Starting phenix.real_space_refine (version: dev) on Mon Feb 20 09:48:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py4_13711/02_2023/7py4_13711.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py4_13711/02_2023/7py4_13711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py4_13711/02_2023/7py4_13711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py4_13711/02_2023/7py4_13711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py4_13711/02_2023/7py4_13711.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py4_13711/02_2023/7py4_13711.pdb" } resolution = 3.1 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= 1.000 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 Process input model Symmetric amino acids flipped Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 304": "OD1" <-> "OD2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 509": "OD1" <-> "OD2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A ASP 540": "OD1" <-> "OD2" Residue "A TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 599": "OD1" <-> "OD2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A GLU 668": "OE1" <-> "OE2" Residue "A GLU 716": "OE1" <-> "OE2" Residue "A ASP 725": "OD1" <-> "OD2" Residue "A GLU 914": "OE1" <-> "OE2" Residue "A PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1176": "OD1" <-> "OD2" Residue "A ASP 1219": "OD1" <-> "OD2" Residue "B ASP 146": "OD1" <-> "OD2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B GLU 277": "OE1" <-> "OE2" Residue "B TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11835 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8989 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 28, 'TRANS': 1083} Chain breaks: 4 Chain: "B" Number of atoms: 2634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2634 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 301} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Unusual residues: {' MG': 1, 'BEF': 1, 'Y01': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.54, per 1000 atoms: 0.64 Number of scatterers: 11835 At special positions: 0 Unit cell: (81.18, 97.68, 180.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 55 16.00 Mg 1 11.99 F 3 9.00 O 2160 8.00 N 1966 7.00 C 7649 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 102 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.04 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=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 402 " - " ASN B 294 " " NAG B 403 " - " ASN B 107 " " NAG C 1 " - " ASN B 180 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.27 Conformation dependent library (CDL) restraints added in 1.9 seconds 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2714 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 10 sheets defined 48.8% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 107 through 118 Processing helix chain 'A' and resid 118 through 133 removed outlier: 3.877A pdb=" N LEU A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 174 removed outlier: 3.734A pdb=" N LEU A 145 " --> pdb=" O TRP A 141 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.740A pdb=" N VAL A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 252 through 259 removed outlier: 3.712A pdb=" N THR A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.501A pdb=" N THR A 317 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 366 removed outlier: 4.032A pdb=" N TYR A 335 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 397 removed outlier: 4.084A pdb=" N TRP A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 403 through 422 Processing helix chain 'A' and resid 442 through 448 removed outlier: 4.174A pdb=" N ILE A 448 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 519 removed outlier: 4.275A pdb=" N ILE A 513 " --> pdb=" O ASP A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 534 removed outlier: 4.032A pdb=" N ARG A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 565 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 635 through 649 Processing helix chain 'A' and resid 662 through 677 Processing helix chain 'A' and resid 682 through 695 removed outlier: 3.603A pdb=" N ILE A 694 " --> pdb=" O VAL A 690 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 695 " --> pdb=" O TYR A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 724 Processing helix chain 'A' and resid 735 through 746 Processing helix chain 'A' and resid 757 through 773 Processing helix chain 'A' and resid 803 through 810 Processing helix chain 'A' and resid 834 through 859 Processing helix chain 'A' and resid 869 through 885 Processing helix chain 'A' and resid 897 through 904 Processing helix chain 'A' and resid 928 through 930 No H-bonds generated for 'chain 'A' and resid 928 through 930' Processing helix chain 'A' and resid 931 through 938 removed outlier: 3.566A pdb=" N LEU A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 969 removed outlier: 3.698A pdb=" N PHE A 961 " --> pdb=" O LYS A 957 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR A 962 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 963 " --> pdb=" O PHE A 959 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL A 964 " --> pdb=" O ALA A 960 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N HIS A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE A 966 " --> pdb=" O THR A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 972 No H-bonds generated for 'chain 'A' and resid 970 through 972' Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 994 through 1003 removed outlier: 3.531A pdb=" N LEU A 998 " --> pdb=" O SER A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1014 removed outlier: 3.542A pdb=" N ARG A1014 " --> pdb=" O LYS A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1018 Processing helix chain 'A' and resid 1019 through 1024 Processing helix chain 'A' and resid 1031 through 1057 Proline residue: A1051 - end of helix removed outlier: 4.131A pdb=" N GLN A1057 " --> pdb=" O GLY A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1092 removed outlier: 3.787A pdb=" N GLY A1089 " --> pdb=" O ASN A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1118 removed outlier: 4.333A pdb=" N ILE A1107 " --> pdb=" O ILE A1103 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A1108 " --> pdb=" O PHE A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1126 Processing helix chain 'A' and resid 1134 through 1140 Processing helix chain 'A' and resid 1142 through 1171 Proline residue: A1159 - end of helix Processing helix chain 'A' and resid 1173 through 