Starting phenix.real_space_refine on Thu Feb 15 09:38:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py4_13711/02_2024/7py4_13711.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py4_13711/02_2024/7py4_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_2024/7py4_13711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py4_13711/02_2024/7py4_13711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py4_13711/02_2024/7py4_13711.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py4_13711/02_2024/7py4_13711.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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 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. 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.01, per 1000 atoms: 0.59 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: 4.67 Conformation dependent library (CDL) restraints added in 2.1 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: 1.22 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: 4.71 Time building geometry restraints manager: 5.06 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 - 23.99: 7093 23.99 - 47.98: 311 47.98 - 71.97: 25 71.97 - 95.95: 23 95.95 - 119.94: 11 Dihedral angle restraints: 7463 sinusoidal: 3253 harmonic: 4210 Sorted by residual: dihedral pdb=" O3 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" C4 NAG C 1 " pdb=" O4 NAG C 1 " ideal model delta sinusoidal sigma weight residual 295.45 175.51 119.94 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C2 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" C4 NAG C 1 " pdb=" O4 NAG C 1 " ideal model delta sinusoidal sigma weight residual 175.11 55.35 119.76 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C5 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" C4 NAG C 1 " pdb=" O3 NAG C 1 " ideal model delta sinusoidal sigma weight residual -174.13 -56.61 -117.52 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 7460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1814 0.129 - 0.258: 21 0.258 - 0.387: 1 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 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: 9.860 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: 0.000 Extract box with map and model: 17.190 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 34.720 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 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: 65.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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= 0.234 Angle : 0.586 12.241 16438 Z= 0.270 Chirality : 0.051 0.644 1841 Planarity : 0.003 0.067 2064 Dihedral : 14.524 119.943 4740 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 % Allowed : 0.08 % Favored : 99.84 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 317 HIS 0.002 0.001 HIS A 449 PHE 0.012 0.001 PHE A1072 TYR 0.010 0.001 TYR B 121 ARG 0.011 0.000 ARG A1184 *********************** 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 : 1.214 Fit side-chains revert: symmetry clash REVERT: A 228 THR cc_start: 0.8219 (p) cc_final: 0.8019 (p) REVERT: A 1000 MET cc_start: 0.8081 (tmm) cc_final: 0.7690 (ttp) REVERT: B 242 MET cc_start: 0.8445 (mpp) cc_final: 0.7840 (mpp) outliers start: 1 outliers final: 1 residues processed: 142 average time/residue: 0.2519 time to fit residues: 51.2442 Evaluate side-chains 118 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 958 ASN 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: 0.7923 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12117 Z= 0.323 Angle : 0.597 9.316 16438 Z= 0.301 Chirality : 0.047 0.555 1841 Planarity : 0.004 0.049 2064 Dihedral : 11.638 109.358 1965 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.95 % Allowed : 5.46 % Favored : 93.59 % 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: 0.62 (0.23), residues: 1427 helix: 1.53 (0.22), residues: 623 sheet: 0.79 (0.37), residues: 196 loop : -0.90 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 260 HIS 0.003 0.001 HIS A1213 PHE 0.020 0.002 PHE A 666 TYR 0.021 0.002 TYR B 241 ARG 0.008 0.000 ARG A1184 *********************** 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 136 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.447 Fit side-chains revert: symmetry clash REVERT: A 1000 MET cc_start: 0.7998 (tmm) cc_final: 0.7681 (ttp) REVERT: B 242 MET cc_start: 0.8475 (mpp) cc_final: 0.7824 (mpp) outliers start: 12 outliers final: 7 residues processed: 133 average time/residue: 0.2445 time to fit residues: 48.3062 Evaluate side-chains 118 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 1025 ASP Chi-restraints excluded: chain A residue 1113 ILE 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: 4.9990 chunk 108 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.7935 