Starting phenix.real_space_refine (version: dev) on Thu Feb 23 16:12:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rmg_4936/02_2023/6rmg_4936_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rmg_4936/02_2023/6rmg_4936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rmg_4936/02_2023/6rmg_4936.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rmg_4936/02_2023/6rmg_4936.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rmg_4936/02_2023/6rmg_4936_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rmg_4936/02_2023/6rmg_4936_trim.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 784 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 85": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 138": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 144": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 255": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 441": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 602": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 824": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 893": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 960": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 982": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 1113": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1114": not complete - not flipped Residue "B ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 19137 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 16284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 16284 Classifications: {'peptide': 1026} Link IDs: {'CIS': 2, 'PTRANS': 45, 'TRANS': 978} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 2369 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 455 Unusual residues: {'NAG': 5, 'Y01': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.14, per 1000 atoms: 0.48 Number of scatterers: 19137 At special positions: 0 Unit cell: (91.9933, 126.186, 140.025, 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) Zn 1 29.99 S 50 16.00 O 1761 8.00 N 1556 7.00 C 6442 6.00 H 9327 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 327 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 304 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A1801 " - " ASN A 312 " " NAG A1802 " - " ASN A 349 " " NAG A1803 " - " ASN A 414 " " NAG A1804 " - " ASN A 875 " " NAG A1807 " - " ASN A 141 " " NAG C 1 " - " ASN A1000 " Time building additional restraints: 15.88 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" NE2 HIS B 140 " pdb="ZN ZN B 201 " - pdb=" ND1 HIS B 182 " 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2204 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 6 sheets defined 58.7% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.589A pdb=" N ALA A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 97 removed outlier: 3.730A pdb=" N LEU A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 114 Processing helix chain 'A' and resid 115 through 119 removed outlier: 3.895A pdb=" N ALA A 118 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.803A pdb=" N TRP A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 147 Processing helix chain 'A' and resid 171 through 187 Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.812A pdb=" N LEU A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 235 through 242 Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.698A pdb=" N PHE A 259 " --> pdb=" O TRP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.529A pdb=" N ILE A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 289 through 294 removed outlier: 3.780A pdb=" N ASP A 293 " --> pdb=" O HIS A 289 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 289 through 294' Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 388 through 409 removed outlier: 4.018A pdb=" N ALA A 392 " --> pdb=" O ASN A 388 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 438 through 458 Processing helix chain 'A' and resid 466 through 491 removed outlier: 3.636A pdb=" N LEU A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 514 through 524 removed outlier: 3.827A pdb=" N LEU A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 544 removed outlier: 3.612A pdb=" N GLU A 539 " --> pdb=" O ASP A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 554 removed outlier: 3.581A pdb=" N ALA A 549 " --> pdb=" O GLY A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 562 Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'A' and resid 575 through 591 removed outlier: 3.583A