1181 Processing helix chain 'A' and resid 1182 through 1185 removed outlier: 3.722A pdb=" N LEU A1185 " --> pdb=" O ARG A1182 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1182 through 1185' Processing helix chain 'A' and resid 1216 through 1223 Processing helix chain 'B' and resid 46 through 74 removed outlier: 3.550A pdb=" N VAL B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Proline residue: B 52 - end of helix Proline residue: B 63 - end of helix Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.637A pdb=" N SER B 96 " --> pdb=" O LYS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 136 Processing helix chain 'B' and resid 141 through 145 Processing helix chain 'B' and resid 146 through 151 removed outlier: 3.786A pdb=" N LEU B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.622A pdb=" N CYS B 157 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 removed outlier: 3.579A pdb=" N ASN B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 222 through 227 removed outlier: 3.564A pdb=" N PHE B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 removed outlier: 3.679A pdb=" N LEU B 243 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP B 244 " --> pdb=" O TYR B 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 240 through 244' Processing helix chain 'B' and resid 254 through 262 removed outlier: 3.801A pdb=" N TRP B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 350 removed outlier: 3.806A pdb=" N GLY B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 67 removed outlier: 4.380A pdb=" N GLY A 277 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190 removed outlier: 11.898A pdb=" N THR A 177 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N LYS A 203 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A 179 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N PHE A 305 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N SER A 217 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N HIS A 307 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 240 removed outlier: 3.890A pdb=" N TYR A 225 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 426 through 427 removed outlier: 3.629A pdb=" N TYR A 427 " --> pdb=" O THR A 432 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 754 through 756 removed outlier: 6.062A pdb=" N THR A 754 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE A 800 " --> pdb=" O THR A 754 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYS A 756 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N THR A 802 " --> pdb=" O CYS A 756 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 862 " --> pdb=" O ARG A 797 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE A 728 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N CYS A 865 " --> pdb=" O ILE A 728 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 730 " --> pdb=" O CYS A 865 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A 451 " --> pdb=" O TRP A 729 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU A 731 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N SER A 453 " --> pdb=" O LEU A 731 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR A 450 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE A 891 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE A 452 " --> pdb=" O ILE A 891 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR A 888 " --> pdb=" O ILE A 906 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N VAL A 908 " --> pdb=" O THR A 888 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA A 890 " --> pdb=" O VAL A 908 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE A 910 " --> pdb=" O ALA A 890 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N GLY A 892 " --> pdb=" O ILE A 910 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A 926 " --> pdb=" O GLY A 909 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 474 through 476 removed outlier: 4.960A pdb=" N ILE A 463 " --> pdb=" O LYS A 709 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA A 705 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N CYS A 469 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA A 703 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE A 471 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N LEU A 701 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU A 656 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA A 703 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A 654 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA A 705 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ARG A 652 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE A 614 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG A 608 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL A 590 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 540 Processing sheet with id=AA8, first strand: chain 'A' and resid 567 through 572 removed outlier: 3.738A pdb=" N LEU A 570 " --> pdb=" O THR A 578 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR A 578 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 78 through 81 removed outlier: 5.733A pdb=" N TYR B 122 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU B 272 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU B 124 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ARG B 270 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 102 through 110 removed outlier: 4.134A pdb=" N CYS B 102 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B 295 " --> pdb=" O CYS B 104 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG B 290 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 182 " --> pdb=" O THR B 296 " (cutoff:3.500A) 541 hydrogen bonds defined for protein. 1536 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: 4.54 Time building geometry restraints manager: 5.