Starting phenix.real_space_refine on Sat Mar 16 03:25:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu3_29452/03_2024/8fu3_29452_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu3_29452/03_2024/8fu3_29452.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu3_29452/03_2024/8fu3_29452_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu3_29452/03_2024/8fu3_29452_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu3_29452/03_2024/8fu3_29452_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu3_29452/03_2024/8fu3_29452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu3_29452/03_2024/8fu3_29452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu3_29452/03_2024/8fu3_29452_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu3_29452/03_2024/8fu3_29452_neut_updated.pdb" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 S 76 5.16 5 C 8652 2.51 5 N 2308 2.21 5 O 2522 1.98 5 F 5 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1054": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1460": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13563 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1367, 11153 Classifications: {'peptide': 1367} Link IDs: {'PTRANS': 47, 'TRANS': 1319} Chain breaks: 3 Chain: "B" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 886 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "C" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 479 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "D" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 468 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "E" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 536 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'YBK': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.34, per 1000 atoms: 0.54 Number of scatterers: 13563 At special positions: 0 Unit cell: (104.96, 134.48, 99.22, 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 76 16.00 F 5 9.00 O 2522 8.00 N 2308 7.00 C 8652 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: 5.20 Conformation dependent library (CDL) restraints added in 2.2 seconds 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3206 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 83 helices and 6 sheets defined 56.5% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.72 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 Processing helix chain 'A' and resid 45 through 52 removed outlier: 3.558A pdb=" N ARG A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 84 through 92 Processing helix chain 'A' and resid 99 through 131 removed outlier: 3.932A pdb=" N VAL A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 202 through 227 Processing helix chain 'A' and resid 266 through 295 Processing helix chain 'A' and resid 307 through 323 Processing helix chain 'A' and resid 326 through 347 Processing helix chain 'A' and resid 350 through 380 removed outlier: 3.895A pdb=" N CYS A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 393 No H-bonds generated for 'chain 'A' and resid 390 through 393' Processing helix chain 'A' and resid 397 through 412 Processing helix chain 'A' and resid 416 through 426 removed outlier: 4.065A pdb=" N TYR A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N PHE A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LEU A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N PHE A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 447 removed outlier: 3.512A pdb=" N ILE A 445 " --> pdb=" O ASP A 441 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASN A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 477 Processing helix chain 'A' and resid 486 through 488 No H-bonds generated for 'chain 'A' and resid 486 through 488' Processing helix chain 'A' and resid 492 through 498 Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 510 through 518 removed outlier: 3.677A pdb=" N GLY A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 536 No H-bonds generated for 'chain 'A' and resid 533 through 536' Processing helix chain 'A' and resid 546 through 552 removed outlier: 4.909A pdb=" N TRP A 550 " --> pdb=" O ASN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 560 through 572 removed outlier: 3.888A pdb=" N LEU A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS A 572 " --> pdb=" O HIS A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 Processing helix chain 'A' and resid 596 through 602 Processing helix chain 'A' and resid 634 through 650 Processing helix chain 'A' and resid 652 through 654 No H-bonds generated for 'chain 'A' and resid 652 through 654' Processing helix chain 'A' and resid 656 through 658 No H-bonds generated for 'chain 'A' and resid 656 through 658' Processing helix chain 'A' and resid 705 through 707 No H-bonds generated for 'chain 'A' and resid 705 through 707' Processing helix chain 'A' and resid 710 through 723 removed outlier: 4.874A pdb=" N ILE A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N CYS A 716 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 760 through 762 No H-bonds generated for 'chain 'A' and resid 760 through 762' Processing helix chain 'A' and resid 782 through 799 Processing helix chain 'A' and resid 829 through 851 Processing helix chain 'A' and resid 869 through 871 No H-bonds generated for 'chain 'A' and resid 869 through 871' Processing helix chain 'A' and resid 884 through 886 No H-bonds generated for 'chain 'A' and resid 884 through 886' Processing helix chain 'A' and resid 901 through 917 removed outlier: 3.893A pdb=" N GLU A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 938 Processing helix chain 'A' and resid 941 through 943 No H-bonds generated for 'chain 'A' and resid 941 through 943' Processing helix chain 'A' and resid 950 through 965 Processing helix chain 'A' and resid 971 through 980 removed outlier: 3.722A pdb=" N ASN A 980 " --> pdb=" O THR A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 985 No H-bonds generated for 'chain 'A' and resid 983 through 985' Processing helix chain 'A' and resid 993 through 996 Processing helix chain 'A' and resid 1004 through 1020 removed outlier: 3.938A pdb=" N TYR A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1044 Processing helix chain 'A' and resid 1053 through 1059 Processing helix chain 'A' and resid 1073 through 1076 No H-bonds generated for 'chain 'A' and resid 1073 through 1076' Processing helix chain 'A' and resid 1078 through 1087 removed outlier: 4.118A pdb=" N THR A1087 " --> pdb=" O GLU A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1098 Processing helix chain 'A' and resid 1100 through 1110 removed outlier: 3.773A pdb=" N ILE A1110 " --> pdb=" O ASP A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1127 Processing helix chain 'A' and resid 1131 through 1143 removed outlier: 3.544A pdb=" N GLY A1143 " --> pdb=" O ASN A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1152 removed outlier: 4.954A pdb=" N LEU A1151 " --> pdb=" O THR A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1179 removed outlier: 4.569A pdb=" N LEU A1176 " --> pdb=" O ASN A1172 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ILE A1177 " --> pdb=" O ILE A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1210 Processing helix chain 'A' and resid 1224 through 1227 No H-bonds generated for 'chain 'A' and resid 1224 through 1227' Processing helix chain 'A' and