pdb=" N LEU A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 605 Processing helix chain 'A' and resid 731 through 739 Processing helix chain 'A' and resid 740 through 745 removed outlier: 3.644A pdb=" N LEU A 744 " --> pdb=" O TYR A 740 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 745 " --> pdb=" O ALA A 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 740 through 745' Processing helix chain 'A' and resid 746 through 770 removed outlier: 4.369A pdb=" N LEU A 761 " --> pdb=" O PHE A 757 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 769 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 770 " --> pdb=" O TYR A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 797 Processing helix chain 'A' and resid 811 through 814 Processing helix chain 'A' and resid 815 through 826 Processing helix chain 'A' and resid 827 through 829 No H-bonds generated for 'chain 'A' and resid 827 through 829' Processing helix chain 'A' and resid 843 through 864 removed outlier: 3.742A pdb=" N GLU A 864 " --> pdb=" O ASP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 888 removed outlier: 3.735A pdb=" N ALA A 883 " --> pdb=" O ASP A 879 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 888 " --> pdb=" O TYR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 902 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.501A pdb=" N GLY A 912 " --> pdb=" O ASP A 909 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE A 913 " --> pdb=" O ALA A 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 909 through 913' Processing helix chain 'A' and resid 918 through 930 Processing helix chain 'A' and resid 930 through 937 Processing helix chain 'A' and resid 983 through 1005 removed outlier: 3.648A pdb=" N LEU A1004 " --> pdb=" O ASN A1000 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A1005 " --> pdb=" O TYR A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1017 removed outlier: 3.502A pdb=" N LEU A1016 " --> pdb=" O GLY A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1020 No H-bonds generated for 'chain 'A' and resid 1018 through 1020' Processing helix chain 'A' and resid 1023 through 1048 removed outlier: 3.645A pdb=" N SER A1033 " --> pdb=" O LEU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1075 removed outlier: 3.545A pdb=" N GLY A1075 " --> pdb=" O MET A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1103 removed outlier: 3.639A pdb=" N VAL A1084 " --> pdb=" O ALA A1080 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLU A1095 " --> pdb=" O GLY A1091 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE A1096 " --> pdb=" O ILE A1092 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS A1099 " --> pdb=" O GLU A1095 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL A1100 " --> pdb=" O PHE A1096 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA A1101 " --> pdb=" O THR A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1121 removed outlier: 3.602A pdb=" N HIS A1121 " --> pdb=" O LEU A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1138 Processing helix chain 'A' and resid 1139 through 1141 No H-bonds generated for 'chain 'A' and resid 1139 through 1141' Processing helix chain 'A' and resid 1152 through 1168 Processing helix chain 'A' and resid 1169 through 1178 removed outlier: 3.925A pdb=" N VAL A1173 " --> pdb=" O VAL A1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 99 through 114 Processing helix chain 'B' and resid 138 through 143 removed outlier: 4.135A pdb=" N GLU B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 156 No H-bonds generated for 'chain 'B' and resid 154 through 156' Processing helix chain 'B' and resid 157 through 169 Processing sheet with id=AA1, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA3, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 349 removed outlier: 7.199A pdb=" N VAL A 347 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 972 through 978 removed outlier: 3.661A pdb=" N ALA A 972 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A 803 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 804 " --> pdb=" O ASN A1011 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER A1007 " --> pdb=" O GLN A 808 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 86 removed outlier: 6.844A pdb=" N ASP B 147 " --> pdb=" O THR B 125 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1332 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: 6.74 Time building geometry restraints manager: 16.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9311 1.03 - 1.22: 29 1.22 - 1.42: 4095 1.42 - 1.61: 5854 1.61 - 1.81: 109 Bond restraints: 19398 Sorted by residual: bond pdb=" CAE Y01 A1814 " pdb=" CBI Y01 A1814 " ideal model delta sigma weight residual 1.532 1.673 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" CAE Y01 A1813 " pdb=" CBI Y01 A1813 " ideal model delta sigma weight residual 1.532 1.666 -0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" CAE Y01 A1817 " pdb=" CBI Y01 A1817 " ideal model delta sigma weight residual 1.532 1.664 -0.132 2.00e-02 2.50e+03 4.34e+01 bond pdb=" CAE Y01 A1811 " pdb=" CBI Y01 A1811 " ideal model delta sigma weight residual 1.532 1.663 -0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" CAV Y01 A1817 " pdb=" CBC Y01 A1817 " ideal model delta sigma weight residual 1.523 1.645 -0.122 2.00e-02 2.50e+03 3.70e+01 ... (remaining 19393 not shown) Histogram of bond angle deviations from ideal: 90.20 - 98.97: 36 98.97 - 107.73: 2712 107.73 - 116.50: 22130 116.50 - 125.26: 9503 125.26 - 134.03: 531 Bond angle restraints: 34912 Sorted by residual: angle pdb=" CAM Y01 A1813 " pdb=" CAY Y01 A1813 " pdb=" OAW Y01 A1813 " ideal model delta sigma weight residual 111.19 127.49 -16.30 3.00e+00 1.11e-01 2.95e+01 angle pdb=" CAM Y01 A1818 " pdb=" CAY Y01 A1818 " pdb=" OAW Y01 A1818 " ideal model delta sigma weight residual 111.19 127.48 -16.29 3.00e+00 1.11e-01 2.95e+01 angle pdb=" CAM Y01 A1808 " pdb=" CAY Y01 A1808 " pdb=" OAW Y01 A1808 " ideal model delta sigma weight residual 111.19 127.43 -16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" CAM Y01 A1809 " pdb=" CAY Y01 A1809 " pdb=" OAW Y01 A1809 " ideal model delta sigma weight residual 111.19 127.35 -16.16 3.00e+00 1.11e-01 2.90e+01 angle pdb=" CAM Y01 A1810 " pdb=" CAY Y01 A1810 " pdb=" OAW Y01 A1810 " ideal model delta sigma weight residual 111.19 127.33 -16.14 3.00e+00 1.11e-01 2.90e+01 ... (remaining 34907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 7707 35.97 - 71.94: 66 71.94 - 107.92: 9 107.92 - 143.89: 0 143.89 - 179.86: 1 Dihedral angle restraints: 7783 sinusoidal: 3636 harmonic: 4147 Sorted by residual: dihedral pdb=" CD ARG A1114 " pdb=" NE ARG A1114 " pdb=" CZ ARG A1114 " pdb=" NH1 ARG A1114 " ideal model delta sinusoidal sigma weight residual 0.00 179.86 -179.86 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA ALA A 75 " pdb=" C ALA A 75 " pdb=" N PRO A 76 " pdb=" CA PRO A 76 " ideal model delta harmonic sigma weight residual 180.00 136.27 43.73 0 5.00e+00 4.00e-02 7.65e+01 dihedral pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " pdb=" SG CYS A 304 " pdb=" CB CYS A 304 " ideal model delta sinusoidal sigma weight residual 93.00 168.12 -75.12 1 1.00e+01 1.00e-02 7.14e+01 ... (remaining 7780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1472 0.103 - 0.206: 76 0.206 - 0.308: 10 0.308 - 0.411: 13 0.411 - 0.514: 11 Chirality restraints: 1582 Sorted by residual: chirality pdb=" CBG Y01 A1816 " pdb=" CAQ Y01 A1816 " pdb=" CBD Y01 A1816 " pdb=" CBI Y01 A1816 " both_signs ideal model delta sigma weight residual False -2.33 -2.85 0.51 2.00e-01 2.50e+01 6.60e+00 chirality pdb=" CBG Y01 A1813 " pdb=" CAQ Y01 A1813 " pdb=" CBD Y01 A1813 " pdb=" CBI Y01 A1813 " both_signs ideal model delta sigma weight residual False -2.33 -2.84 0.51 2.00e-01 2.50e+01 6.49e+00 chirality pdb=" CBG Y01 A1810 " pdb=" CAQ Y01 A1810 " pdb=" CBD Y01 A1810 " pdb=" CBI Y01 A1810 " both_signs ideal model delta sigma weight residual False -2.33 -2.83 0.50 2.00e-01 2.50e+01 6.33e+00 ... (remaining 1579 not shown) Planarity restraints: 2799 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 310 " 0.237 2.00e-02 2.50e+03 3.16e-01 1.50e+03 pdb=" CG ASN A 310 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 310 " -0.231 2.00e-02 2.50e+03 pdb=" ND2 ASN A 310 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 310 " -0.486 2.00e-02 2.50e+03 pdb="HD22 ASN A 310 " 0.504 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 915 " 0.216 2.00e-02 2.50e+03 2.66e-01 1.06e+03 pdb=" CG ASN A 915 " -0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN A 915 " -0.215 2.00e-02 2.50e+03 pdb=" ND2 ASN A 915 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN A 915 " -0.408 2.00e-02 2.50e+03 pdb="HD22 ASN A 915 " 0.407 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 417 " -0.186 2.00e-02 2.50e+03 2.08e-01 6.46e+02 pdb=" CD GLN A 417 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLN A 417 " 0.171 2.00e-02 2.50e+03 pdb=" NE2 GLN A 417 " 0.003 2.00e-02 2.50e+03 