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2282 1.33 - 1.45: 3007 1.45 - 1.57: 6743 1.57 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 12117 Sorted by residual: bond pdb=" CAX Y01 A1303 " pdb=" OAH Y01 A1303 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" CAX Y01 B 401 " pdb=" OAH Y01 B 401 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" CAX Y01 A1304 " pdb=" OAH Y01 A1304 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" CAX Y01 A1305 " pdb=" OAH Y01 A1305 " ideal model delta sigma weight residual 1.248 1.341 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" F2 BEF A1302 " pdb="BE BEF A1302 " ideal model delta sigma weight residual 1.476 1.559 -0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 12112 not shown) Histogram of bond angle deviations from ideal: 97.97 - 105.18: 183 105.18 - 112.38: 6150 112.38 - 119.59: 4039 119.59 - 126.80: 5910 126.80 - 134.01: 156 Bond angle restraints: 16438 Sorted by residual: angle pdb=" F2 BEF A1302 " pdb="BE BEF A1302 " pdb=" F3 BEF A1302 " ideal model delta sigma weight residual 119.96 107.72 12.24 3.00e+00 1.11e-01 1.67e+01 angle pdb=" F1 BEF A1302 " pdb="BE BEF A1302 " pdb=" F3 BEF A1302 " ideal model delta sigma weight residual 120.12 110.60 9.52 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CAM Y01 A1305 " pdb=" CAY Y01 A1305 " pdb=" OAW Y01 A1305 " ideal model delta sigma weight residual 111.19 120.15 -8.96 3.00e+00 1.11e-01 8.91e+00 angle pdb=" CAM Y01 A1304 " pdb=" CAY Y01 A1304 " pdb=" OAW Y01 A1304 " ideal model delta sigma weight residual 111.19 120.11 -8.92 3.00e+00 1.11e-01 8.84e+00 angle pdb=" CAM Y01 B 401 " pdb=" CAY Y01 B 401 " pdb=" OAW Y01 B 401 " ideal model delta sigma weight residual 111.19 119.88 -8.69 3.00e+00 1.11e-01 8.38e+00 ... (remaining 16433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.71: 6799 22.71 - 45.42: 331 45.42 - 68.13: 21 68.13 - 90.84: 8 90.84 - 113.55: 3 Dihedral angle restraints: 7162 sinusoidal: 2952 harmonic: 4210 Sorted by residual: dihedral pdb=" C2 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" C4 NAG C 1 " pdb=" C5 NAG C 1 " ideal model delta sinusoidal sigma weight residual 50.00 -63.55 113.55 1 2.00e+01 2.50e-03 3.36e+01 dihedral pdb=" C2 NAG B 402 " pdb=" C3 NAG B 402 " pdb=" C4 NAG B 402 " pdb=" C5 NAG B 402 " ideal model delta sinusoidal sigma weight residual 50.00 -55.74 105.74 1 2.00e+01 2.50e-03 3.05e+01 dihedral pdb=" C1 NAG C 1 " pdb=" C2 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" C4 NAG C 1 " ideal model delta sinusoidal sigma weight residual -50.00 40.93 -90.93 1 2.00e+01 2.50e-03 2.44e+01 ... (remaining 7159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1816 0.129 - 0.258: 20 0.258 - 0.387: 0 0.387 - 0.516: 4 0.516 - 0.644: 1 Chirality restraints: 1841 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN B 180 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" CBG Y01 B 401 " pdb=" CAQ Y01 B 401 " pdb=" CBD Y01 B 401 " pdb=" CBI Y01 B 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.76 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CBG Y01 A1305 " pdb=" CAQ Y01 A1305 " pdb=" CBD Y01 A1305 " pdb=" CBI Y01 A1305 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 1838 not shown) Planarity restraints: 2067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 108 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO A 109 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 169 " -0.033 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO B 170 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 170 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 170 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1184 " -0.150 9.50e-02 1.11e+02 6.74e-02 3.18e+00 pdb=" NE ARG A1184 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A1184 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A1184 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A1184 " -0.002 2.00e-02 2.50e+03 ... (remaining 2064 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 19 2.30 - 2.95: 5660 2.95 - 3.60: 16525 3.60 - 4.25: 26530 4.25 - 4.90: 46813 Nonbonded interactions: 95547 Sorted by model distance: nonbonded pdb=" OD2 ASP A 454 " pdb=" F3 BEF A1302 " model vdw 1.650 2.390 nonbonded pdb=" O LEU A 441 " pdb=" OH TYR A 924 " model vdw 1.963 2.440 nonbonded pdb=" O ASN B 298 " pdb=" O3 NAG C 1 " model vdw 1.964 2.440 nonbonded pdb=" O LEU A 445 " pdb=" OH TYR A1019 " model vdw 2.078 2.440 nonbonded pdb=" O THR A 456 " pdb="MG MG A1301 " model vdw 2.085 2.170 ... (remaining 95542 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 55 5.16 5 Be 1 3.05 5 C 7649 2.51 5 N 1966 2.21 5 O 2160 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 3.990 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: 15.860 Check model and map are aligned: 0.190 Process input model: 35.550 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 : 0.004 0.094 12117 Z= 0.225 Angle : 0.573 12.241 16438 Z= 0.269 Chirality : 0.050 0.644 1841 Planarity : 0.003 0.067 2064 Dihedral : 12.727 113.551 4439 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.23), residues: 1427 helix: 1.85 (0.23), residues: 607 sheet: 0.70 (0.37), residues: 202 loop : -0.82 (0.25), residues: 618 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 1.311 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 142 average time/residue: 0.2765 time to fit residues: 55.9551 Evaluate side-chains 117 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 1.369 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1122 time to fit residues: 2.2289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.9980 chunk 108 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 12117 Z= 0.324 Angle : 0.573 9.508 16438 Z= 0.300 Chirality : 0.047 0.586 1841 Planarity : 0.004 0.049 2064 Dihedral : 7.886 112.676 1662 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1427 helix: 1.52 (0.22), residues: 623 sheet: 0.79 (0.36), residues: 197 loop : -0.90 (0.25), residues: 607 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 1.477 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 135 average time/residue: 0.2572 time to fit residues: 50.9517 Evaluate side-chains 122 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 1.418 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1111 time to fit residues: 3.8603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 140 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 HIS A 848 GLN B 74 ASN B 152 ASN B 249 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 12117 Z= 0.222 Angle : 0.515 8.255 16438 Z= 0.270 Chirality : 0.045 0.582 1841 Planarity : 0.004 0.037 2064 Dihedral : 7.829 111.012 1662 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.23), residues: 1427 helix: 1.56 (0.22), residues: 632 sheet: 0.79 (0.36), residues: 201 loop : -0.91 (0.25), residues: 594 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 1.386 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 133 average time/residue: 0.2006 time to fit residues: 39.6595 Evaluate side-chains 120 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0875 time to fit residues: 1.9234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 130 optimal weight: 0.4980 chunk 138 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: