) REVERT: A 100 LYS cc_start: 0.8830 (mttt) cc_final: 0.8162 (tmmt) REVERT: A 104 ASP cc_start: 0.8925 (m-30) cc_final: 0.8366 (m-30) REVERT: A 118 GLU cc_start: 0.8420 (tt0) cc_final: 0.7718 (mm-30) REVERT: A 164 ASN cc_start: 0.7984 (t0) cc_final: 0.7720 (t0) REVERT: A 183 THR cc_start: 0.5033 (p) cc_final: 0.4825 (p) REVERT: A 202 GLU cc_start: 0.8538 (tp30) cc_final: 0.8295 (mm-30) REVERT: A 220 LYS cc_start: 0.9091 (mttm) cc_final: 0.8845 (mtmt) REVERT: A 376 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8115 (mt-10) REVERT: A 402 GLN cc_start: 0.8465 (mp-120) cc_final: 0.7739 (mp10) REVERT: A 606 GLU cc_start: 0.7944 (mp0) cc_final: 0.7660 (mp0) REVERT: A 667 ASP cc_start: 0.7918 (m-30) cc_final: 0.7459 (p0) REVERT: A 772 ASN cc_start: 0.7296 (t0) cc_final: 0.6788 (t0) REVERT: A 795 MET cc_start: 0.7753 (mtp) cc_final: 0.7422 (mtp) REVERT: A 819 ASP cc_start: 0.7475 (m-30) cc_final: 0.7129 (p0) REVERT: A 838 GLU cc_start: 0.8497 (tp30) cc_final: 0.8242 (tp30) REVERT: A 934 ARG cc_start: 0.6003 (OUTLIER) cc_final: 0.5519 (ptt90) REVERT: A 974 ARG cc_start: 0.7650 (ptm160) cc_final: 0.7381 (ptm160) REVERT: A 979 MET cc_start: 0.8119 (mtt) cc_final: 0.7328 (mpp) REVERT: A 1011 MET cc_start: 0.8979 (ttt) cc_final: 0.8387 (tmm) REVERT: A 1032 GLU cc_start: 0.8483 (tt0) cc_final: 0.7941 (tm-30) REVERT: A 1070 ASP cc_start: 0.8272 (p0) cc_final: 0.7930 (p0) REVERT: A 1099 ASP cc_start: 0.6117 (t70) cc_final: 0.5308 (t70) REVERT: A 1167 GLU cc_start: 0.7759 (mp0) cc_final: 0.7463 (pt0) REVERT: A 1195 MET cc_start: 0.7915 (mmm) cc_final: 0.7396 (mmt) REVERT: A 1226 GLN cc_start: 0.6427 (tp-100) cc_final: 0.5978 (tt0) REVERT: A 1273 GLU cc_start: 0.8207 (tt0) cc_final: 0.7831 (tt0) REVERT: A 1453 TRP cc_start: 0.8511 (t60) cc_final: 0.8250 (t60) REVERT: A 1459 ASN cc_start: 0.8704 (m110) cc_final: 0.8354 (m-40) outliers start: 26 outliers final: 16 residues processed: 211 average time/residue: 0.2735 time to fit residues: 79.5594 Evaluate side-chains 169 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 934 ARG Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1429 PHE Chi-restraints excluded: chain A residue 1445 VAL Chi-restraints excluded: chain A residue 1451 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 chunk 116 optimal weight: 0.0980 chunk 129 optimal weight: 3.9990 chunk 44 optimal weight: 0.1980 chunk 105 optimal weight: 6.9990 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 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11560 Z= 0.181 Angle : 0.762 15.428 15708 Z= 0.384 Chirality : 0.044 0.224 1790 Planarity : 0.005 0.065 2015 Dihedral : 12.609 88.955 1749 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % Rotamer: Outliers : 2.14 % Allowed : 11.55 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -3.52 (0.20), residues: 1423 helix: -0.77 (0.22), residues: 507 sheet: -2.51 (0.31), residues: 236 loop : -3.59 (0.20), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1170 HIS 0.004 0.001 HIS A 528 PHE 0.022 0.002 PHE A1112 TYR 0.016 0.002 TYR A1446 ARG 0.008 0.001 ARG A1093 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 