pdb="HE21 GLN A 417 " 0.307 2.00e-02 2.50e+03 pdb="HE22 GLN A 417 " -0.317 2.00e-02 2.50e+03 ... (remaining 2796 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 1913 2.25 - 2.84: 42325 2.84 - 3.42: 48394 3.42 - 4.01: 65874 4.01 - 4.60: 102270 Nonbonded interactions: 260776 Sorted by model distance: nonbonded pdb=" HE2 HIS A 178 " pdb=" OG1 THR A 362 " model vdw 1.661 1.850 nonbonded pdb=" O ALA A 412 " pdb=" H SER A 415 " model vdw 1.686 1.850 nonbonded pdb=" O THR B 55 " pdb=" H GLY B 60 " model vdw 1.697 1.850 nonbonded pdb="HH21 ARG A 135 " pdb=" OE2 GLU A1019 " model vdw 1.699 1.850 nonbonded pdb=" O THR B 40 " pdb=" HE ARG B 163 " model vdw 1.713 1.850 ... (remaining 260771 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 50 5.16 5 C 6442 2.51 5 N 1556 2.21 5 O 1761 1.98 5 H 9327 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.290 Extract box with map and model: 6.910 Check model and map are aligned: 0.290 Process input model: 64.530 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.170 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 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 : 0.011 0.141 10071 Z= 0.741 Angle : 1.444 16.299 13740 Z= 0.613 Chirality : 0.075 0.514 1582 Planarity : 0.006 0.081 1670 Dihedral : 11.907 179.859 3633 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.21), residues: 1170 helix: -2.64 (0.16), residues: 609 sheet: -2.58 (0.55), residues: 70 loop : -2.46 (0.27), residues: 491 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.6389 time to fit residues: 191.6559 Evaluate side-chains 118 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.451 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 91 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN A 872 ASN A 889 GLN ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 929 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 10071 Z= 0.199 Angle : 0.648 8.242 13740 Z= 0.330 Chirality : 0.039 0.176 1582 Planarity : 0.005 0.065 1670 Dihedral : 10.861 178.471 1462 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: -1.99 (0.24), residues: 1170 helix: -0.76 (0.19), residues: 618 sheet: -1.99 (0.61), residues: 67 loop : -1.86 (0.29), residues: 485 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 144 average time/residue: 0.4375 time to fit residues: 92.8301 Evaluate side-chains 116 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 1.505 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 6 average time/residue: 0.2232 time to fit residues: 4.5769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 408 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10071 Z= 0.202 Angle : 0.594 8.251 13740 Z= 0.303 Chirality : 0.039 0.175 1582 Planarity : 0.004 0.062 1670 Dihedral : 10.060 178.859 1462 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: -0.99 (0.25), residues: 1170 helix: 0.18 (0.21), residues: 622 sheet: -1.70 (0.62), residues: 67 loop : -1.56 (0.30), residues: 481 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 131 average time/residue: 0.4822 time to fit residues: 91.0595 Evaluate side-chains 118 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 1.639 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 12 average time/residue: 0.2812 time to fit residues: 8.0927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 10071 Z= 0.317 Angle : 0.625 8.707 13740 Z= 0.323 Chirality : 0.041 0.169 1582 Planarity : 0.004 0.063 1670 Dihedral : 10.153 178.983 1462 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: -0.80 (0.25), residues: 1170 helix: 0.37 (0.21), residues: 622 sheet: -1.65 (0.60), residues: 77 loop : -1.50 (0.30), residues: 471 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 120 average time/residue: 0.4547 time to fit residues: 80.7923 Evaluate side-chains 109 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 1.516 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2444 time to fit residues: 4.1116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A1121 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 10071 Z= 0.235 Angle : 0.588 8.512 13740 Z= 0.301 Chirality : 0.039 0.163 1582 Planarity : 0.004 0.063 1670 Dihedral : 9.936 179.500 1462 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: -0.44 (0.26), residues: 1170 helix: 0.71 (0.22), residues: 621 sheet: -1.29 (0.64), residues: 67 loop : -1.47 (0.30), residues: 482 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 112 average time/residue: 0.4383 time to fit residues: 73.1030 Evaluate side-chains 