Starting phenix.real_space_refine (version: dev) on Tue Apr 5 06:08:22 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n8o_3601/04_2022/5n8o_3601_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n8o_3601/04_2022/5n8o_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_3601/04_2022/5n8o_3601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n8o_3601/04_2022/5n8o_3601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n8o_3601/04_2022/5n8o_3601_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n8o_3601/04_2022/5n8o_3601_neut.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Convert atoms to be neutral 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: {'PTRANS': 51, 'CIS': 7, 'TRANS': 1372, 'PCIS': 1} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 1432, 10991 Classifications: {'peptide': 1432} Link IDs: {'PTRANS': 51, 'CIS': 7, 'TRANS': 1372, 'PCIS': 1} 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: 11.61, per 1000 atoms: 1.02 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: 4.58 Conformation dependent library (CDL) restraints added in 3.2 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: 3.30 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: 4.68 Time building geometry restraints manager: 4.95 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 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 angle pdb=" C VAL A 353 " pdb=" N ILE A 354 " pdb=" CA ILE A 354 " ideal model delta sigma weight residual 121.70 130.13 -8.43 1.80e+00 3.09e-01 2.19e+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 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. 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: 0.370 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: 2.650 Check model and map are aligned: 0.170 Convert atoms to be neutral: 0.100 Process input model: 43.390 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 : 1.257 19.196 15708 Z= 0.658 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 % 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 *********************** 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 : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.3085 time to fit residues: 122.3200 Evaluate side-chains 164 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.315 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8074 ------------------------------------------------------------------------------- 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: 0.2980 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 A 152 GLN 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 ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.131 11560 Z= 0.211 Angle : 0.831 17.413 15708 Z= 0.419 Chirality : 0.047 0.318 1790 Planarity : 0.006 0.075 2015 Dihedral : 12.884 89.226 1749 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.82 % Favored : 86.97 % Rotamer Outliers : 1.80 % 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: -4.28 (0.19), residues: 1423 helix: -1.73 (0.20), residues: 516 sheet: -2.81 (0.30), residues: 237 loop : -3.82 (0.20), residues: 670 *********************** 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 226 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 205 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 216 average time/residue: 0.2518 time to fit residues: 76.7709 Evaluate side-chains 148 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 1.309 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1130 time to fit residues: 3.8692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 116 optimal weight: 0.3980 chunk 129 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 HIS ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1283 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.126 11560 Z= 0.209 Angle : 0.791 15.450 15708 Z= 0.398 Chirality : 0.045 0.215 1790 Planarity : 0.005 0.058 2015 Dihedral : 12.635 88.719 1749 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.82 % Favored : 87.11 % Rotamer Outliers : 2.05 % 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: -3.54 (0.20), residues: 1423 helix: -0.83 (0.22), residues: 507 sheet: -2.43 (0.32), residues: 238 loop : -3.62 (0.20), residues: 678 *********************** 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 189 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 9 residues processed: 178 average time/residue: 0.2747 time to fit residues: 68.8828 Evaluate side-chains 148 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 139 time to evaluate : 1.367 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1185 time to fit residues: 3.7920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 124 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 GLN ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1226 GLN ** 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: 0.7732 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.118 11560 Z= 0.257 Angle : 0.814 14.795 15708 Z= 0.408 Chirality : 0.046 0.186 1790 Planarity : 0.005 0.063 2015 Dihedral : 12.612 89.120 1749 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.68 % Favored : 87.25 % Rotamer Outliers : 1.80 % 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: -0.53 (0.22), residues: 524 sheet: -2.09 (0.33), residues: 226 loop : -3.65 (0.20), residues: 673 *********************** 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 170 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 149 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 162 average time/residue: 0.2722 time to fit residues: 62.8098 Evaluate side-chains 150 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 1.375 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1435 time to fit residues: 4.5726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 6.9990 chunk 79 optimal weight: 0.0270 chunk 2 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 124 optimal weight: 0.4980 chunk 35 optimal weight: 0.0870 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1077 ASN ** A1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1403 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.124 11560 Z= 0.180 Angle : 0.765 14.466 15708 Z= 0.378 Chirality : 0.044 0.190 1790 Planarity : 0.005 0.070 2015 Dihedral : 12.376 88.995 1749 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer Outliers : 0.68 % 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: -2.82 (0.21), residues: 1423 helix: -0.11 (0.23), residues: 512 sheet: -1.87 (0.33), residues: 226 loop : -3.38 (0.21), residues: 685 *********************** 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 179 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 171 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 176 average time/residue: 0.2586 time to fit residues: 64.3309 Evaluate side-chains 141 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 1.276 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1117 time to fit residues: 2.1929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 64 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 529 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.138 11560 Z= 0.208 Angle : 0.782 13.889 15708 Z= 0.387 Chirality : 0.044 0.176 1790 Planarity : 0.005 0.073 2015 Dihedral : 12.370 89.199 1749 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.96 % Favored : 86.97 % Rotamer Outliers : 0.94 % 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: -2.68 (0.22), residues: 1423 helix: 0.03 (0.23), residues: 520 sheet: -1.92 (0.33), residues: 224 loop : -3.31 (0.21), residues: 679 *********************** 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 165 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 154 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 160 average time/residue: 0.2611 time to fit residues: 59.5180 Evaluate side-chains 145 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 140 time to evaluate : 1.338 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1260 time to fit residues: 2.9912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 138 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 0.3980 chunk 64 optimal weight: 20.0000 chunk 85 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 529 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.154 11560 Z= 0.202 Angle : 0.789 14.888 15708 Z= 0.387 Chirality : 0.044 0.186 1790 Planarity : 0.005 0.084 2015 Dihedral : 12.291 87.995 1749 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.18 % Favored : 87.82 % Rotamer Outliers : 0.60 % 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: -2.51 (0.22), residues: 1423 helix: 0.20 (0.24), residues: 516 sheet: -1.79 (0.34), residues: 218 loop : -3.23 (0.22), residues: 689 *********************** 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 161 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 157 average time/residue: 0.2535 time to fit residues: 56.9411 Evaluate side-chains 139 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 1.372 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1185 time to fit residues: 2.2762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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 861 HIS ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.153 11560 Z= 0.415 Angle : 0.941 14.471 15708 Z= 0.472 Chirality : 0.050 0.217 1790 Planarity : 0.006 0.090 2015 Dihedral : 12.676 84.965 1749 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 15.14 % Favored : 84.72 % Rotamer Outliers : 1.80 % 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: -2.81 (0.21), residues: 1423 helix: -0.15 (0.23), residues: 528 sheet: -1.91 (0.33), residues: 228 loop : -3.39 (0.22), residues: 667 *********************** 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 157 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 150 average time/residue: 0.2591 time to fit residues: 55.9304 Evaluate side-chains 135 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 1.439 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1198 time to fit residues: 4.1672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 0.0570 chunk 116 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1077 ASN ** A1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.139 11560 Z= 0.204 Angle : 0.826 15.404 15708 Z= 0.406 Chirality : 0.045 0.257 1790 Planarity : 0.005 0.069 2015 Dihedral : 12.400 87.088 1749 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.83 % Favored : 88.10 % Rotamer Outliers : 0.51 % 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: -2.56 (0.22), residues: 1423 helix: 0.10 (0.23), residues: 521 sheet: -1.80 (0.34), residues: 215 loop : -3.22 (0.22), residues: 687 *********************** 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 154 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 148 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 152 average time/residue: 0.2542 time to fit residues: 55.5574 Evaluate side-chains 139 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 136 time to evaluate : 1.367 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1122 time to fit residues: 2.4893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 95 optimal weight: 0.1980 chunk 143 optimal weight: 8.9990 chunk 132 optimal weight: 0.0970 chunk 114 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** A1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1459 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.125 11560 Z= 0.266 Angle : 0.859 15.989 15708 Z= 0.423 Chirality : 0.046 0.189 1790 Planarity : 0.006 0.101 2015 Dihedral : 12.472 85.236 1749 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.80 % Favored : 86.13 % Rotamer Outliers : 0.43 % 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: -2.58 (0.22), residues: 1423 helix: 0.13 (0.23), residues: 519 sheet: -1.88 (0.34), residues: 220 loop : -3.26 (0.22), residues: 684 ********************** 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 141 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 138 average time/residue: 0.2684 time to fit residues: 53.1050 Evaluate side-chains 133 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 1.368 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1123 time to fit residues: 2.2864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 chunk 117 optimal weight: 0.3980 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 0.3980 chunk 100 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.114087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.093464 restraints weight = 62848.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.097778 restraints weight = 28298.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.099643 restraints weight = 15654.263| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3731 r_free = 0.3731 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.122 11560 Z= 0.205 Angle : 0.846 17.450 15708 Z= 0.413 Chirality : 0.044 0.164 1790 Planarity : 0.005 0.057 2015 Dihedral : 12.354 86.511 1749 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.32 % Favored : 87.68 % Rotamer Outliers : 0.17 % 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 (0.24), residues: 510 sheet: -1.83 (0.34), residues: 221 loop : -3.18 (0.22), residues: 692 =============================================================================== Job complete usr+sys time: 2249.57 seconds wall clock time: 41 minutes 48.06 seconds (2508.06 seconds total)