190 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8558 (mtt90) cc_final: 0.7966 (ttm-80) REVERT: A 60 LEU cc_start: 0.8666 (mt) cc_final: 0.8412 (tp) REVERT: A 100 LYS cc_start: 0.8760 (mttt) cc_final: 0.8108 (tmmt) REVERT: A 104 ASP cc_start: 0.9002 (m-30) cc_final: 0.8399 (m-30) REVERT: A 118 GLU cc_start: 0.8314 (tt0) cc_final: 0.7699 (mm-30) REVERT: A 226 MET cc_start: 0.8297 (mtt) cc_final: 0.8015 (mtt) REVERT: A 376 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8081 (mt-10) REVERT: A 486 LEU cc_start: 0.6502 (pp) cc_final: 0.5762 (tp) REVERT: A 606 GLU cc_start: 0.7972 (mp0) cc_final: 0.7719 (mp0) REVERT: A 772 ASN cc_start: 0.7228 (t0) cc_final: 0.6643 (t0) REVERT: A 795 MET cc_start: 0.7662 (mtp) cc_final: 0.7445 (mtp) REVERT: A 819 ASP cc_start: 0.7439 (m-30) cc_final: 0.7055 (p0) REVERT: A 934 ARG cc_start: 0.6007 (OUTLIER) cc_final: 0.5573 (ptt90) REVERT: A 1011 MET cc_start: 0.8961 (ttt) cc_final: 0.8487 (tmm) REVERT: A 1032 GLU cc_start: 0.8443 (tt0) cc_final: 0.7833 (tm-30) REVERT: A 1033 MET cc_start: 0.8450 (mtp) cc_final: 0.8096 (mtp) REVERT: A 1070 ASP cc_start: 0.8261 (p0) cc_final: 0.8036 (p0) REVERT: A 1099 ASP cc_start: 0.5770 (t70) cc_final: 0.4993 (t0) REVERT: A 1167 GLU cc_start: 0.7715 (mp0) cc_final: 0.7353 (pt0) REVERT: A 1195 MET cc_start: 0.7559 (mmm) cc_final: 0.7287 (mmt) REVERT: A 1270 ARG cc_start: 0.7708 (mtt180) cc_final: 0.7233 (mtt180) REVERT: A 1273 GLU cc_start: 0.8294 (tt0) cc_final: 0.8001 (tt0) REVERT: A 1459 ASN cc_start: 0.8695 (m110) cc_final: 0.8402 (m-40) outliers start: 25 outliers final: 10 residues processed: 203 average time/residue: 0.2598 time to fit residues: 73.5056 Evaluate side-chains 163 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 152 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 934 ARG Chi-restraints excluded: chain A residue 938 GLU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1445 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 87 optimal weight: 0.1980 chunk 131 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 GLN ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11560 Z= 0.228 Angle : 0.782 15.742 15708 Z= 0.393 Chirality : 0.045 0.184 1790 Planarity : 0.005 0.064 2015 Dihedral : 12.542 89.944 1749 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.96 % Favored : 86.97 % Rotamer: Outliers : 2.74 % Allowed : 12.57 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -3.26 (0.21), residues: 1423 helix: -0.55 (0.23), residues: 519 sheet: -2.14 (0.33), residues: 224 loop : -3.59 (0.20), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1170 HIS 0.007 0.001 HIS A 528 PHE 0.021 0.002 PHE A 894 TYR 0.010 0.002 TYR A 213 ARG 0.009 0.001 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8648 (mtt90) cc_final: 0.8007 (ttm-80) REVERT: A 100 LYS cc_start: 0.8753 (mttt) cc_final: 0.8105 (tmmt) REVERT: A 104 ASP cc_start: 0.9032 (m-30) cc_final: 0.8433 (m-30) REVERT: A 118 GLU cc_start: 0.8401 (tt0) cc_final: 0.7859 (mm-30) REVERT: A 376 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8140 (mt-10) REVERT: A 486 LEU cc_start: 0.6555 (pp) cc_final: 