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12117 Z= 0.312 Angle : 0.581 9.235 16438 Z= 0.293 Chirality : 0.046 0.548 1841 Planarity : 0.004 0.038 2064 Dihedral : 10.313 108.525 1963 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.58 % Allowed : 8.07 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.23), residues: 1427 helix: 1.41 (0.21), residues: 630 sheet: 0.82 (0.37), residues: 197 loop : -0.99 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 260 HIS 0.003 0.001 HIS A1213 PHE 0.025 0.002 PHE A 666 TYR 0.014 0.001 TYR B 241 ARG 0.006 0.000 ARG A 166 *********************** 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 141 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 1.319 Fit side-chains REVERT: A 206 ASP cc_start: 0.7436 (m-30) cc_final: 0.7016 (m-30) REVERT: A 514 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: A 1000 MET cc_start: 0.8000 (tmm) cc_final: 0.7740 (ttp) REVERT: A 1215 ARG cc_start: 0.7919 (ptm160) cc_final: 0.7633 (ptp90) REVERT: B 242 MET cc_start: 0.8503 (mpp) cc_final: 0.7816 (mpp) outliers start: 20 outliers final: 12 residues processed: 135 average time/residue: 0.2386 time to fit residues: 47.0910 Evaluate side-chains 129 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 1025 ASP Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 146 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 67 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 HIS A 526 GLN B 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12117 Z= 0.202 Angle : 0.521 8.527 16438 Z= 0.264 Chirality : 0.044 0.540 1841 Planarity : 0.003 0.040 2064 Dihedral : 9.514 106.555 1963 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.27 % Allowed : 10.13 % Favored : 88.61 % 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: 0.68 (0.23), residues: 1427 helix: 1.59 (0.22), residues: 630 sheet: 0.85 (0.36), residues: 201 loop : -0.93 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 317 HIS 0.002 0.001 HIS A 449 PHE 0.016 0.001 PHE A 955 TYR 0.013 0.001 TYR B 303 ARG 0.006 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 4 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: 16 poor density : 123 time to evaluate : 1.325 Fit side-chains REVERT: A 206 ASP cc_start: 0.7416 (m-30) cc_final: 0.7011 (m-30) REVERT: A 514 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: A 1000 MET cc_start: 0.7947 (tmm) cc_final: 0.7713 (ttp) REVERT: B 242 MET cc_start: 0.8516 (mpp) cc_final: 0.7826 (mpp) outliers start: 16 outliers final: 12 residues processed: 134 average time/residue: 0.2388 time to fit residues: 47.5199 Evaluate side-chains 127 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 1025 ASP Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 146 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 0.0980 chunk 78 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 HIS A 526 GLN B 74 ASN B 235 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12117 Z= 0.201 Angle : 0.512 7.477 16438 Z= 0.259 Chirality : 0.043 0.534 1841 Planarity : 0.003 0.039 2064 Dihedral : 9.274 105.595 1963 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.34 % Allowed : 11.55 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.23), residues: 1427 helix: 1.64 (0.22), residues: 633 sheet: 0.93 (0.36), residues: 199 loop : -0.93 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 317 HIS 0.002 0.001 HIS A 449 PHE 0.015 0.001 PHE A 955 TYR 0.014 0.001 TYR B 303 ARG 0.006 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 5 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 137 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 1.350 Fit side-chains REVERT: A 514 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: A 1000 MET cc_start: 0.8003 (tmm) cc_final: 0.7686 (ttp) REVERT: A 1215 ARG cc_start: 0.7858 (ptm160) cc_final: 0.7592 (ptp90) REVERT: B 242 MET cc_start: 0.8500 (mpp) cc_final: 0.7835 (mpp) outliers start: 17 outliers final: 13 residues processed: 130 average time/residue: 0.2652 time to fit residues: 50.6582 Evaluate side-chains 125 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 1025 ASP Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 240 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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: 0.7930 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12117 Z= 0.282 Angle : 0.543 8.434 16438 Z= 0.275 Chirality : 0.045 0.540 1841 Planarity : 0.004 0.043 2064 Dihedral : 9.324 105.946 1963 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.74 % Allowed : 11.95 % Favored : 86.31 % 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: 0.62 (0.23), residues: 1427 helix: 1.54 (0.21), residues: 630 sheet: 0.86 (0.37), residues: 200 loop : -0.99 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 260 HIS 0.003 0.001 HIS A 449 PHE 0.016 0.001 PHE A 