Starting phenix.real_space_refine on Fri Dec 8 22:47:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk4_14754/12_2023/7zk4_14754.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk4_14754/12_2023/7zk4_14754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk4_14754/12_2023/7zk4_14754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk4_14754/12_2023/7zk4_14754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk4_14754/12_2023/7zk4_14754.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk4_14754/12_2023/7zk4_14754.pdb" } resolution = 2.6 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= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 31 5.16 5 C 6028 2.51 5 N 1554 2.21 5 O 1716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 180": "OE1" <-> "OE2" Residue "A PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 441": "OD1" <-> "OD2" Residue "A ASP 450": "OD1" <-> "OD2" Residue "A TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "A TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 993": "OD1" <-> "OD2" Residue "A GLU 1009": "OE1" <-> "OE2" Residue "A TYR 1083": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1093": "OD1" <-> "OD2" Residue "A GLU 1096": "OE1" <-> "OE2" Residue "A ASP 1120": "OD1" <-> "OD2" Residue "A ASP 1131": "OD1" <-> "OD2" Residue "A GLU 1140": "OE1" <-> "OE2" Residue "A GLU 1147": "OE1" <-> "OE2" Residue "A ASP 1155": "OD1" <-> "OD2" Residue "A TYR 1161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1207": "OE1" <-> "OE2" Residue "A ASP 1237": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9337 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1189, 9337 Unusual residues: {' MG': 2, 'ATP': 2, 'Y01': 5} Classifications: {'peptide': 1176, 'undetermined': 9, 'water': 4} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 29, 'TRANS': 1146, None: 13} Not linked: pdbres="VAL A1269 " pdbres="ATP A2001 " Not linked: pdbres="ATP A2001 " pdbres=" MG A2002 " Not linked: pdbres=" MG A2002 " pdbres="ATP A2003 " Not linked: pdbres="ATP A2003 " pdbres=" MG A2004 " Not linked: pdbres=" MG A2004 " pdbres="Y01 A2005 " ... (remaining 8 not shown) Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 5.52, per 1000 atoms: 0.59 Number of scatterers: 9337 At special positions: 0 Unit cell: (71.982, 87.048, 148.986, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 31 16.00 P 6 15.00 Mg 2 11.99 O 1716 8.00 N 1554 7.00 C 6028 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: 3.85 Conformation dependent library (CDL) restraints added in 1.7 seconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 71.9% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 42 through 69 removed outlier: 3.805A pdb=" N ASP A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 74 through 83 removed outlier: 3.524A pdb=" N VAL A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 154 removed outlier: 6.143A pdb=" N ARG A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ALA A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 180 removed outlier: 4.216A pdb=" N VAL A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 208 removed outlier: 3.854A pdb=" N GLY A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP A 208 " --> pdb=" O PHE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 216 removed outlier: 3.508A pdb=" N VAL A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 256 Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 265 through 319 Processing helix chain 'A' and resid 323 through 344 Processing helix chain 'A' and resid 344 through 367 removed outlier: 3.756A pdb=" N TYR A 359 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLU A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.946A pdb=" N LYS A 401 " --> pdb=" O PRO A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 437 removed outlier: 3.511A pdb=" N GLN A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.752A pdb=" N THR A 518 " --> pdb=" O GLN A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 528 through 542 Processing helix chain 'A' and resid 558 through 572 removed outlier: 3.700A pdb=" N ALA A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 590 removed outlier: 3.567A pdb=" N VAL A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 Processing helix chain 'A' and resid 616 through 624 removed outlier: 3.503A pdb=" N LYS A 620 " --> pdb=" O GLY A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 699 Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 703 through 737 removed outlier: 3.678A pdb=" N ASN A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 721 " --> pdb=" O ASN A 717 " (cutoff:3.500A) Proline residue: A 722 - end of helix removed outlier: 4.073A pdb=" N SER A 725 " --> pdb=" O GLN A 721 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A 726 " --> pdb=" O PRO A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 795 removed outlier: 3.548A pdb=" N PHE A 773 " --> pdb=" O GLN A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 802 removed outlier: 3.534A pdb=" N PHE A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 825 removed outlier: 3.932A pdb=" N ALA A 824 " --> pdb=" O GLN A 820 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 825 " --> pdb=" O VAL A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 850 removed outlier: 3.820A pdb=" N GLY A 842 " --> pdb=" O ASN A 838 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE A 843 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 844 " --> pdb=" O GLY A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 899 removed outlier: 4.077A pdb=" N LEU A 857 " --> pdb=" O LEU A 853 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 858 " --> pdb=" O THR A 854 " (cutoff:3.500A) Proline residue: A 862 - end of helix removed outlier: 3.871A pdb=" N GLU A 871 " --> pdb=" O ALA A 867 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS A 881 " --> pdb=" O GLY A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 906 Processing helix chain 'A' and resid 908 through 919 Processing helix chain 'A' and resid 920 through 962 removed outlier: 3.706A pdb=" N HIS A 932 " --> pdb=" O MET A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 982 Processing helix chain 'A' and resid 983 through 990 Processing helix chain 'A' and resid 990 through 1009 removed outlier: 3.522A pdb=" N LYS A 996 " --> pdb=" O PRO A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1080 removed outlier: 3.631A pdb=" N VAL A1076 " --> pdb=" O LYS A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1108 Processing helix chain 'A' and resid 1122 through 1129 Processing helix chain 'A' and resid 1137 through 1148 Processing helix chain 'A' and resid 1150 through 1157 Processing helix chain 'A' and resid 1159 through 1163 Processing helix chain 'A' and resid 1166 through 1170 removed outlier: 3.525A pdb=" N THR A1170 " --> pdb=" O ASP A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1188 removed outlier: 3.976A pdb=" N ARG A1188 " --> pdb=" O ARG A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1217 Processing helix chain 'A' and resid 1229 through 1233 Processing helix chain 'A' and resid 1252 through 1259 removed outlier: 3.512A pdb=" N GLN A1259 " --> pdb=" O GLN A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1269 Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 413 removed outlier: 6.789A pdb=" N LYS A 407 " --> pdb=" O HIS A 394 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N HIS A 394 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU A 409 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A 393 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP A 444 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 466 through 469 removed outlier: 6.489A pdb=" N GLY A 467 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ASP A 551 " --> pdb=" O GLY A 467 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 469 " --> pdb=" O ASP A 551 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 548 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE A 581 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A 550 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU A 604 " --> pdb=" O GLY A 596 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP A 598 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1049 through 1056 removed outlier: 6.881A pdb=" N GLN A1050 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A1037 " --> pdb=" O GLN A1050 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU A1052 " --> pdb=" O GLY A1035 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL A1036 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA A1087 " --> pdb=" O VAL A1036 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1109 through 1112 removed outlier: 6.384A pdb=" N GLY A1110 " --> pdb=" O LEU A1194 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASP A1196 " --> pdb=" O GLY A1110 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A1112 " --> pdb=" O ASP A1196 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU A1193 " --> pdb=" O ILE A1224 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE A1226 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU A1195 " --> pdb=" O ILE A1226 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU A1062 " --> pdb=" O VAL A1225 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N THR A1061 " --> pdb=" O LEU A1238 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL A1240 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ALA A1063 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE A1242 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A1065 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A1249 " --> pdb=" O VAL A1241 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLN A1243 " --> pdb=" O VAL A1247 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL A1247 " --> pdb=" O GLN A1243 " (cutoff:3.500A) 631 hydrogen bonds defined for protein. 1851 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: 3.50 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1509 1.28 - 1.42: 2367 1.42 - 1.55: 5560 1.55 - 1.69: 21 1.69 - 1.82: 61 Bond restraints: 9518 Sorted by residual: bond pdb=" C LEU A 48 " pdb=" O LEU A 48 " ideal model delta sigma weight residual 1.236 1.146 0.090 1.29e-02 6.01e+03 4.89e+01 bond pdb=" C HIS A 932 " pdb=" O HIS A 932 " ideal model delta sigma weight residual 1.237 1.158 0.079 1.19e-02 7.06e+03 4.37e+01 bond pdb=" C MET A 928 " pdb=" O MET A 928 " ideal model delta sigma weight residual 1.236 1.157 0.080 1.26e-02 6.30e+03 3.99e+01 bond pdb=" C LEU A 134 " pdb=" O LEU A 134 " ideal model delta sigma weight residual 1.237 1.166 0.070 1.19e-02 7.06e+03 3.47e+01 bond pdb=" CA ALA A 943 " pdb=" CB ALA A 943 " ideal model delta sigma weight residual 1.531 1.446 0.085 1.59e-02 3.96e+03 2.84e+01 ... (remaining 9513 not shown) Histogram of bond angle deviations from ideal: 95.96 - 104.76: 150 104.76 - 113.56: 5413 113.56 - 122.36: 6288 122.36 - 131.16: 1037 131.16 - 139.96: 25 Bond angle restraints: 12913 Sorted by residual: angle pdb=" N ILE A 127 " pdb=" CA ILE A 127 " pdb=" C ILE A 127 " ideal model delta sigma weight residual 111.00 101.28 9.72 1.09e+00 8.42e-01 7.95e+01 angle pdb=" N SER A 88 " pdb=" CA SER A 88 " pdb=" C SER A 88 " ideal model delta sigma weight residual 111.07 103.21 7.86 1.07e+00 8.73e-01 5.40e+01 angle pdb=" N MET A 91 " pdb=" CA MET A 91 " pdb=" C MET A 91 " ideal model delta sigma weight residual 111.54 101.60 9.94 1.36e+00 5.41e-01 5.34e+01 angle pdb=" O2B ATP A2001 " pdb=" PB ATP A2001 " pdb=" O3B ATP A2001 " ideal model delta sigma weight residual 106.94 119.22 -12.28 1.88e+00 2.83e-01 4.27e+01 angle pdb=" C ARG A 954 " pdb=" CA ARG A 954 " pdb=" CB ARG A 954 " ideal model delta sigma weight residual 110.85 100.62 10.23 1.70e+00 3.46e-01 3.62e+01 ... (remaining 12908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.49: 5554 23.49 - 46.98: 305 46.98 - 70.47: 54 70.47 - 93.96: 19 93.96 - 117.44: 3 Dihedral angle restraints: 5935 sinusoidal: 2567 harmonic: 3368 Sorted by residual: dihedral pdb=" C ARG A 954 " pdb=" N ARG A 954 " pdb=" CA ARG A 954 " pdb=" CB ARG A 954 " ideal model delta harmonic sigma weight residual -122.60 -107.79 -14.81 0 2.50e+00 1.60e-01 3.51e+01 dihedral pdb=" C ILE A 860 " pdb=" N ILE A 860 " pdb=" CA ILE A 860 " pdb=" CB ILE A 860 " ideal model delta harmonic sigma weight residual -122.00 -134.06 12.06 0 2.50e+00 1.60e-01 2.33e+01 dihedral pdb=" C TYR A 946 " pdb=" N TYR A 946 " pdb=" CA TYR A 946 " pdb=" CB TYR A 946 " ideal model delta harmonic sigma weight residual -122.60 -134.22 11.62 0 2.50e+00 1.60e-01 2.16e+01 ... (remaining 5932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1328 0.075 - 0.151: 134 0.151 - 0.226: 18 0.226 - 0.302: 6 0.302 - 0.377: 4 Chirality restraints: 1490 Sorted by residual: chirality pdb=" CA TYR A 946 " pdb=" N TYR A 946 " pdb=" C TYR A 946 " pdb=" CB TYR A 946 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CA ARG A 954 " pdb=" N ARG A 954 " pdb=" C ARG A 954 " pdb=" CB ARG A 954 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA ILE A 860 " pdb=" N ILE A 860 " pdb=" C ILE A 860 " pdb=" CB ILE A 860 " both_signs ideal model delta sigma weight residual False 2.43 2.11 0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 1487 not shown) Planarity restraints: 1606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 858 " -0.023 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C LEU A 858 " 0.081 2.00e-02 2.50e+03 pdb=" O LEU A 858 " -0.030 2.00e-02 2.50e+03 pdb=" N ALA A 859 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 860 " -0.021 2.00e-02 2.50e+03 4.26e-02 1.81e+01 pdb=" C ILE A 860 " 0.074 2.00e-02 2.50e+03 pdb=" O ILE A 860 " -0.027 2.00e-02 2.50e+03 pdb=" N VAL A 861 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 79 " -0.018 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C ALA A 79 " 0.064 2.00e-02 2.50e+03 pdb=" O ALA A 79 " -0.024 2.00e-02 2.50e+03 pdb=" N SER A 80 " -0.022 2.00e-02 2.50e+03 ... (remaining 1603 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 73 2.59 - 3.16: 8192 3.16 - 3.74: 15320 3.74 - 4.32: 21459 4.32 - 4.90: 34768 Nonbonded interactions: 79812 Sorted by model distance: nonbonded pdb=" OG SER A 430 " pdb="MG MG A2002 " model vdw 2.008 2.170 nonbonded pdb="MG MG A2004 " pdb=" O HOH A2102 " model vdw 2.053 2.170 nonbonded pdb="MG MG A2002 " pdb=" O HOH A2101 " model vdw 2.061 2.170 nonbonded pdb="MG MG A2002 " pdb=" O HOH A2103 " model vdw 2.063 2.170 nonbonded pdb=" OG SER A1073 " pdb="MG MG A2004 " model vdw 2.076 2.170 ... (remaining 79807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.930 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: 5.160 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.200 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 9518 Z= 0.393 Angle : 0.861 15.278 12913 Z= 0.554 Chirality : 0.053 0.377 1490 Planarity : 0.005 0.047 1606 Dihedral : 15.323 117.445 3777 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.10 % Allowed : 0.94 % Favored : 98.95 % Cbeta Deviations : 0.56 % 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: 1.26 (0.24), residues: 1172 helix: 1.29 (0.18), residues: 791 sheet: 0.48 (0.63), residues: 70 loop : -0.05 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 228 HIS 0.008 0.001 HIS A 932 PHE 0.041 0.002 PHE A 974 TYR 0.023 0.002 TYR A 958 ARG 0.007 0.000 ARG A 954 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 1.036 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 1.5434 time to fit residues: 238.8927 Evaluate side-chains 121 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.258 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 35 optimal weight: 0.0000 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN A 392 ASN A 404 GLN A 452 GLN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1030 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9518 Z= 0.168 Angle : 0.549 9.680 12913 Z= 0.286 Chirality : 0.040 0.155 1490 Planarity : 0.003 0.033 1606 Dihedral : 11.328 87.505 1685 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.20 % Allowed : 8.81 % Favored : 88.98 % 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 (0.24), residues: 1172 helix: 1.80 (0.18), residues: 788 sheet: 0.54 (0.64), residues: 70 loop : -0.17 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.003 0.001 HIS A 608 PHE 0.028 0.002 PHE A 332 TYR 0.016 0.001 TYR A 506 ARG 0.003 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 1.115 Fit side-chains outliers start: 21 outliers final: 4 residues processed: 129 average time/residue: 1.5361 time to fit residues: 210.2760 Evaluate side-chains 119 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.1721 time to fit residues: 2.0160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 5.9990 chunk 33 optimal weight: 0.0170 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 95 optimal weight: 0.0000 chunk 106 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 overall best weight: 0.4622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 GLN ** A1003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9518 Z= 0.145 Angle : 0.503 9.327 12913 Z= 0.261 Chirality : 0.038 0.153 1490 Planarity : 0.003 0.030 1606 Dihedral : 10.522 89.066 1685 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.96 % Favored : 97.95 % Rotamer: Outliers : 2.10 % Allowed : 11.23 % Favored : 86.67 % 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: 1.92 (0.24), residues: 1172 helix: 1.93 (0.18), residues: 792 sheet: 0.67 (0.64), residues: 70 loop : -0.25 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 228 HIS 0.004 0.001 HIS A1003 PHE 0.016 0.001 PHE A 508 TYR 0.010 0.001 TYR A 312 ARG 0.003 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 1.124 Fit side-chains outliers start: 20 outliers final: 5 residues processed: 132 average time/residue: 1.4907 time to fit residues: 209.1227 Evaluate side-chains 118 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 1.104 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.1639 time to fit residues: 