0.5834 (tp) REVERT: A 772 ASN cc_start: 0.7449 (t0) cc_final: 0.6889 (t0) REVERT: A 795 MET cc_start: 0.7743 (mtp) cc_final: 0.7541 (mtp) REVERT: A 819 ASP cc_start: 0.7421 (m-30) cc_final: 0.7056 (p0) REVERT: A 884 MET cc_start: 0.6679 (mmm) cc_final: 0.6456 (mmm) REVERT: A 934 ARG cc_start: 0.5952 (OUTLIER) cc_final: 0.5682 (ptt90) REVERT: A 943 ILE cc_start: 0.9085 (mt) cc_final: 0.8778 (pt) REVERT: A 985 ASP cc_start: 0.8019 (t70) cc_final: 0.7338 (m-30) REVERT: A 1011 MET cc_start: 0.8999 (ttt) cc_final: 0.8417 (tmm) REVERT: A 1032 GLU cc_start: 0.8409 (tt0) cc_final: 0.7938 (tm-30) REVERT: A 1033 MET cc_start: 0.8625 (mtp) cc_final: 0.8226 (mtt) REVERT: A 1070 ASP cc_start: 0.8309 (p0) cc_final: 0.7877 (p0) REVERT: A 1099 ASP cc_start: 0.5537 (t70) cc_final: 0.5003 (t0) REVERT: A 1195 MET cc_start: 0.7347 (mmm) cc_final: 0.7138 (mmt) REVERT: A 1273 GLU cc_start: 0.8358 (tt0) cc_final: 0.8140 (tt0) REVERT: A 1459 ASN cc_start: 0.8757 (m110) cc_final: 0.8480 (m-40) outliers start: 32 outliers final: 15 residues processed: 181 average time/residue: 0.2605 time to fit residues: 66.1916 Evaluate side-chains 161 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 934 ARG Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1401 THR Chi-restraints excluded: chain A residue 1445 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 2 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1226 GLN ** A1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11560 Z= 0.208 Angle : 0.755 14.338 15708 Z= 0.379 Chirality : 0.044 0.185 1790 Planarity : 0.005 0.066 2015 Dihedral : 12.450 89.310 1749 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.89 % Favored : 87.04 % Rotamer: Outliers : 2.31 % Allowed : 13.60 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -3.01 (0.21), residues: 1423 helix: -0.28 (0.23), residues: 518 sheet: -1.88 (0.34), residues: 216 loop : -3.54 (0.20), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A1170 HIS 0.006 0.001 HIS A 528 PHE 0.018 0.002 PHE A1412 TYR 0.015 0.001 TYR A1209 ARG 0.007 0.001 ARG A1214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8653 (mtt90) cc_final: 0.7871 (ttm-80) REVERT: A 60 LEU cc_start: 0.8835 (mt) cc_final: 0.8521 (tp) REVERT: A 92 MET cc_start: 0.8898 (ttp) cc_final: 0.8488 (tmm) REVERT: A 100 LYS cc_start: 0.8738 (mttt) cc_final: 0.8099 (tmmt) REVERT: A 104 ASP cc_start: 0.9037 (m-30) cc_final: 0.8436 (m-30) REVERT: A 111 ASP cc_start: 0.8881 (t0) cc_final: 0.8603 (t0) REVERT: A 223 MET cc_start: 0.7438 (mtm) cc_final: 0.7176 (mtp) REVERT: A 486 LEU cc_start: 0.6556 (pp) cc_final: 0.5904 (tp) REVERT: A 631 MET cc_start: 0.7921 (tpt) cc_final: 0.7167 (tpt) REVERT: A 664 ARG cc_start: 0.8205 (mtm-85) cc_final: 0.7975 (mtp85) REVERT: A 772 ASN cc_start: 0.7473 (t0) cc_final: 0.6918 (t0) REVERT: A 795 MET cc_start: 0.7781 (mtp) cc_final: 0.7513 (mtp) REVERT: A 819 ASP cc_start: 0.7386 (m-30) cc_final: 0.7019 (p0) REVERT: A 934 ARG cc_start: 0.6004 (OUTLIER) cc_final: 0.5737 (ptt90) REVERT: A 943 ILE cc_start: 0.9134 (mt) cc_final: 0.8842 (pt) REVERT: A 985 ASP cc_start: 0.8076 (t70) cc_final: 0.7453 (m-30) REVERT: A 1011 MET cc_start: 0.9013 (ttt) cc_final: 0.8430 (tmm) REVERT: A 1032 GLU cc_start: 0.8437 (tt0) cc_final: 0.7964 (tm-30) REVERT: A 1033 MET cc_start: 0.8648 (mtp) cc_final: 0.8281 (mtt) REVERT: A 1070 ASP cc_start: 0.8317 (p0) cc_final: 0.7919 (p0) REVERT: A 1099 ASP cc_start: 0.5376 (t70) cc_final: 0.4901 (t0) REVERT: A 1260 MET cc_start: 0.8152 (mmt) cc_final: 0.7933 (mmp) REVERT: A 1392 GLN cc_start: 0.8392 (mm-40) cc_final: 0.7150 (mp10) REVERT: A 1459 ASN cc_start: 0.8755 (m110) cc_final: 0.8540 (m-40) outliers start: 27 outliers final: 20 residues processed: 173 average time/residue: 0.2554 time to fit residues: 63.1071 Evaluate side-chains 167 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 146 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 934 ARG Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1401 THR Chi-restraints excluded: chain A residue 1429 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 8.9990 chunk 125 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 64 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 73 optimal weight: 0.3980 chunk 134 optimal weight: 0.0970 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 ASN A 155 GLN ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11560 Z= 0.183 Angle : 0.735 15.056 15708 Z= 0.366 Chirality : 0.043 0.176 1790 Planarity : 0.005 0.064 2015 Dihedral : 12.295 89.270 1749 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer: Outliers : 1.88 % Allowed : 14.37 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -2.73 (0.22), residues: 1423 helix: -0.03 (0.23), residues: 519 sheet: -1.79 (0.34), residues: 211 loop : -3.36 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A1170 HIS 0.005 0.001 HIS A 528 PHE 0.018 0.002 PHE A1412 TYR 0.017 0.001 TYR A1332 ARG 0.005 0.000 ARG A1093 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 178 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8624 (mtt90) cc_final: 0.7860 (ttm-80) REVERT: A 60 LEU cc_start: 0.8853 (mt) cc_final: 0.8546 (tp) REVERT: A 92 MET cc_start: 0.8754 (ttp) cc_final: 0.8490 (ppp) REVERT: A 100 LYS cc_start: 0.8704 (mttt) cc_final: 0.8115 (tmmt) REVERT: A 104 ASP cc_start: 0.9063 (m-30) cc_final: 0.8466 (m-30) REVERT: A 223 MET cc_start: 0.7370 (mtm) cc_final: 0.7154 (mtp) REVERT: A 278 MET cc_start: 0.8216 (tmm) cc_final: 0.8007 (tmm) REVERT: A 486 LEU cc_start: 0.6635 (pp) cc_final: 0.6089 (tp) REVERT: A 631 MET cc_start: 0.7910 (tpt) cc_final: 0.7074 (tpt) REVERT: A 664 ARG cc_start: 0.8212 (mtm-85) cc_final: 0.8007 (mtp85) REVERT: A 772 ASN cc_start: 0.7418 (t0) cc_final: 0.6826 (t0) REVERT: A 795 MET cc_start: 0.7728 (mtp) cc_final: 0.7445 (mtp) REVERT: A 819 ASP cc_start: 0.7418 (m-30) cc_final: 0.7081 (p0) REVERT: A 857 LYS cc_start: 0.8931 (tptp) cc_final: 0.8617 (tptm) REVERT: A 985 ASP cc_start: 0.8168 (t70) cc_final: 0.7595 (m-30) REVERT: A 991 GLN cc_start: 0.8509 (tp-100) cc_final: 0.8224 (tp-100) REVERT: A 1011 MET cc_start: 0.8971 (ttt) cc_final: 0.8362 (tmm) REVERT: A 1032 GLU cc_start: 0.8361 (tt0) cc_final: 0.7971 (tm-30) REVERT: A 1159 LYS cc_start: 0.8617 (mttt) cc_final: 