109 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 1.558 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.2707 time to fit residues: 4.3700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 109 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 10071 Z= 0.213 Angle : 0.573 8.426 13740 Z= 0.292 Chirality : 0.038 0.162 1582 Planarity : 0.004 0.060 1670 Dihedral : 9.764 179.885 1462 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: -0.21 (0.26), residues: 1170 helix: 0.91 (0.22), residues: 622 sheet: -1.14 (0.66), residues: 67 loop : -1.37 (0.30), residues: 481 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 115 average time/residue: 0.4301 time to fit residues: 73.0018 Evaluate side-chains 108 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 1.521 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.2413 time to fit residues: 3.1579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10071 Z= 0.186 Angle : 0.562 8.207 13740 Z= 0.284 Chirality : 0.038 0.159 1582 Planarity : 0.004 0.058 1670 Dihedral : 9.614 179.796 1462 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: -0.00 (0.26), residues: 1170 helix: 1.10 (0.22), residues: 621 sheet: -1.02 (0.67), residues: 67 loop : -1.31 (0.30), residues: 482 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 111 average time/residue: 0.4506 time to fit residues: 73.8394 Evaluate side-chains 106 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 1.516 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2445 time to fit residues: 3.9660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 10071 Z= 0.218 Angle : 0.568 8.270 13740 Z= 0.289 Chirality : 0.038 0.161 1582 Planarity : 0.004 0.056 1670 Dihedral : 9.550 179.260 1462 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1170 helix: 1.20 (0.22), residues: 621 sheet: -1.02 (0.67), residues: 67 loop : -1.28 (0.30), residues: 482 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 109 average time/residue: 0.4266 time to fit residues: 68.9836 Evaluate side-chains 103 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 1.510 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2543 time to fit residues: 2.7641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 10071 Z= 0.326 Angle : 0.631 10.333 13740 Z= 0.322 Chirality : 0.041 0.173 1582 Planarity : 0.004 0.058 1670 Dihedral : 9.764 178.762 1462 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: 0.02 (0.26), residues: 1170 helix: 1.13 (0.22), residues: 620 sheet: -1.15 (0.65), residues: 67 loop : -1.29 (0.30), residues: 483 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 113 average time/residue: 0.4347 time to fit residues: 73.1326 Evaluate side-chains 105 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 1.444 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2359 time to fit residues: 3.7035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 52 optimal weight: 0.0970 chunk 77 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 10071 Z= 0.165 Angle : 0.567 8.103 13740 Z= 0.286 Chirality : 0.038 0.175 1582 Planarity : 0.004 0.056 1670 Dihedral : 9.525 179.057 1462 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: 0.30 (0.26), residues: 1170 helix: 1.35 (0.22), residues: 624 sheet: -1.05 (0.66), residues: 67 loop : -1.16 (0.31), residues: 479 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 738 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.4300 time to fit residues: 68.5409 Evaluate side-chains 100 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.430 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 95 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A1121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.113131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.090607 restraints weight = 48285.620| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.60 r_work: 0.3006 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 10071 Z= 0.165 Angle : 0.555 8.047 13740 Z= 0.280 Chirality : 0.038 0.177 1582 Planarity : 0.004 0.053 1670 Dihedral : 9.337 178.230 1462 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 2.00 % 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: 0.45 (0.26), residues: 1170 helix: 1.52 (0.22), residues: 622 sheet: -1.01 (0.66), residues: 67 loop : -1.15 (0.30), residues: 481 =============================================================================== Job complete usr+sys time: 4284.90 seconds wall clock time: 76 minutes 31.99 seconds (4591.99 seconds total)