1.9844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 0.0030 chunk 72 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 GLN ** A1003 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1030 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9518 Z= 0.204 Angle : 0.515 7.500 12913 Z= 0.271 Chirality : 0.040 0.169 1490 Planarity : 0.003 0.030 1606 Dihedral : 10.276 88.963 1685 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.79 % Favored : 98.12 % Rotamer: Outliers : 2.41 % Allowed : 12.59 % Favored : 84.99 % 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: 1.77 (0.24), residues: 1172 helix: 1.75 (0.18), residues: 800 sheet: 0.71 (0.64), residues: 70 loop : -0.15 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 228 HIS 0.004 0.001 HIS A1151 PHE 0.023 0.002 PHE A 763 TYR 0.012 0.001 TYR A 312 ARG 0.002 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.246 Fit side-chains outliers start: 23 outliers final: 8 residues processed: 131 average time/residue: 1.5365 time to fit residues: 213.4371 Evaluate side-chains 124 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 5 average time/residue: 0.3396 time to fit residues: 3.4650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN A 404 GLN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1003 HIS A1030 ASN A1099 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9518 Z= 0.205 Angle : 0.511 7.346 12913 Z= 0.269 Chirality : 0.040 0.156 1490 Planarity : 0.003 0.030 1606 Dihedral : 10.113 87.661 1685 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.13 % Favored : 97.78 % Rotamer: Outliers : 3.25 % Allowed : 13.12 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.24), residues: 1172 helix: 1.71 (0.18), residues: 798 sheet: 0.73 (0.64), residues: 70 loop : -0.18 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.004 0.001 HIS A1003 PHE 0.023 0.002 PHE A 508 TYR 0.010 0.001 TYR A 849 ARG 0.002 0.000 ARG A 785 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 1.087 Fit side-chains outliers start: 31 outliers final: 7 residues processed: 139 average time/residue: 1.3602 time to fit residues: 201.9492 Evaluate side-chains 125 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.1823 time to fit residues: 2.5245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 404 GLN A 452 GLN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1030 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9518 Z= 0.278 Angle : 0.563 7.424 12913 Z= 0.296 Chirality : 0.042 0.174 1490 Planarity : 0.004 0.035 1606 Dihedral : 10.337 87.876 1685 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.30 % Favored : 97.61 % Rotamer: Outliers : 2.83 % Allowed : 13.96 % Favored : 83.21 % 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: 1.49 (0.24), residues: 1172 helix: 1.53 (0.18), residues: 798 sheet: 0.70 (0.64), residues: 70 loop : -0.26 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 228 HIS 0.005 0.001 HIS A1151 PHE 0.026 0.002 PHE A 508 TYR 0.014 0.002 TYR A 849 ARG 0.005 0.000 ARG A 954 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 0.937 Fit side-chains outliers start: 27 outliers final: 10 residues processed: 139 average time/residue: 1.3104 time to fit residues: 194.8261 Evaluate side-chains 128 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 0.953 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 0.3951 time to fit residues: 3.3347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 0.3980 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN A 452 GLN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1030 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9518 Z= 0.164 Angle : 0.514 8.565 12913 Z= 0.267 Chirality : 0.039 0.203 1490 Planarity : 0.003 0.030 1606 Dihedral : 10.171 87.619 1685 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.22 % Favored : 97.70 % Rotamer: Outliers : 2.20 % Allowed : 16.16 % Favored : 81.64 % 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: 1.76 (0.24), residues: 1172 helix: 1.78 (0.18), residues: 796 sheet: 0.69 (0.64), residues: 70 loop : -0.25 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 228 HIS 0.003 0.001 HIS A 141 PHE 0.020 0.001 PHE A 332 TYR 0.012 0.001 TYR A 110 ARG 0.003 0.000 ARG A 954 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.166 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 132 average time/residue: 1.4070 time to fit residues: 198.2063 Evaluate side-chains 130 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 1.085 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.3514 time to fit residues: 3.6988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 72 optimal weight: 0.0980 chunk 77 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 89 optimal weight: 0.0030 chunk 103 optimal weight: 4.