0.8371 (mtmm) REVERT: A 1210 GLU cc_start: 0.7725 (mp0) cc_final: 0.6842 (mp0) REVERT: A 1335 ASP cc_start: 0.7638 (m-30) cc_final: 0.7333 (m-30) REVERT: A 1392 GLN cc_start: 0.8385 (mm-40) cc_final: 0.7073 (mp10) REVERT: A 1425 LEU cc_start: 0.7336 (mm) cc_final: 0.7049 (mt) REVERT: A 1453 TRP cc_start: 0.7954 (t60) cc_final: 0.7550 (t60) outliers start: 22 outliers final: 16 residues processed: 188 average time/residue: 0.2875 time to fit residues: 74.8117 Evaluate side-chains 182 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1429 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 9.9990 chunk 79 optimal weight: 0.4980 chunk 101 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 138 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 64 optimal weight: 20.0000 chunk 85 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1001 GLN ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11560 Z= 0.188 Angle : 0.759 14.580 15708 Z= 0.376 Chirality : 0.043 0.217 1790 Planarity : 0.004 0.063 2015 Dihedral : 12.200 89.140 1749 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.97 % Favored : 88.03 % Rotamer: Outliers : 2.14 % Allowed : 14.97 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -2.53 (0.22), residues: 1423 helix: 0.12 (0.23), residues: 522 sheet: -1.83 (0.33), residues: 224 loop : -3.20 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A1170 HIS 0.006 0.001 HIS A 528 PHE 0.017 0.002 PHE A1412 TYR 0.013 0.001 TYR A 937 ARG 0.007 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 174 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8587 (mtt90) cc_final: 0.7903 (ttm-80) REVERT: A 92 MET cc_start: 0.8828 (ttp) cc_final: 0.8454 (ppp) REVERT: A 100 LYS cc_start: 0.8696 (mttt) cc_final: 0.8123 (tmmt) REVERT: A 104 ASP cc_start: 0.9045 (m-30) cc_final: 0.8475 (m-30) REVERT: A 118 GLU cc_start: 0.8330 (tt0) cc_final: 0.7612 (mm-30) REVERT: A 223 MET cc_start: 0.7358 (mtm) cc_final: 0.7084 (mtp) REVERT: A 278 MET cc_start: 0.8334 (tmm) cc_final: 0.7965 (tmm) REVERT: A 486 LEU cc_start: 0.6519 (pp) cc_final: 0.5981 (tp) REVERT: A 631 MET cc_start: 0.7880 (tpt) cc_final: 0.7056 (tpt) REVERT: A 772 ASN cc_start: 0.7411 (t0) cc_final: 0.6823 (t0) REVERT: A 795 MET cc_start: 0.7627 (mtp) cc_final: 0.7314 (mtp) REVERT: A 819 ASP cc_start: 0.7391 (m-30) cc_final: 0.7058 (p0) REVERT: A 857 LYS cc_start: 0.8912 (tptp) cc_final: 0.8630 (tptm) REVERT: A 937 TYR cc_start: 0.7905 (t80) cc_final: 0.7657 (t80) REVERT: A 960 ARG cc_start: 0.5878 (tpt-90) cc_final: 0.5366 (mmm-85) REVERT: A 985 ASP cc_start: 0.8235 (t70) cc_final: 0.7643 (m-30) REVERT: A 991 GLN cc_start: 0.8480 (tp-100) cc_final: 0.8174 (tp-100) REVERT: A 1011 MET cc_start: 0.8972 (ttt) cc_final: 0.8303 (tmm) REVERT: A 1032 GLU cc_start: 0.8333 (tt0) cc_final: 0.7986 (tm-30) REVERT: A 1070 ASP cc_start: 0.8692 (p0) cc_final: 0.7630 (p0) REVERT: A 1210 GLU cc_start: 0.7610 (mp0) cc_final: 0.6830 (mp0) REVERT: A 1238 ARG cc_start: 0.7987 (ttm-80) cc_final: 0.7711 (ttm170) REVERT: A 1335 ASP cc_start: 0.7688 (m-30) cc_final: 0.7177 (m-30) REVERT: A 1345 MET cc_start: 0.8658 (tpp) cc_final: 0.8370 (mmt) REVERT: A 1392 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7054 (mp10) outliers start: 25 outliers final: 17 residues processed: 188 average time/residue: 0.2709 time to fit residues: 71.2611 Evaluate side-chains 174 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 157 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1429 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 7.9990 chunk 82 optimal weight: 0.0470 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 126 optimal weight: 0.0570 overall best weight: 3.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 GLN A 856 GLN ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11560 Z= 0.286 Angle : 0.810 14.047 15708 Z= 0.407 Chirality : 0.046 0.180 1790 Planarity : 0.005 0.063 2015 Dihedral : 12.371 87.123 1749 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.52 % Favored : 86.34 % Rotamer: Outliers : 2.31 % Allowed : 16.08 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -2.61 (0.22), residues: 1423 helix: 0.10 (0.23), residues: 526 sheet: -1.82 (0.34), residues: 223 loop : -3.33 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A1170 HIS 0.008 0.001 HIS A 528 PHE 0.027 0.002 PHE A 894 TYR 0.018 0.002 TYR A1141 ARG 0.009 0.001 ARG A1146 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8656 (mtt90) cc_final: 0.7928 (ttm-80) REVERT: A 60 LEU cc_start: 0.8865 (mt) cc_final: 0.8579 (tp) REVERT: A 100 LYS cc_start: 0.8696 (mttt) cc_final: 0.8148 (tmmt) REVERT: A 104 ASP cc_start: 0.9064 (m-30) cc_final: 0.8439 (m-30) REVERT: A 111 ASP cc_start: 0.8899 (t0) cc_final: 0.8537 (t0) REVERT: A 223 MET cc_start: 0.7472 (mtm) cc_final: 0.7264 (mtp) REVERT: A 278 MET cc_start: 0.8296 (tmm) cc_final: 0.8044 (tmm) REVERT: A 486 LEU cc_start: 0.6633 (pp) cc_final: 0.6124 (tp) REVERT: A 499 PHE cc_start: 0.7837 (p90) cc_final: 0.7633 (p90) REVERT: A 631 MET cc_start: 0.7989 (tpt) cc_final: 0.7182 (tpt) REVERT: A 772 ASN cc_start: 0.7796 (t0) cc_final: 0.7313 (t0) REVERT: A 795 MET cc_start: 0.7697 (mtp) cc_final: 0.7411 (mtp) REVERT: A 819 ASP cc_start: 0.7535 (m-30) cc_final: 0.7224 (p0) REVERT: A 857 LYS cc_start: 0.9002 (tptp) cc_final: 0.8652 (tptm) REVERT: A 985 ASP cc_start: 0.8206 (t70) cc_final: 0.7582 (m-30) REVERT: A 1011 MET cc_start: 0.8959 (ttt) cc_final: 0.8333 (tmm) REVERT: A 1032 GLU cc_start: 0.8347 (tt0) cc_final: 0.7982 (tm-30) REVERT: A 1070 ASP cc_start: 0.8636 (p0) cc_final: 0.7744 (p0) REVERT: A 1137 ARG cc_start: 0.7374 (tmt-80) cc_final: 0.5744 (mmt90) REVERT: A 1210 GLU cc_start: 0.7694 (mp0) cc_final: 0.6925 (mp0) REVERT: A 1392 GLN cc_start: 0.8396 (mm-40) cc_final: 0.7152 (mp10) REVERT: A 1417 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6775 (mm-30) outliers start: 27 outliers final: 20 residues processed: 173 average time/residue: 0.2795 time to fit residues: 66.8494 Evaluate side-chains 173 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1429 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1403 HIS ** A1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11560 Z= 0.202 Angle : 0.808 14.806 15708 Z= 0.394 Chirality : 0.044 0.234 1790 Planarity : 0.005 0.065 2015 Dihedral : 12.272 86.877 1749 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.18 % Favored : 87.75 % Rotamer: Outliers : 1.97 % Allowed : 16.00 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -2.49 (0.22), residues: 1423 helix: 0.24 (0.23), residues: 521 sheet: -1.84 (0.33), residues: 223 loop : -3.24 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A1170 HIS 0.007 0.001 HIS A 528 PHE 0.018 0.002 PHE A1412 TYR 0.013 0.001 TYR A1141 ARG 0.007 0.001 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 155 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8613 (mtt90) cc_final: 0.7919 (ttm-80) REVERT: A 60 LEU cc_start: 0.8853 (mt) cc_final: 0.8586 (tp) REVERT: A 92 MET cc_start: 0.8679 (ttp) cc_final: 0.8432 (tmm) REVERT: A 111 ASP cc_start: 0.8887 (t0) cc_final: 0.8526 (t0) REVERT: A 118 GLU cc_start: 0.8360 (tt0) cc_final: 0.7740 (mm-30) REVERT: A 223 MET cc_start: 0.7405 (mtm) cc_final: 0.7178 (mtp) REVERT: A 278 MET cc_start: 0.8313 (tmm) cc_final: 0.8013 (tmm) REVERT: A 486 LEU cc_start: 0.6648 (pp) cc_final: 0.6146 (tp) REVERT: A 499 PHE cc_start: 0.7782 (p90) cc_final: 0.7533 (p90) REVERT: A 631 MET cc_start: 0.7983 (tpt) cc_final: 0.7176 (tpt) REVERT: A 772 ASN cc_start: 0.7682 (t0) cc_final: 0.7114 (t0) REVERT: A 795 MET cc_start: 0.7652 (mtp) cc_final: 0.7322 (mtp) REVERT: A 819 ASP cc_start: 0.7506 (m-30) cc_final: 0.7255 (p0) REVERT: A 857 LYS cc_start: 0.8976 (tptp) cc_final: 0.8659 (tptm) REVERT: A 960 ARG cc_start: 0.5983 (tpt-90) cc_final: 0.5452 (mmm-85) REVERT: A 985 ASP cc_start: 0.8227 (t70) cc_final: 0.7669 (m-30) REVERT: A 1011 MET cc_start: 0.8964 (ttt) cc_final: 0.8298 (tmm) REVERT: A 1032 GLU cc_start: 0.8325 (tt0) cc_final: 0.7950 (tm-30) REVERT: A 1070 ASP cc_start: 0.8572 (p0) cc_final: 0.8043 (p0) REVERT: A 1210 GLU cc_start: 0.7729 (mp0) cc_final: 0.6977 (mp0) REVERT: A 1345 MET cc_start: 0.8638 (tpp) cc_final: 0.8283 (mmt) REVERT: A 1392 GLN cc_start: 0.8390 (mm-40) cc_final: 0.7161 (mp10) outliers start: 23 outliers final: 18 residues processed: 168 average time/residue: 0.2644 time to fit residues: 62.3157 Evaluate side-chains 163 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1429 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.0010 chunk 83 optimal weight: 0.1980 chunk 64 optimal weight: 6.9990 chunk 95 optimal weight: 0.2980 chunk 143 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 0.0030 chunk 90 optimal weight: 0.0670 overall best weight: 0.1134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11560 Z= 0.182 Angle : 0.796 16.581 15708 Z= 0.388 Chirality : 0.044 0.370 1790 Planarity : 0.004 0.064 2015 Dihedral : 12.095 88.425 1749 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.39 % Favored : 87.61 % Rotamer: Outliers : 1.37 % Allowed : 16.94 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -2.27 (0.22), residues: 1423 helix: 0.40 (0.24), residues: 514 sheet: -1.81 (0.33), residues: 222 loop : -3.01 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A1170 HIS 0.006 0.001 HIS A 106 PHE 0.019 0.002 PHE A1112 TYR 0.023 0.001 TYR A 937 ARG 0.013 0.001 ARG A 