resid 1278 through 1280 No H-bonds generated for 'chain 'A' and resid 1278 through 1280' Processing helix chain 'A' and resid 1283 through 1298 Processing helix chain 'A' and resid 1305 through 1316 Processing helix chain 'A' and resid 1321 through 1326 removed outlier: 3.944A pdb=" N LYS A1326 " --> pdb=" O GLU A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1338 No H-bonds generated for 'chain 'A' and resid 1336 through 1338' Processing helix chain 'A' and resid 1355 through 1360 removed outlier: 3.542A pdb=" N THR A1359 " --> pdb=" O TYR A1356 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN A1360 " --> pdb=" O ARG A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1376 Processing helix chain 'A' and resid 1385 through 1403 Processing helix chain 'A' and resid 1416 through 1418 No H-bonds generated for 'chain 'A' and resid 1416 through 1418' Processing helix chain 'A' and resid 1433 through 1442 Processing helix chain 'A' and resid 1444 through 1446 No H-bonds generated for 'chain 'A' and resid 1444 through 1446' Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 4.042A pdb=" N GLU A1458 " --> pdb=" O THR A1454 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A1459 " --> pdb=" O GLN A1455 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE A1460 " --> pdb=" O TYR A1456 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 151 Processing helix chain 'B' and resid 174 through 182 Processing helix chain 'B' and resid 191 through 198 Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 218 through 227 Processing helix chain 'C' and resid 131 through 156 Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'D' and resid 129 through 156 Processing helix chain 'D' and resid 160 through 186 Processing helix chain 'E' and resid 132 through 157 removed outlier: 3.807A pdb=" N VAL E 154 " --> pdb=" O THR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 198 removed outlier: 4.004A pdb=" N LEU E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 80 through 82 removed outlier: 4.412A pdb=" N VAL A 263 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 629 through 632 Processing sheet with id= C, first strand: chain 'A' and resid 860 through 863 removed outlier: 3.839A pdb=" N TYR A 691 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 873 through 875 removed outlier: 3.880A pdb=" N ILE A 873 " --> pdb=" O TYR A 880 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1228 through 1231 Processing sheet with id= F, first strand: chain 'B' and resid 152 through 154 660 hydrogen bonds defined for protein. 1812 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.19 Time building geometry restraints manager: 5.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2368 1.31 - 1.44: 3422 1.44 - 1.57: 7886 1.57 - 1.70: 1 1.70 - 1.82: 129 Bond restraints: 13806 Sorted by residual: bond pdb=" C25 YBK A2201 " pdb=" C27 YBK A2201 " ideal model delta sigma weight residual 1.541 1.395 0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" C21 YBK A2201 " pdb=" C22 YBK A2201 " ideal model delta sigma weight residual 1.362 1.440 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" N PRO A 528 " pdb=" CA PRO A 528 " ideal model delta sigma weight residual 1.466 1.427 0.039 1.17e-02 7.31e+03 1.13e+01 bond pdb=" CB HIS A 961 " pdb=" CG HIS A 961 " ideal model delta sigma weight residual 1.497 1.450 0.047 1.40e-02 5.10e+03 1.12e+01 bond pdb=" CB HIS A1011 " pdb=" CG HIS A1011 " ideal model delta sigma weight residual 1.497 1.452 0.045 1.40e-02 5.10e+03 1.03e+01 ... (remaining 13801 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.33: 307 106.33 - 113.25: 7664 113.25 - 120.17: 4882 120.17 - 127.09: 5725 127.09 - 134.01: 88 Bond angle restraints: 18666 Sorted by residual: angle pdb=" C ALA A 749 " pdb=" N PRO A 750 " pdb=" CA PRO A 750 " ideal model delta sigma weight residual 119.66 125.42 -5.76 7.20e-01 1.93e+00 6.41e+01 angle pdb=" C TYR A 880 " pdb=" N PRO A 881 " pdb=" CA PRO A 881 " ideal model delta sigma weight residual 120.03 127.58 -7.55 9.90e-01 1.02e+00 5.82e+01 angle pdb=" C LEU A 527 " pdb=" N PRO A 528 " pdb=" CA PRO A 528 " ideal model delta sigma weight residual 119.90 127.45 -7.55 1.02e+00 9.61e-01 5.48e+01 angle pdb=" C LEU A1129 " pdb=" N PRO A1130 " pdb=" CA PRO A1130 " ideal model delta sigma weight residual 119.56 126.97 -7.41 1.02e+00 9.61e-01 5.28e+01 angle pdb=" C LEU A1447 " pdb=" N PRO A1448 " pdb=" CA PRO A1448 " ideal model delta sigma weight residual 120.21 127.00 -6.79 9.60e-01 1.09e+00 5.00e+01 ... (remaining 18661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 8102 17.72 - 35.45: 234 35.45 - 53.17: 71 53.17 - 70.89: 17 70.89 - 88.61: 5 Dihedral angle restraints: 8429 sinusoidal: 3490 harmonic: 4939 Sorted by residual: dihedral pdb=" CA GLY D 158 " pdb=" C GLY D 158 " pdb=" N PRO D 159 " pdb=" CA PRO D 159 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA LEU A 527 " pdb=" C LEU A 527 " pdb=" N PRO A 528 " pdb=" CA PRO A 528 " ideal model delta harmonic sigma weight residual 180.00 163.90 16.10 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CG ARG C 182 " pdb=" CD ARG C 182 " pdb=" NE ARG C 182 " pdb=" CZ ARG C 182 " ideal model delta sinusoidal sigma weight residual 180.00 -139.23 -40.77 2 1.50e+01 4.44e-03 9.10e+00 ... (remaining 8426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1538 0.064 - 0.128: 545 0.128 - 0.192: 66 0.192 - 0.256: 4 0.256 - 0.320: 1 Chirality restraints: 2154 Sorted by residual: chirality pdb=" CA PRO A 528 " pdb=" N PRO A 528 " pdb=" C PRO A 528 " pdb=" CB PRO A 528 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA ILE A1353 " pdb=" N ILE A1353 " pdb=" C ILE A1353 " pdb=" CB ILE A1353 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA TRP A 932 " pdb=" N TRP A 932 " pdb=" C TRP A 932 " pdb=" CB TRP A 932 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2151 not shown) Planarity restraints: 2347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 426 " -0.035 2.00e-02 2.50e+03 2.16e-02 8.14e+00 pdb=" CG PHE A 426 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 426 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 426 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE A 426 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 426 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 426 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 710 " -0.037 2.00e-02 2.50e+03 1.96e-02 7.68e+00 pdb=" CG TYR A 710 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 710 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 710 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 710 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR A 710 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 710 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 710 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 586 " -0.036 2.00e-02 2.50e+03 1.88e-02 7.07e+00 pdb=" CG TYR A 586 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 586 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 586 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR A 586 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 586 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 586 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 586 " -0.025 2.00e-02 2.50e+03 ... (remaining 2344 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4870 2.84 - 3.36: 14429 3.36 - 3.87: 24449 3.87 - 4.39: 30066 4.39 - 4.90: 47375 Nonbonded interactions: 121189 Sorted by model distance: nonbonded pdb=" O HIS A 325 " pdb=" N GLU A 327 " model vdw 2.330 2.520 nonbonded pdb=" O ILE A 514 " pdb=" OG SER A 517 " model vdw 2.357 2.440 nonbonded pdb=" OG SER A 543 " pdb=" OG SER A 615 " model vdw 2.359 2.440 nonbonded pdb=" OD2 ASP A1290 " pdb=" NZ LYS A1294 " model vdw 2.370 2.520 nonbonded pdb=" OE1 GLU A 534 " pdb=" NZ LYS A1136 " model vdw 2.390 2.520 ... (remaining 121184 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and resid 131 through 188) selection = (chain 'D' and resid 131 through 188) selection = (chain 'E' and resid 131 through 188) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 5.480 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 39.040 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 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:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 : 0.014 0.146 13806 Z= 0.933 Angle : 1.151 9.070 18666 Z= 0.806 Chirality : 0.060 0.320 2154 Planarity : 0.005 0.036 2347 Dihedral : 10.524 88.613 5223 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.57 % Favored : 97.89 % Rotamer: Outliers : 0.07 % Allowed : 0.59 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.19), residues: 1657 helix: 0.51 (0.15), residues: 955 sheet: 0.42 (0.58), residues: 73 loop : 0.79 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.006 TRP A 207 HIS 0.005 0.001 HIS A1011 PHE 0.035 0.004 PHE A 426 TYR 0.037 0.005 TYR A 710 ARG 0.004 0.001 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 368 time to evaluate : 1.740 Fit side-chains REVERT: A 63 LYS cc_start: 0.7371 (mttt) cc_final: 0.6893 (pttp) REVERT: A 83 GLU cc_start: 0.7972 (tt0) cc_final: 0.7328 (tt0) REVERT: A 101 GLU cc_start: 0.5735 (tt0) cc_final: 0.5397 (tt0) REVERT: A 129 ASN cc_start: 0.7880 (t0) cc_final: 0.7626 (t0) REVERT: A 198 GLN cc_start: 0.7275 (pt0) cc_final: 0.7017 (pt0) REVERT: A 203 TRP cc_start: 0.6379 (m100) cc_final: 0.5689 (m100) REVERT: A 220 GLN cc_start: 0.7322 (tt0) cc_final: 0.6983 (mt0) REVERT: A 312 GLN cc_start: 0.6675 (mm-40) cc_final: 0.6468 (mt0) REVERT: A 340 MET cc_start: 0.6414 (tpt) cc_final: 0.5454 (mtp) REVERT: A 354 LYS cc_start: 0.7148 (tttt) cc_final: 0.6386 (mmtp) REVERT: A 370 LYS cc_start: 0.7630 (tttt) cc_final: 0.7366 (ttmt) REVERT: A 373 LYS cc_start: 0.8096 (tttt) cc_final: 0.7704 (tttm) REVERT: A 386 LYS cc_start: 0.7778 (mmtm) cc_final: 0.7572 (mtmp) REVERT: A 413 ASP cc_start: 0.7022 (t0) cc_final: 0.6770 (t0) REVERT: A 434 VAL cc_start: 0.7040 (t) cc_final: 0.6674 (p) REVERT: A 445 ILE cc_start: 0.7973 (tp) cc_final: 0.7673 (mm) REVERT: A 446 ASN cc_start: 0.6309 (m-40) cc_final: 0.6107 (m-40) REVERT: A 449 GLU cc_start: 0.6705 (tt0) cc_final: 0.6403 (tt0) REVERT: A 450 THR cc_start: 0.7171 (m) cc_final: 0.6806 (m) REVERT: A 567 GLU cc_start: 0.6770 (mm-30) cc_final: 0.6556 (mt-10) REVERT: A 594 GLU cc_start: 0.7292 (mp0) cc_final: 0.6973 (mm-30) REVERT: A 718 ASP cc_start: 0.6672 (t70) cc_final: 0.6150 (m-30) REVERT: A 801 LYS cc_start: 0.6977 (mmtm) cc_final: 0.6441 (mppt) REVERT: A 803 SER cc_start: 0.7644 (t) cc_final: 0.7349 (p) REVERT: A 805 THR cc_start: 0.7559 (m) cc_final: 0.7289 (t) REVERT: A 848 TYR cc_start: 0.6837 (m-80) cc_final: 0.6506 (m-80) REVERT: A 859 GLU cc_start: 0.6118 (mt-10) cc_final: 0.5712 (mp0) REVERT: A 902 LYS cc_start: 0.7293 (mmtt) cc_final: 0.6766 (tttp) REVERT: A 967 ASN cc_start: 0.8076 (t0) cc_final: 0.7775 (t0) REVERT: A 1071 LYS cc_start: 0.6408 (mmtp) cc_final: 0.5975 (mmtt) REVERT: A 1091 LYS cc_start: 0.7861 (mttt) cc_final: 0.7472 (mmmt) REVERT: A 1145 LYS cc_start: 0.6600 (mtmt) cc_final: 0.6075 (ptpt) REVERT: A 1171 LYS cc_start: 0.7032 (mttt) cc_final: 0.6733 (mtpt) REVERT: A 1244 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7508 (mp0) REVERT: A 1272 THR cc_start: 0.7442 (m) cc_final: 0.7158 (p) REVERT: A 1290 ASP cc_start: 0.6910 (t70) cc_final: 0.6413 (m-30) REVERT: A 1322 GLU cc_start: 0.5971 (mp0) cc_final: 0.5700 (mp0) REVERT: A 1339 ARG cc_start: 0.7589 (mmt90) cc_final: 0.6214 (mtm180) REVERT: A 1364 ASP cc_start: 0.7565 (t0) cc_final: 0.7091 (t0) REVERT: A 1379 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7098 (mm-30) REVERT: A 1409 ARG cc_start: 0.7713 (ptp-110) cc_final: 0.7444 (ptp-170) REVERT: A 1421 LEU cc_start: 0.8567 (tp) cc_final: 0.8365 (tm) REVERT: A 1423 LYS cc_start: 0.8005 (pttt) cc_final: 0.7485 (pttm) REVERT: A 1437 LYS cc_start: 0.6898 (ttmm) cc_final: 0.6467 (ttpp) REVERT: B 187 MET cc_start: 0.3333 (mtm) cc_final: 0.2618 (ppp) REVERT: B 213 GLU cc_start: 0.6622 (tt0) cc_final: 0.6092 (mp0) REVERT: C 170 MET cc_start: 0.7545 (mtp) cc_final: 0.7157 (mtp) REVERT: D 170 MET cc_start: 0.5344 (mmm) cc_final: 0.5129 (mmm) outliers start: 1 outliers final: 0 residues processed: 369 average time/residue: 1.2428 time to fit residues: 501.8717 Evaluate side-chains 214 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 247 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN A 547 ASN A 563 GLN ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 HIS A 874 GLN ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1069 GLN A1247 ASN ** A1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1360 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13806 Z= 0.204 Angle : 0.532 6.989 18666 Z= 0.285 Chirality : 0.039 0.175 2154 Planarity : 0.004 0.035 2347 Dihedral : 4.876 86.492 1831 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.87 % Favored : 98.07 % Rotamer: Outliers : 3.07 % Allowed : 8.69 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.20), residues: 1657 helix: 1.58 (0.16), residues: 958 sheet: 0.38 (0.63), residues: 68 loop : 0.75 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 932 HIS 0.004 0.001 HIS A 773 PHE 0.021 0.002 PHE A1385 TYR 0.014 0.002 TYR A 746 ARG 0.007 0.001 ARG A1370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 238 time to evaluate : 1.752 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7535 (m-30) REVERT: A 59 MET cc_start: 0.7672 (mtp) cc_final: 0.7276 (mtt) REVERT: A 63 LYS cc_start: 0.7438 (mttt) cc_final: 0.6908 (pttp) REVERT: A 129 ASN cc_start: 0.7816 (t0) cc_final: 0.7531 (t0) REVERT: A 198 GLN cc_start: 0.7357 (pt0) cc_final: 0.6967 (mt0) REVERT: A 203 TRP cc_start: 0.6390 (m100) cc_final: 0.5502 (m100) REVERT: A 220 GLN cc_start: 0.7438 (tt0) cc_final: 0.6898 (mt0) REVERT: A 312 GLN cc_start: 0.7211 (mm-40) cc_final: 0.6891 (mt0) REVERT: A 333 LYS cc_start: 0.7031 (tttt) cc_final: 0.6766 (ttpp) REVERT: A 340 MET cc_start: 0.6146 (tpt) cc_final: 0.5271 (mtp) REVERT: A 354 LYS cc_start: 0.6992 (tttt) cc_final: 0.6781 (tttp) REVERT: A 373 LYS cc_start: 0.8034 (tttt) cc_final: 0.7652 (tttm) REVERT: A 413 ASP cc_start: 0.7058 (t0) cc_final: 0.6805 (t0) REVERT: A 445 ILE cc_start: 0.7902 (tp) cc_final: 0.7451 (mm) REVERT: A 446 ASN cc_start: 0.6624 (m-40) cc_final: 0.6280 (t0) REVERT: A 536 ILE cc_start: 0.7497 (mm) cc_final: 0.6508 (pt) REVERT: A 584 GLU cc_start: 0.6930 (mp0) cc_final: 0.6455 (tt0) REVERT: A 594 GLU cc_start: 0.7279 (mp0) cc_final: 0.6901 (mm-30) REVERT: A 694 LYS cc_start: 0.7144 (mttt) cc_final: 0.5706 (pttp) REVERT: A 782 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6777 (tp-100) REVERT: A 783 LYS cc_start: 0.6263 (mmtt) cc_final: 0.6039 (mttm) REVERT: A 801 LYS cc_start: 0.7208 (mmtm) cc_final: 0.6570 (mppt) REVERT: A 848 TYR cc_start: 0.6856 (m-80) cc_final: 0.6506 (m-80) REVERT: A 856 LYS cc_start: 0.7975 (mttp) cc_final: 0.7711 (mttm) REVERT: A 859 GLU cc_start: 0.6267 (mt-10) cc_final: 0.5919 (mp0) REVERT: A 863 SER cc_start: 0.7999 (OUTLIER) cc_final: 0.7507 (t) REVERT: A 902 LYS cc_start: 0.7450 (mmtt) cc_final: 0.6732 (ttpp) REVERT: A 1071 LYS cc_start: 0.6431 (mmtp) cc_final: 0.6027 (mmtt) REVERT: A 1091 LYS cc_start: 0.7784 (mttt) cc_final: 0.7345 (mmmt) REVERT: A 1145 LYS cc_start: 0.6702 (mtmt) cc_final: 0.5970 (ptpt) REVERT: A 1158 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7322 (m-30) REVERT: A 1171 LYS cc_start: 0.6953 (mttt) cc_final: 0.6642 (mtpt) REVERT: A 1244 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7525 (mt-10) REVERT: A 1272 THR cc_start: 0.7358 (m) cc_final: 0.6982 (p) REVERT: A 1290 ASP cc_start: 0.6842 (t70) cc_final: 0.6467 (m-30) REVERT: A 1323 LYS cc_start: 0.7032 (mttt) cc_final: 0.6805 (mtmt) REVERT: A 1339 ARG cc_start: 0.7669 (mmt90) cc_final: 0.6236 (mtm180) REVERT: A 1364 ASP cc_start: 0.7682 (t0) cc_final: 0.7457 (t0) REVERT: A 1378 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6646 (t0) REVERT: A 1379 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6939 (mp0) REVERT: A 1423 LYS cc_start: 0.8103 (pttt) cc_final: 0.7574 (pttm) REVERT: B 187 MET cc_start: 0.3558 (mtm) cc_final: 0.2602 (ptm) REVERT: B 213 GLU cc_start: 0.6376 (tt0) cc_final: 0.6075 (mp0) REVERT: B 220 SER cc_start: 0.6912 (t) cc_final: 0.6160 (m) REVERT: B 221 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6119 (mt-10) REVERT: B 222 LYS cc_start: 0.6341 (tttt) cc_final: 0.6139 (tttp) REVERT: C 170 MET cc_start: 0.7696 (mtp) cc_final: 0.7319 (mtp) REVERT: E 195 MET cc_start: 0.4069 (mmm) cc_final: 0.3789 (mmm) outliers start: 47 outliers final: 17 residues processed: 269 average time/residue: 1.2396 time to fit residues: 365.9325 Evaluate side-chains 224 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 202 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1104 GLU Chi-restraints excluded: chain A residue 1158 ASP Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1334 VAL Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1378 ASP Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1405 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain E residue 148 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 162 optimal weight: 0.0970 chunk 133 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 120 optimal weight: 0.0870 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 247 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 GLN A1037 ASN A1279 GLN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 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 : 0.002 0.032 13806 Z= 0.154 Angle : 0.469 6.119 18666 Z= 0.249 Chirality : 0.038 0.171 2154 Planarity : 0.003 0.041 2347 Dihedral : 4.687 86.591 1831 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.23 % Favored : 97.71 % Rotamer: Outliers : 3.14 % Allowed : 10.98 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.21), residues: 1657 helix: 1.70 (0.16), residues: 964 sheet: 0.12 (0.63), residues: 73 loop : 0.72 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 932 HIS 0.003 0.001 HIS A 568 PHE 0.019 0.002 PHE A1385 TYR 0.012 0.001 TYR A 746 ARG 0.004 0.000 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 215 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: A 59 MET cc_start: 0.7622 (mtp) cc_final: 0.7243 (mtt) REVERT: A 63 LYS cc_start: 0.7426 (mttt) cc_final: 0.6914 (pttp) REVERT: A 97 MET cc_start: 0.5481 (ttm) cc_final: 0.5032 (ttt) REVERT: A 129 ASN cc_start: 0.7728 (t0) cc_final: 0.7424 (t0) REVERT: A 198 GLN cc_start: 0.7258 (pt0) cc_final: 0.6955 (mt0) REVERT: A 203 TRP cc_start: 0.6355 (m100) cc_final: 0.5476 (m100) REVERT: A 220 GLN cc_start: 0.7352 (tt0) cc_final: 0.6874 (mt0) REVERT: A 243 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7742 (tp40) REVERT: A 312 GLN cc_start: 0.7137 (mm-40) cc_final: 0.6817 (mt0) REVERT: A 336 GLU cc_start: 0.7061 (tt0) cc_final: 0.6566 (mt-10) REVERT: A 340 MET cc_start: 0.6164 (tpt) cc_final: 0.5267 (mtp) REVERT: A 354 LYS cc_start: 0.7049 (tttt) cc_final: 0.6845 (tttp) REVERT: A 373 LYS cc_start: 0.7970 (tttt) cc_final: 0.7479 (ttpm) REVERT: A 413 ASP cc_start: 0.7070 (t0) cc_final: 0.6790 (t0) REVERT: A 445 ILE cc_start: 0.7851 (tp) cc_final: 0.7401 (mm) REVERT: A 446 ASN cc_start: 0.6716 (m-40) cc_final: 0.6484 (t0) REVERT: A 584 GLU cc_start: 0.7045 (mp0) cc_final: 0.6480 (tt0) REVERT: A 594 GLU cc_start: 0.7238 (mp0) cc_final: 0.6837 (mm-30) REVERT: A 694 LYS cc_start: 0.7125 (mttt) cc_final: 0.5662 (pttp) REVERT: A 783 LYS cc_start: 0.6185 (mmtt) cc_final: 0.5934 (mttm) REVERT: A 801 LYS cc_start: 0.7313 (mmtm) cc_final: 0.6713 (mppt) REVERT: A 848 TYR cc_start: 0.6871 (m-80) cc_final: 0.6615 (m-80) REVERT: A 863 SER cc_start: 0.7809 (OUTLIER) cc_final: 0.7438 (t) REVERT: A 902 LYS cc_start: 0.7422 (mmtt) cc_final: 0.6884 (ttpp) REVERT: A 1071 LYS cc_start: 0.6710 (mmtp) cc_final: 0.6235 (mmtt) REVERT: A 1091 LYS cc_start: 0.7773 (mttt) cc_final: 0.7291 (mmmt) REVERT: A 1145 LYS cc_start: 0.6847 (mtmt) cc_final: 0.6129 (ptpt) REVERT: A 1158 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7254 (m-30) REVERT: A 1171 LYS cc_start: 0.6858 (mttt) cc_final: 0.6563 (mtpt) REVERT: A 1244 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7568 (mt-10) REVERT: A 1272 THR cc_start: 0.7290 (m) cc_final: 0.6879 (p) REVERT: A 1290 ASP cc_start: 0.6797 (t70) cc_final: 0.6405 (m-30) REVERT: A 1323 LYS cc_start: 0.7034 (mttt) cc_final: 0.6830 (mtmt) REVERT: A 1339 ARG cc_start: 0.7577 (mmt90) cc_final: 0.6152 (mtm180) REVERT: A 1364 ASP cc_start: 0.7734 (t0) cc_final: 0.7463 (t0) REVERT: A 1423 LYS cc_start: 0.8051 (pttt) cc_final: 0.7586 (pttm) REVERT: A 1437 LYS cc_start: 0.7486 (ttmt) cc_final: 0.7274 (mppt) REVERT: B 187 MET cc_start: 0.3567 (mtm) cc_final: 0.2644 (ptm) REVERT: B 213 GLU cc_start: 0.6404 (tt0) cc_final: 0.6086 (mp0) REVERT: B 220 SER cc_start: 0.6791 (t) cc_final: 0.6056 (m) REVERT: B 222 LYS cc_start: 0.6387 (tttt) cc_final: 0.6182 (tttp) REVERT: C 170 MET cc_start: 0.7584 (mtp) cc_final: 0.7211 (mtp) REVERT: D 170 MET cc_start: 0.5275 (mmm) cc_final: 0.5021 (mmm) REVERT: E 195 MET cc_start: 0.4165 (mmm) cc_final: 0.3769 (mmm) outliers start: 48 outliers final: 19 residues processed: 245 average time/residue: 1.1865 time to fit residues: 319.7484 Evaluate side-chains 214 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 191 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1104 GLU Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1158 ASP Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1265 SER Chi-restraints excluded: chain A residue 1334 VAL Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1409 ARG Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain E residue 148 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 2.9990 chunk 112 optimal weight: 0.0470 chunk 77 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 150 optimal weight: 0.0970 chunk 159 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 overall best weight: 1.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 812 ASN A 936 GLN A1029 GLN ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1279 GLN A1360 ASN B 217 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13806 Z= 0.202 Angle : 0.492 6.570 18666 Z= 0.255 Chirality : 0.039 0.183 2154 Planarity : 0.004 0.043 2347 Dihedral : 4.702 88.845 1831 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.23 % Favored : 97.71 % Rotamer: Outliers : 3.33 % Allowed : 11.70 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.21), residues: 1657 helix: 1.62 (0.16), residues: 958 sheet: -0.04 (0.63), residues: 73 loop : 0.69 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 932 HIS 0.003 0.001 HIS A1420 PHE 0.024 0.002 PHE A 314 TYR 0.014 0.001 TYR A 746 ARG 0.007 0.000 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 201 time to evaluate : 1.383 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7560 (m-30) REVERT: A 63 LYS cc_start: 0.7395 (mttt) cc_final: 0.6918 (pttp) REVERT: A 129 ASN cc_start: 0.7682 (t0) cc_final: 0.7443 (t0) REVERT: A 198 GLN cc_start: 0.7306 (pt0) cc_final: 0.6971 (mt0) REVERT: A 203 TRP cc_start: 0.6434 (m100) cc_final: 0.5535 (m100) REVERT: A 220 GLN cc_start: 0.7449 (tt0) cc_final: 0.6927 (mt0) REVERT: A 243 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7701 (tp40) REVERT: A 314 PHE cc_start: 0.5452 (t80) cc_final: 0.4987 (t80) REVERT: A 336 GLU cc_start: 0.7262 (tt0) cc_final: 0.6701 (mt-10) REVERT: A 340 MET cc_start: 0.6152 (tpt) cc_final: 0.5223 (mtp) REVERT: A 354 LYS cc_start: 0.7091 (tttt) cc_final: 0.6858 (tttp) REVERT: A 413 ASP cc_start: 0.7213 (t0) cc_final: 0.6897 (t0) REVERT: A 445 ILE cc_start: 0.7858 (tp) cc_final: 0.7411 (mm) REVERT: A 584 GLU cc_start: 0.7043 (mp0) cc_final: 0.6518 (tt0) REVERT: A 594 GLU cc_start: 0.7155 (mp0) cc_final: 0.6861 (mm-30) REVERT: A 692 ILE cc_start: 0.6468 (OUTLIER) cc_final: 0.6039 (tp) REVERT: A 694 LYS cc_start: 0.7184 (mttt) cc_final: 0.5648 (pttp) REVERT: A 782 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.6776 (tp-100) REVERT: A 783 LYS cc_start: 0.6250 (mmtt) cc_final: 0.5996 (mttm) REVERT: A 801 LYS cc_start: 0.7378 (mmtm) cc_final: 0.6821 (mppt) REVERT: A 848 TYR cc_start: 0.6925 (m-80) cc_final: 0.6663 (m-80) REVERT: A 863 SER cc_start: 0.7806 (OUTLIER) cc_final: 0.7454 (t) REVERT: A 902 LYS cc_start: 0.7361 (mmtt) cc_final: 0.6762 (ttpp) REVERT: A 1026 ASP cc_start: 0.6137 (OUTLIER) cc_final: 0.5806 (p0) REVERT: A 1071 LYS cc_start: 0.6975 (mmtp) cc_final: 0.6391 (mmtt) REVERT: A 1091 LYS cc_start: 0.7836 (mttt) cc_final: 0.7355 (mmmt) REVERT: A 1145 LYS cc_start: 0.7042 (mtmt) cc_final: 0.6308 (ptpt) REVERT: A 1167 GLU cc_start: 0.6680 (mm-30) cc_final: 0.6108 (mp0) REVERT: A 1171 LYS cc_start: 0.6855 (mttt) cc_final: 0.6550 (mtpt) REVERT: A 1244 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7567 (mt-10) REVERT: A 1272 THR cc_start: 0.7274 (m) cc_final: 0.6822 (p) REVERT: A 1290 ASP cc_start: 0.6824 (t70) cc_final: 0.6428 (m-30) REVERT: A 1304 ASN cc_start: 0.7705 (t0) cc_final: 0.7361 (t160) REVERT: A 1323 LYS cc_start: 0.7130 (mttt) cc_final: 0.6915 (mtmt) REVERT: A 1339 ARG cc_start: 0.7591 (mmt90) cc_final: 0.6184 (mtm180) REVERT: A 1423 LYS cc_start: 0.8068 (pttt) cc_final: 0.7640 (pttm) REVERT: B 187 MET cc_start: 0.3757 (mtm) cc_final: 0.2818 (ptm) REVERT: B 213 GLU cc_start: 0.6343 (tt0) cc_final: 0.6035 (mp0) REVERT: B 220 SER cc_start: 0.6822 (t) cc_final: 0.6106 (m) REVERT: B 222 LYS cc_start: 0.6339 (tttt) cc_final: 0.6025 (tttp) REVERT: C 170 MET cc_start: 0.7627 (mtp) cc_final: 0.7233 (mtp) outliers start: 51 outliers final: 20 residues processed: 232 average time/residue: 1.2667 time to fit residues: 323.2152 Evaluate side-chains 210 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 184 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1334 VAL Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1450 LYS Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 160 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 0.0040 chunk 136 optimal weight: 0.4980 chunk 110 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 143 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 812 ASN A1029 GLN ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1279 GLN A1360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13806 Z= 0.155 Angle : 0.453 6.757 18666 Z= 0.237 Chirality : 0.038 0.168 2154 Planarity : 0.003 0.045 2347 Dihedral : 4.587 88.580 1831 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.17 % Favored : 97.77 % Rotamer: Outliers : 3.01 % Allowed : 12.81 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.21), residues: 1657 helix: 1.64 (0.16), residues: 966 sheet: -0.02 (0.64), residues: 73 loop : 0.63 (0.27), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 932 HIS 0.003 0.001 HIS A 773 PHE 0.018 0.001 PHE A1385 TYR 0.017 0.001 TYR A 565 ARG 0.004 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 204 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7532 (m-30) REVERT: A 59 MET cc_start: 0.7595 (mtp) cc_final: 0.7196 (mtt) REVERT: A 63 LYS cc_start: 0.7356 (mttt) cc_final: 0.6867 (pttp) REVERT: A 129 ASN cc_start: 0.7675 (t0) cc_final: 0.7432 (t0) REVERT: A 198 GLN cc_start: 0.7294 (pt0) cc_final: 0.6989 (mt0) REVERT: A 203 TRP cc_start: 0.6436 (m100) cc_final: 0.5533 (m100) REVERT: A 220 GLN cc_start: 0.7436 (tt0) cc_final: 0.6915 (mt0) REVERT: A 243 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7687 (tp40) REVERT: A 279 ARG cc_start: 0.6150 (mmp80) cc_final: 0.5614 (mtp180) REVERT: A 314 PHE cc_start: 0.5598 (t80) cc_final: 0.4798 (t80) REVERT: A 336 GLU cc_start: 0.7294 (tt0) cc_final: 0.6765 (mt-10) REVERT: A 340 MET cc_start: 0.6089 (tpt) cc_final: 0.5180 (mtp) REVERT: A 354 LYS cc_start: 0.7091 (tttt) cc_final: 0.6863 (tttp) REVERT: A 359 SER cc_start: 0.7469 (t) cc_final: 0.6886 (m) REVERT: A 413 ASP cc_start: 0.7149 (t0) cc_final: 0.6858 (t0) REVERT: A 445 ILE cc_start: 0.7862 (tp) cc_final: 0.7418 (mm) REVERT: A 507 GLU cc_start: 0.7129 (pt0) cc_final: 0.6572 (pm20) REVERT: A 584 GLU cc_start: 0.7054 (mp0) cc_final: 0.6575 (tt0) REVERT: A 594 GLU cc_start: 0.7089 (mp0) cc_final: 0.6842 (mm-30) REVERT: A 694 LYS cc_start: 0.7193 (mttt) cc_final: 0.5690 (pttp) REVERT: A 783 LYS cc_start: 0.6199 (mmtt) cc_final: 0.5952 (mttm) REVERT: A 801 LYS cc_start: 0.7340 (mmtm) cc_final: 0.6792 (mppt) REVERT: A 818 SER cc_start: 0.8277 (OUTLIER) cc_final: 0.8061 (m) REVERT: A 848 TYR cc_start: 0.6888 (m-80) cc_final: 0.6630 (m-80) REVERT: A 863 SER cc_start: 0.7839 (OUTLIER) cc_final: 0.7430 (t) REVERT: A 902 LYS cc_start: 0.7356 (mmtt) cc_final: 0.6744 (ttpp) REVERT: A 1026 ASP cc_start: 0.6164 (OUTLIER) cc_final: 0.5937 (p0) REVERT: A 1071 LYS cc_start: 0.7002 (mmtp) cc_final: 0.6407 (mmtt) REVERT: A 1091 LYS cc_start: 0.7879 (mttt) cc_final: 0.7389 (mmmt) REVERT: A 1145 LYS cc_start: 0.7073 (mtmt) cc_final: 0.6386 (ptpt) REVERT: A 1167 GLU cc_start: 0.6624 (mm-30) cc_final: 0.6111 (mp0) REVERT: A 1171 LYS cc_start: 0.6734 (mttt) cc_final: 0.6411 (mtpt) REVERT: A 1231 LYS cc_start: 0.7356 (mmtt) cc_final: 0.7098 (mmtt) REVERT: A 1244 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7612 (mt-10) REVERT: A 1270 LYS cc_start: 0.6545 (tttt) cc_final: 0.5956 (mmtt) REVERT: A 1272 THR cc_start: 0.7247 (m) cc_final: 0.6760 (p) REVERT: A 1290 ASP cc_start: 0.6852 (t70) cc_final: 0.6474 (m-30) REVERT: A 1304 ASN cc_start: 0.7601 (t0) cc_final: 0.6992 (t0) REVERT: A 1305 LYS cc_start: 0.7294 (tmmt) cc_final: 0.7067 (tttt) REVERT: A 1339 ARG cc_start: 0.7595 (mmt90) cc_final: 0.6207 (mtm180) REVERT: A 1423 LYS cc_start: 0.8056 (pttt) cc_final: 0.7653 (pttm) REVERT: A 1426 ILE cc_start: 0.7715 (mm) cc_final: 0.7499 (mp) REVERT: B 187 MET cc_start: 0.3847 (mtm) cc_final: 0.2857 (ptm) REVERT: B 213 GLU cc_start: 0.6336 (tt0) cc_final: 0.6029 (mp0) REVERT: B 220 SER cc_start: 0.6810 (t) cc_final: 0.6085 (m) REVERT: B 222 LYS cc_start: 0.6375 (tttt) cc_final: 0.6033 (tttp) REVERT: C 170 MET cc_start: 0.7572 (mtp) cc_final: 0.7189 (mtp) outliers start: 46 outliers final: 21 residues processed: 232 average time/residue: 1.1944 time to fit residues: 304.6035 Evaluate side-chains 217 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 191 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1334 VAL Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1409 ARG Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain E residue 148 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 5.9990 chunk 143 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 73 optimal weight: 0.0870 chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 ASN ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1279 GLN A1360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13806 Z= 0.148 Angle : 0.445 6.621 18666 Z= 0.232 Chirality : 0.038 0.176 2154 Planarity : 0.003 0.047 2347 Dihedral : 4.513 88.673 1831 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.35 % Favored : 97.59 % Rotamer: Outliers : 2.75 % Allowed : 13.53 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.21), residues: 1657 helix: 1.75 (0.17), residues: 960 sheet: 0.14 (0.65), residues: 73 loop : 0.64 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 932 HIS 0.002 0.001 HIS A 773 PHE 0.017 0.001 PHE A1385 TYR 0.013 0.001 TYR A 746 ARG 0.003 0.000 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 199 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7527 (m-30) REVERT: A 63 LYS cc_start: 0.7341 (mttt) cc_final: 0.6855 (pttm) REVERT: A 129 ASN cc_start: 0.7639 (t0) cc_final: 0.7426 (t0) REVERT: A 198 GLN cc_start: 0.7262 (pt0) cc_final: 0.6995 (mt0) REVERT: A 203 TRP cc_start: 0.6445 (m100) cc_final: 0.5536 (m100) REVERT: A 220 GLN cc_start: 0.7436 (tt0) cc_final: 0.6893 (mt0) REVERT: A 243 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7663 (tp40) REVERT: A 279 ARG cc_start: 0.6115 (mmp80) cc_final: 0.5413 (tpt90) REVERT: A 314 PHE cc_start: 0.5610 (t80) cc_final: 0.3955 (t80) REVERT: A 336 GLU cc_start: 0.7358 (tt0) cc_final: 0.6766 (mt-10) REVERT: A 340 MET cc_start: 0.6062 (tpt) cc_final: 0.5163 (mtp) REVERT: A 354 LYS cc_start: 0.7109 (tttt) cc_final: 0.6880 (tttp) REVERT: A 359 SER cc_start: 0.7422 (t) cc_final: 0.6849 (m) REVERT: A 386 LYS cc_start: 0.8137 (mmtm) cc_final: 0.7856 (mmtt) REVERT: A 413 ASP cc_start: 0.7211 (t0) cc_final: 0.6908 (t0) REVERT: A 445 ILE cc_start: 0.7836 (tp) cc_final: 0.7428 (mm) REVERT: A 507 GLU cc_start: 0.7089 (pt0) cc_final: 0.6475 (pm20) REVERT: A 584 GLU cc_start: 0.7057 (mp0) cc_final: 0.6577 (tt0) REVERT: A 694 LYS cc_start: 0.7271 (mttt) cc_final: 0.5735 (pttp) REVERT: A 782 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.6772 (tp-100) REVERT: A 783 LYS cc_start: 0.6231 (mmtt) cc_final: 0.6000 (mttm) REVERT: A 801 LYS cc_start: 0.7446 (mmtm) cc_final: 0.6975 (mppt) REVERT: A 848 TYR cc_start: 0.6896 (m-80) cc_final: 0.6628 (m-80) REVERT: A 863 SER cc_start: 0.7858 (OUTLIER) cc_final: 0.7453 (t) REVERT: A 902 LYS cc_start: 0.7442 (mmtt) cc_final: 0.6785 (ttpp) REVERT: A 1071 LYS cc_start: 0.6896 (mmtp) cc_final: 0.6364 (mmtt) REVERT: A 1091 LYS cc_start: 0.7900 (mttt) cc_final: 0.7448 (mmmt) REVERT: A 1167 GLU cc_start: 0.6668 (mm-30) cc_final: 0.6145 (mp0) REVERT: A 1171 LYS cc_start: 0.6731 (mttt) cc_final: 0.6405 (mtpt) REVERT: A 1244 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7577 (mt-10) REVERT: A 1270 LYS cc_start: 0.6531 (tttt) cc_final: 0.5993 (mmtt) REVERT: A 1272 THR cc_start: 0.7250 (m) cc_final: 0.6739 (p) REVERT: A 1290 ASP cc_start: 0.6868 (t70) cc_final: 0.6506 (m-30) REVERT: A 1304 ASN cc_start: 0.7634 (t0) cc_final: 0.6979 (t0) REVERT: A 1305 LYS cc_start: 0.7346 (tmmt) cc_final: 0.7093 (tttt) REVERT: A 1339 ARG cc_start: 0.7611 (mmt90) cc_final: 0.6177 (mtm180) REVERT: A 1423 LYS cc_start: 0.8034 (pttt) cc_final: 0.7648 (pttm) REVERT: A 1426 ILE cc_start: 0.7714 (mm) cc_final: 0.7509 (mp) REVERT: B 187 MET cc_start: 0.3888 (mtm) cc_final: 0.2906 (ptm) REVERT: B 213 GLU cc_start: 0.6293 (tt0) cc_final: 0.5972 (mp0) REVERT: B 220 SER cc_start: 0.6820 (t) cc_final: 0.6091 (m) REVERT: B 221 GLU cc_start: 0.6937 (mm-30) cc_final: 0.6074 (mt-10) REVERT: B 222 LYS cc_start: 0.6357 (tttt) cc_final: 0.6005 (tttp) REVERT: C 170 MET cc_start: 0.7597 (mtp) cc_final: 0.7217 (mtp) REVERT: D 170 MET cc_start: 0.5418 (mmm) cc_final: 0.5063 (mmm) outliers start: 42 outliers final: 22 residues processed: 225 average time/residue: 1.1902 time to fit residues: 295.1325 Evaluate side-chains 222 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 196 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1334 VAL Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain E residue 148 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 90 optimal weight: 0.2980 chunk 116 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 159 optimal weight: 0.4980 chunk 99 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 727 GLN A 809 ASN A 812 ASN ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1279 GLN A1360 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13806 Z= 0.153 Angle : 0.449 7.070 18666 Z= 0.233 Chirality : 0.038 0.174 2154 Planarity : 0.003 0.048 2347 Dihedral : 4.482 88.625 1831 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.35 % Favored : 97.59 % Rotamer: Outliers : 2.94 % Allowed : 13.79 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.21), residues: 1657 helix: 1.72 (0.17), residues: 967 sheet: 0.16 (0.64), residues: 73 loop : 0.61 (0.27), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 932 HIS 0.002 0.001 HIS A 773 PHE 0.016 0.001 PHE A1385 TYR 0.014 0.001 TYR A 746 ARG 0.005 0.000 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 204 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7530 (m-30) REVERT: A 59 MET cc_start: 0.7617 (mtp) cc_final: 0.7301 (mtt) REVERT: A 63 LYS cc_start: 0.7345 (mttt) cc_final: 0.6850 (pttp) REVERT: A 198 GLN cc_start: 0.7260 (pt0) cc_final: 0.6972 (mt0) REVERT: A 203 TRP cc_start: 0.6459 (m100) cc_final: 0.5553 (m100) REVERT: A 220 GLN cc_start: 0.7450 (tt0) cc_final: 0.6893 (mt0) REVERT: A 243 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7680 (tp40) REVERT: A 314 PHE cc_start: 0.5549 (t80) cc_final: 0.3817 (t80) REVERT: A 336 GLU cc_start: 0.7353 (tt0) cc_final: 0.6756 (mt-10) REVERT: A 340 MET cc_start: 0.6042 (tpt) cc_final: 0.5138 (mtp) REVERT: A 354 LYS cc_start: 0.7128 (tttt) cc_final: 0.6891 (tttp) REVERT: A 359 SER cc_start: 0.7419 (t) cc_final: 0.6847 (m) REVERT: A 386 LYS cc_start: 0.8072 (mmtm) cc_final: 0.7803 (mmtt) REVERT: A 413 ASP cc_start: 0.7236 (t0) cc_final: 0.6943 (t0) REVERT: A 445 ILE cc_start: 0.7798 (tp) cc_final: 0.7378 (mm) REVERT: A 507 GLU cc_start: 0.7066 (pt0) cc_final: 0.6447 (pm20) REVERT: A 584 GLU cc_start: 0.7053 (mp0) cc_final: 0.6582 (tt0) REVERT: A 593 ASN cc_start: 0.6710 (OUTLIER) cc_final: 0.6494 (t0) REVERT: A 692 ILE cc_start: 0.6417 (OUTLIER) cc_final: 0.6101 (tp) REVERT: A 694 LYS cc_start: 0.7331 (mttt) cc_final: 0.5759 (pttp) REVERT: A 782 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.6774 (tp-100) REVERT: A 783 LYS cc_start: 0.6232 (mmtt) cc_final: 0.6009 (mttm) REVERT: A 801 LYS cc_start: 0.7407 (mmtm) cc_final: 0.6878 (mppt) REVERT: A 848 TYR cc_start: 0.6889 (m-80) cc_final: 0.6608 (m-80) REVERT: A 863 SER cc_start: 0.7875 (OUTLIER) cc_final: 0.7436 (t) REVERT: A 902 LYS cc_start: 0.7453 (mmtt) cc_final: 0.6781 (ttpp) REVERT: A 1071 LYS cc_start: 0.6859 (mmtp) cc_final: 0.6341 (mmtt) REVERT: A 1083 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6788 (mt-10) REVERT: A 1091 LYS cc_start: 0.7890 (mttt) cc_final: 0.7415 (mmmt) REVERT: A 1167 GLU cc_start: 0.6711 (mm-30) cc_final: 0.6426 (mm-30) REVERT: A 1171 LYS cc_start: 0.6737 (mttt) cc_final: 0.6393 (mtpt) REVERT: A 1195 GLU cc_start: 0.6553 (mm-30) cc_final: 0.5992 (tt0) REVERT: A 1244 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7513 (mt-10) REVERT: A 1270 LYS cc_start: 0.6531 (tttt) cc_final: 0.6028 (mmtt) REVERT: A 1290 ASP cc_start: 0.6820 (t70) cc_final: 0.6446 (m-30) REVERT: A 1304 ASN cc_start: 0.7627 (t0) cc_final: 0.6975 (t0) REVERT: A 1305 LYS cc_start: 0.7402 (tmmt) cc_final: 0.7153 (tttt) REVERT: A 1339 ARG cc_start: 0.7639 (mmt90) cc_final: 0.6219 (mtm180) REVERT: A 1423 LYS cc_start: 0.8062 (pttt) cc_final: 0.7662 (pttm) REVERT: B 213 GLU cc_start: 0.6306 (tt0) cc_final: 0.5994 (mp0) REVERT: B 220 SER cc_start: 0.6826 (t) cc_final: 0.6102 (m) REVERT: B 221 GLU cc_start: 0.6794 (mm-30) cc_final: 0.5951 (mt-10) REVERT: B 222 LYS cc_start: 0.6346 (tttt) cc_final: 0.5996 (tttp) REVERT: C 170 MET cc_start: 0.7551 (mtp) cc_final: 0.7145 (mtp) outliers start: 45 outliers final: 24 residues processed: 230 average time/residue: 1.2074 time to fit residues: 306.6106 Evaluate side-chains 223 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 193 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1334 VAL Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1409 ARG Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain E residue 148 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 108 optimal weight: 0.3980 chunk 78 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 812 ASN ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1279 GLN A1330 GLN A1360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13806 Z= 0.284 Angle : 0.542 7.352 18666 Z= 0.278 Chirality : 0.041 0.180 2154 Planarity : 0.004 0.045 2347 Dihedral : 4.757 84.392 1831 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.60 % Favored : 97.34 % Rotamer: Outliers : 2.88 % Allowed : 14.05 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.21), residues: 1657 helix: 1.47 (0.16), residues: 955 sheet: -0.15 (0.63), residues: 75 loop : 0.45 (0.26), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 932 HIS 0.004 0.001 HIS A 773 PHE 0.022 0.002 PHE A1054 TYR 0.020 0.002 TYR A 746 ARG 0.004 0.000 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 204 time to evaluate : 1.825 Fit side-chains revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7583 (m-30) REVERT: A 63 LYS cc_start: 0.7471 (mttt) cc_final: 0.6955 (pttm) REVERT: A 198 GLN cc_start: 0.7294 (pt0) cc_final: 0.6985 (mt0) REVERT: A 203 TRP cc_start: 0.6536 (m100) cc_final: 0.5595 (m100) REVERT: A 220 GLN cc_start: 0.7649 (tt0) cc_final: 0.6983 (mt0) REVERT: A 243 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7675 (tp40) REVERT: A 336 GLU cc_start: 0.7432 (tt0) cc_final: 0.6845 (mt-10) REVERT: A 340 MET cc_start: 0.6029 (tpt) cc_final: 0.5098 (mtp) REVERT: A 354 LYS cc_start: 0.7032 (tttt) cc_final: 0.6805 (tttp) REVERT: A 386 LYS cc_start: 0.8035 (mmtm) cc_final: 0.7767 (mmtt) REVERT: A 413 ASP cc_start: 0.7449 (t0) cc_final: 0.7137 (t0) REVERT: A 445 ILE cc_start: 0.7805 (tp) cc_final: 0.7377 (mm) REVERT: A 584 GLU cc_start: 0.7025 (mp0) cc_final: 0.6567 (tt0) REVERT: A 694 LYS cc_start: 0.7443 (mttt) cc_final: 0.5832 (pttp) REVERT: A 782 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.6788 (tp-100) REVERT: A 783 LYS cc_start: 0.6304 (mmtt) cc_final: 0.6026 (mttm) REVERT: A 801 LYS cc_start: 0.7357 (mmtm) cc_final: 0.6816 (mppt) REVERT: A 848 TYR cc_start: 0.7008 (m-80) cc_final: 0.6800 (m-80) REVERT: A 863 SER cc_start: 0.7840 (OUTLIER) cc_final: 0.7442 (t) REVERT: A 902 LYS cc_start: 0.7418 (mmtt) cc_final: 0.6721 (ttpp) REVERT: A 1071 LYS cc_start: 0.7042 (mmtp) cc_final: 0.6482 (mmtt) REVERT: A 1091 LYS cc_start: 0.7973 (mttt) cc_final: 0.7573 (mmmt) REVERT: A 1167 GLU cc_start: 0.6721 (mm-30) cc_final: 0.6424 (mm-30) REVERT: A 1171 LYS cc_start: 0.6809 (mttt) cc_final: 0.6462 (mtpt) REVERT: A 1229 ASP cc_start: 0.7697 (m-30) cc_final: 0.7412 (m-30) REVERT: A 1244 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7538 (mt-10) REVERT: A 1270 LYS cc_start: 0.6514 (tttt) cc_final: 0.5992 (mmtt) REVERT: A 1290 ASP cc_start: 0.6859 (t70) cc_final: 0.6478 (m-30) REVERT: A 1304 ASN cc_start: 0.7672 (t0) cc_final: 0.7206 (t160) REVERT: A 1305 LYS cc_start: 0.7482 (tmmt) cc_final: 0.7190 (tttt) REVERT: A 1339 ARG cc_start: 0.7654 (mmt90) cc_final: 0.6226 (mtm180) REVERT: A 1378 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6688 (m-30) REVERT: A 1423 LYS cc_start: 0.8187 (pttt) cc_final: 0.7714 (pttm) REVERT: B 213 GLU cc_start: 0.6330 (tt0) cc_final: 0.5973 (mp0) REVERT: B 220 SER cc_start: 0.6942 (t) cc_final: 0.6215 (m) REVERT: B 222 LYS cc_start: 0.6379 (tttt) cc_final: 0.6089 (tttp) REVERT: C 170 MET cc_start: 0.7592 (mtp) cc_final: 0.7197 (mtp) outliers start: 44 outliers final: 28 residues processed: 228 average time/residue: 1.1861 time to fit residues: 297.8692 Evaluate side-chains 226 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 193 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 1153 LYS Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1334 VAL Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1378 ASP Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 160 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 0.2980 chunk 140 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 809 ASN A 812 ASN A1022 HIS ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1279 GLN A1330 GLN A1360 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13806 Z= 0.164 Angle : 0.471 9.078 18666 Z= 0.243 Chirality : 0.038 0.175 2154 Planarity : 0.003 0.048 2347 Dihedral : 4.610 88.302 1831 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.23 % Favored : 97.71 % Rotamer: Outliers : 2.35 % Allowed : 14.71 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.21), residues: 1657 helix: 1.56 (0.17), residues: 952 sheet: 0.02 (0.64), residues: 74 loop : 0.53 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 932 HIS 0.004 0.001 HIS A1022 PHE 0.017 0.001 PHE A1054 TYR 0.016 0.001 TYR A 746 ARG 0.005 0.000 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 196 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: A 59 MET cc_start: 0.7615 (mtp) cc_final: 0.7213 (mtt) REVERT: A 63 LYS cc_start: 0.7379 (mttt) cc_final: 0.6861 (pttm) REVERT: A 198 GLN cc_start: 0.7259 (pt0) cc_final: 0.6953 (mt0) REVERT: A 203 TRP cc_start: 0.6518 (m100) cc_final: 0.5594 (m100) REVERT: A 220 GLN cc_start: 0.7534 (tt0) cc_final: 0.6956 (mt0) REVERT: A 243 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7681 (tp40) REVERT: A 279 ARG cc_start: 0.6285 (mmp80) cc_final: 0.5683 (mtp180) REVERT: A 314 PHE cc_start: 0.5660 (t80) cc_final: 0.4978 (t80) REVERT: A 336 GLU cc_start: 0.7410 (tt0) cc_final: 0.6819 (mt-10) REVERT: A 340 MET cc_start: 0.6049 (tpt) cc_final: 0.5121 (mtp) REVERT: A 354 LYS cc_start: 0.7110 (tttt) cc_final: 0.6879 (tttp) REVERT: A 359 SER cc_start: 0.7466 (t) cc_final: 0.6895 (m) REVERT: A 386 LYS cc_start: 0.8000 (mmtm) cc_final: 0.7711 (mmtt) REVERT: A 413 ASP cc_start: 0.7457 (t0) cc_final: 0.7146 (t0) REVERT: A 445 ILE cc_start: 0.7758 (tp) cc_final: 0.7313 (mm) REVERT: A 584 GLU cc_start: 0.7029 (mp0) cc_final: 0.6556 (tt0) REVERT: A 694 LYS cc_start: 0.7393 (mttt) cc_final: 0.5831 (pttp) REVERT: A 782 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.6742 (tp-100) REVERT: A 783 LYS cc_start: 0.6265 (mmtt) cc_final: 0.5978 (mttm) REVERT: A 801 LYS cc_start: 0.7342 (mmtm) cc_final: 0.6795 (mppt) REVERT: A 863 SER cc_start: 0.7878 (OUTLIER) cc_final: 0.7479 (t) REVERT: A 902 LYS cc_start: 0.7437 (mmtt) cc_final: 0.6744 (tttm) REVERT: A 1071 LYS cc_start: 0.6954 (mmtp) cc_final: 0.6428 (mmtt) REVERT: A 1091 LYS cc_start: 0.7935 (mttt) cc_final: 0.7526 (mmmt) REVERT: A 1167 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6454 (mm-30) REVERT: A 1171 LYS cc_start: 0.6748 (mttt) cc_final: 0.6394 (mtpt) REVERT: A 1244 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7500 (mt-10) REVERT: A 1270 LYS cc_start: 0.6498 (tttt) cc_final: 0.6006 (mmtt) REVERT: A 1290 ASP cc_start: 0.6854 (t70) cc_final: 0.6482 (m-30) REVERT: A 1304 ASN cc_start: 0.7618 (t0) cc_final: 0.6966 (t0) REVERT: A 1305 LYS cc_start: 0.7467 (tmmt) cc_final: 0.7171 (tttt) REVERT: A 1339 ARG cc_start: 0.7653 (mmt90) cc_final: 0.6198 (mtm180) REVERT: A 1423 LYS cc_start: 0.8169 (pttt) cc_final: 0.7768 (pttm) REVERT: B 213 GLU cc_start: 0.6360 (tt0) cc_final: 0.6017 (mp0) REVERT: B 220 SER cc_start: 0.6859 (t) cc_final: 0.6124 (m) REVERT: B 222 LYS cc_start: 0.6409 (tttt) cc_final: 0.6203 (tttp) REVERT: C 170 MET cc_start: 0.7578 (mtp) cc_final: 0.7234 (mtp) outliers start: 36 outliers final: 21 residues processed: 218 average time/residue: 1.1722 time to fit residues: 281.9390 Evaluate side-chains 217 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1334 VAL Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain C residue 156 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 809 ASN A 812 ASN ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1249 ASN A1279 GLN A1330 GLN A1360 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13806 Z= 0.195 Angle : 0.490 9.223 18666 Z= 0.252 Chirality : 0.039 0.182 2154 Planarity : 0.003 0.047 2347 Dihedral : 4.616 88.990 1831 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.78 % Favored : 97.16 % Rotamer: Outliers : 2.09 % Allowed : 15.10 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.21), residues: 1657 helix: 1.54 (0.17), residues: 952 sheet: -0.03 (0.64), residues: 74 loop : 0.52 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 932 HIS 0.003 0.001 HIS A 829 PHE 0.022 0.002 PHE A1308 TYR 0.016 0.001 TYR A 746 ARG 0.004 0.000 ARG A 511 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3314 Ramachandran restraints generated. 1657 Oldfield, 0 Emsley, 1657 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 192 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7564 (m-30) REVERT: A 63 LYS cc_start: 0.7398 (mttt) cc_final: 0.6877 (pttm) REVERT: A 198 GLN cc_start: 0.7284 (pt0) cc_final: 0.6962 (mt0) REVERT: A 203 TRP cc_start: 0.6528 (m100) cc_final: 0.5600 (m100) REVERT: A 220 GLN cc_start: 0.7544 (tt0) cc_final: 0.6917 (mt0) REVERT: A 243 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7663 (tp40) REVERT: A 314 PHE cc_start: 0.5708 (t80) cc_final: 0.4803 (t80) REVERT: A 336 GLU cc_start: 0.7446 (tt0) cc_final: 0.6861 (mt-10) REVERT: A 340 MET cc_start: 0.6048 (tpt) cc_final: 0.5120 (mtp) REVERT: A 354 LYS cc_start: 0.7078 (tttt) cc_final: 0.6848 (tttp) REVERT: A 386 LYS cc_start: 0.7962 (mmtm) cc_final: 0.7692 (mmtt) REVERT: A 413 ASP cc_start: 0.7453 (t0) cc_final: 0.7157 (t0) REVERT: A 445 ILE cc_start: 0.7765 (tp) cc_final: 0.7319 (mm) REVERT: A 584 GLU cc_start: 0.6994 (mp0) cc_final: 0.6553 (tt0) REVERT: A 694 LYS cc_start: 0.7450 (mttt) cc_final: 0.5865 (pttp) REVERT: A 782 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.6792 (tp-100) REVERT: A 783 LYS cc_start: 0.6302 (mmtt) cc_final: 0.5991 (mttm) REVERT: A 801 LYS cc_start: 0.7355 (mmtm) cc_final: 0.6806 (mppt) REVERT: A 863 SER cc_start: 0.7861 (OUTLIER) cc_final: 0.7472 (t) REVERT: A 902 LYS cc_start: 0.7453 (mmtt) cc_final: 0.6756 (tttm) REVERT: A 1071 LYS cc_start: 0.6920 (mmtp) cc_final: 0.6438 (mmtt) REVERT: A 1091 LYS cc_start: 0.7953 (mttt) cc_final: 0.7533 (mmmt) REVERT: A 1167 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6459 (mm-30) REVERT: A 1171 LYS cc_start: 0.6765 (mttt) cc_final: 0.6414 (mtpt) REVERT: A 1244 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7511 (mt-10) REVERT: A 1270 LYS cc_start: 0.6507 (tttt) cc_final: 0.6029 (mmtt) REVERT: A 1290 ASP cc_start: 0.6862 (t70) cc_final: 0.6492 (m-30) REVERT: A 1304 ASN cc_start: 0.7614 (t0) cc_final: 0.6968 (t0) REVERT: A 1305 LYS cc_start: 0.7473 (tmmt) cc_final: 0.7189 (tttt) REVERT: A 1339 ARG cc_start: 0.7651 (mmt90) cc_final: 0.6194 (mtm180) REVERT: A 1423 LYS cc_start: 0.8169 (pttt) cc_final: 0.7758 (pttm) REVERT: B 213 GLU cc_start: 0.6403 (tt0) cc_final: 0.6029 (mp0) REVERT: B 220 SER cc_start: 0.6867 (t) cc_final: 0.6135 (m) REVERT: B 222 LYS cc_start: 0.6415 (tttt) cc_final: 0.6130 (tttp) REVERT: C 170 MET cc_start: 0.7588 (mtp) cc_final: 0.7236 (mtp) outliers start: 32 outliers final: 21 residues processed: 212 average time/residue: 1.2146 time to fit residues: 284.5133 Evaluate side-chains 214 residues out of total 1530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 189 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 243 GLN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1275 VAL Chi-restraints excluded: chain A residue 1334 VAL Chi-restraints excluded: chain A residue 1347 CYS Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain C residue 156 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 134 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 812 ASN ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1249 ASN A1279 GLN A1360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.163416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.134018 restraints weight = 15392.259| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.61 r_work: 0.3433 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13806 Z= 0.245 Angle : 0.522 9.355 18666 Z= 0.267 Chirality : 0.040 0.186 2154 Planarity : 0.004 0.046 2347 Dihedral : 4.714 86.635 1831 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.84 % Favored : 97.10 % Rotamer: Outliers : 2.09 % Allowed : 15.16 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.21), residues: 1657 helix: 1.44 (0.17), residues: 950 sheet: -0.02 (0.65), residues: 73 loop : 0.42 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 932 HIS 0.004 0.001 HIS A 773 PHE 0.019 0.002 PHE A1054 TYR 0.018 0.002 TYR A 746 ARG 0.005 0.000 ARG A 511 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5478.31 seconds wall clock time: 97 minutes 58.39 seconds (5878.39 seconds total)