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN A 452 GLN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9518 Z= 0.143 Angle : 0.490 8.181 12913 Z= 0.256 Chirality : 0.038 0.185 1490 Planarity : 0.003 0.031 1606 Dihedral : 9.864 89.224 1685 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.22 % Favored : 97.70 % Rotamer: Outliers : 1.89 % Allowed : 16.47 % Favored : 81.64 % 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: 1.79 (0.24), residues: 1172 helix: 1.83 (0.18), residues: 802 sheet: 0.73 (0.64), residues: 70 loop : -0.39 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 228 HIS 0.003 0.001 HIS A 608 PHE 0.019 0.001 PHE A 332 TYR 0.011 0.001 TYR A 312 ARG 0.003 0.000 ARG A 613 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 1.083 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 126 average time/residue: 1.4574 time to fit residues: 195.6239 Evaluate side-chains 127 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 0.1898 time to fit residues: 2.6164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9980 chunk 99 optimal weight: 0.0570 chunk 105 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 0.0170 chunk 100 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN A 452 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9518 Z= 0.152 Angle : 0.488 8.001 12913 Z= 0.256 Chirality : 0.038 0.182 1490 Planarity : 0.003 0.031 1606 Dihedral : 9.765 88.663 1685 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.13 % Favored : 97.78 % Rotamer: Outliers : 1.36 % Allowed : 17.31 % Favored : 81.32 % 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: 1.86 (0.24), residues: 1172 helix: 1.87 (0.18), residues: 803 sheet: 0.79 (0.64), residues: 70 loop : -0.35 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 228 HIS 0.003 0.001 HIS A 141 PHE 0.023 0.001 PHE A 332 TYR 0.018 0.001 TYR A 506 ARG 0.002 0.000 ARG A 785 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 0.991 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 124 average time/residue: 1.4101 time to fit residues: 186.6751 Evaluate side-chains 123 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 1.127 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.1808 time to fit residues: 2.3240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN A 452 GLN A1030 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9518 Z= 0.232 Angle : 0.553 11.507 12913 Z= 0.288 Chirality : 0.041 0.268 1490 Planarity : 0.004 0.031 1606 Dihedral : 10.036 87.430 1685 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.39 % Favored : 97.53 % Rotamer: Outliers : 1.15 % Allowed : 17.84 % Favored : 81.01 % 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: 1.59 (0.24), residues: 1172 helix: 1.64 (0.18), residues: 802 sheet: 0.74 (0.64), residues: 70 loop : -0.35 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 228 HIS 0.004 0.001 HIS A1151 PHE 0.024 0.002 PHE A 508 TYR 0.016 0.002 TYR A 312 ARG 0.003 0.000 ARG A 785 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 1.134 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 125 average time/residue: 1.4531 time to fit residues: 193.6941 Evaluate side-chains 124 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 1.175 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.4572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.178298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.126238 restraints weight = 8620.158| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.67 r_work: 0.3237 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9518 Z= 0.252 Angle : 0.559 8.683 12913 Z= 0.293 Chirality : 0.041 0.239 1490 Planarity : 0.004 0.031 1606 Dihedral : 10.063 87.857 1685 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.39 % Favored : 97.53 % Rotamer: Outliers : 1.57 % Allowed : 17.63 % Favored : 80.80 % 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: 1.44 (0.24), residues: 1172 helix: 1.51 (0.18), residues: 803 sheet: 0.63 (0.64), residues: 70 loop : -0.37 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 228 HIS 0.004 0.001 HIS A1151 PHE 0.030 0.002 PHE A 332 TYR 0.021 0.002 TYR A 506 ARG 0.003 0.000 ARG A 785 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3923.90 seconds wall clock time: 70 minutes 10.66 seconds (4210.66 seconds total)