934 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 176 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8524 (mtt90) cc_final: 0.7845 (ttm-80) REVERT: A 60 LEU cc_start: 0.8854 (mt) cc_final: 0.8596 (tp) REVERT: A 111 ASP cc_start: 0.8889 (t0) cc_final: 0.8547 (t0) REVERT: A 118 GLU cc_start: 0.8224 (tt0) cc_final: 0.7499 (mm-30) REVERT: A 278 MET cc_start: 0.8305 (tmm) cc_final: 0.8010 (tmm) REVERT: A 486 LEU cc_start: 0.6557 (pp) cc_final: 0.6056 (tp) REVERT: A 499 PHE cc_start: 0.7661 (p90) cc_final: 0.7325 (p90) REVERT: A 631 MET cc_start: 0.7890 (tpt) cc_final: 0.7060 (tpt) REVERT: A 772 ASN cc_start: 0.7398 (t0) cc_final: 0.6801 (t0) REVERT: A 795 MET cc_start: 0.7601 (mtp) cc_final: 0.7259 (mtp) REVERT: A 819 ASP cc_start: 0.7378 (m-30) cc_final: 0.7137 (p0) REVERT: A 857 LYS cc_start: 0.8906 (tptp) cc_final: 0.8668 (tptm) REVERT: A 884 MET cc_start: 0.7024 (mmm) cc_final: 0.6805 (mmm) REVERT: A 960 ARG cc_start: 0.5690 (tpt-90) cc_final: 0.5054 (mmm-85) REVERT: A 985 ASP cc_start: 0.8364 (t70) cc_final: 0.7727 (m-30) REVERT: A 1011 MET cc_start: 0.8922 (ttt) cc_final: 0.8274 (tmm) REVERT: A 1032 GLU cc_start: 0.8222 (tt0) cc_final: 0.7919 (tm-30) REVERT: A 1070 ASP cc_start: 0.8592 (p0) cc_final: 0.8154 (p0) REVERT: A 1210 GLU cc_start: 0.7434 (mp0) cc_final: 0.6734 (mp0) REVERT: A 1238 ARG cc_start: 0.7987 (ttm-80) cc_final: 0.7772 (ttp-170) REVERT: A 1335 ASP cc_start: 0.7705 (m-30) cc_final: 0.6986 (m-30) REVERT: A 1345 MET cc_start: 0.8689 (tpp) cc_final: 0.8471 (mmt) REVERT: A 1392 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7065 (mp10) outliers start: 16 outliers final: 13 residues processed: 187 average time/residue: 0.2542 time to fit residues: 67.3683 Evaluate side-chains 164 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 TYR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1429 PHE Chi-restraints excluded: chain A residue 1467 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 GLN ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.111430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.090730 restraints weight = 63377.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.095039 restraints weight = 28035.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.098644 restraints weight = 14728.659| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 11560 Z= 0.305 Angle : 0.861 15.972 15708 Z= 0.425 Chirality : 0.047 0.249 1790 Planarity : 0.005 0.065 2015 Dihedral : 12.325 86.714 1749 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.24 % Favored : 86.62 % Rotamer: Outliers : 1.54 % Allowed : 17.02 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.51 % 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: -2.48 (0.22), residues: 1423 helix: 0.18 (0.23), residues: 519 sheet: -1.80 (0.33), residues: 227 loop : -3.17 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A1170 HIS 0.009 0.001 HIS A 528 PHE 0.031 0.002 PHE A 894 TYR 0.020 0.002 TYR A 937 ARG 0.012 0.001 ARG A 934 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2483.27 seconds wall clock time: 45 minutes 59.20 seconds (2759.20 seconds total)