527 TYR 0.014 0.001 TYR B 303 ARG 0.006 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 6 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 137 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 1.374 Fit side-chains REVERT: A 514 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: A 1000 MET cc_start: 0.8029 (tmm) cc_final: 0.7680 (ttp) REVERT: A 1168 MET cc_start: 0.7183 (ttm) cc_final: 0.6975 (ttp) REVERT: B 242 MET cc_start: 0.8535 (mpp) cc_final: 0.7825 (mpp) outliers start: 22 outliers final: 20 residues processed: 130 average time/residue: 0.2224 time to fit residues: 43.4660 Evaluate side-chains 132 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1025 ASP Chi-restraints excluded: chain A residue 1029 ASN Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 240 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.7908 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12117 Z= 0.210 Angle : 0.508 7.338 16438 Z= 0.258 Chirality : 0.043 0.528 1841 Planarity : 0.003 0.040 2064 Dihedral : 9.242 105.155 1963 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.29 % Allowed : 12.26 % Favored : 85.44 % 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: 0.76 (0.23), residues: 1427 helix: 1.63 (0.22), residues: 637 sheet: 0.96 (0.37), residues: 199 loop : -0.93 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 317 HIS 0.003 0.001 HIS B 302 PHE 0.014 0.001 PHE A 955 TYR 0.013 0.001 TYR B 121 ARG 0.008 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 7 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 148 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 1.269 Fit side-chains REVERT: A 206 ASP cc_start: 0.7412 (m-30) cc_final: 0.6998 (m-30) REVERT: A 514 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: A 1000 MET cc_start: 0.7979 (tmm) cc_final: 0.7695 (ttp) REVERT: A 1064 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6278 (mt-10) REVERT: A 1215 ARG cc_start: 0.7858 (ptm160) cc_final: 0.7597 (ptp90) REVERT: B 224 GLU cc_start: 0.7866 (tp30) cc_final: 0.7385 (tp30) REVERT: B 242 MET cc_start: 0.8530 (mpp) cc_final: 0.7822 (mpp) outliers start: 29 outliers final: 20 residues processed: 138 average time/residue: 0.2320 time to fit residues: 47.5863 Evaluate side-chains 140 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1025 ASP Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 240 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 108 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 HIS ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12117 Z= 0.164 Angle : 0.499 6.783 16438 Z= 0.251 Chirality : 0.043 0.515 1841 Planarity : 0.003 0.043 2064 Dihedral : 9.136 104.333 1963 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.14 % Allowed : 12.82 % Favored : 85.05 % 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: 0.92 (0.23), residues: 1427 helix: 1.81 (0.22), residues: 637 sheet: 0.88 (0.37), residues: 204 loop : -0.85 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 317 HIS 0.002 0.001 HIS A 449 PHE 0.013 0.001 PHE A 955 TYR 0.012 0.001 TYR B 121 ARG 0.008 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 8 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 152 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 1.240 Fit side-chains REVERT: A 206 ASP cc_start: 0.7399 (m-30) cc_final: 0.6982 (m-30) REVERT: A 271 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7565 (ttt90) REVERT: A 514 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: A 589 ASN cc_start: 0.7848 (t0) cc_final: 0.7628 (t0) REVERT: A 1000 MET cc_start: 0.7993 (tmm) cc_final: 0.7675 (ttp) REVERT: A 1064 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6226 (mt-10) REVERT: A 1215 ARG cc_start: 0.7856 (ptm160) cc_final: 0.7570 (ptp90) REVERT: B 224 GLU cc_start: 0.7859 (tp30) cc_final: 0.7429 (tp30) REVERT: B 242 MET cc_start: 0.8506 (mpp) cc_final: 0.7840 (mpp) outliers start: 27 outliers final: 17 residues processed: 143 average time/residue: 0.2314 time to fit residues: 48.4244 Evaluate side-chains 138 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1025 ASP Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 240 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 0.0870 chunk 120 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 HIS ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12117 Z= 0.232 Angle : 0.523 7.419 16438 Z= 0.265 Chirality : 0.044 0.521 1841 Planarity : 0.004 0.050 2064 Dihedral : 9.219 104.329 1963 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.74 % Allowed : 13.45 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.23), residues: 1427 helix: 1.75 (0.21), residues: 638 sheet: 0.85 (0.37), residues: 204 loop : -0.87 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 317 HIS 0.003 0.001 HIS A 167 PHE 0.015 0.001 PHE A 527 TYR 0.013 0.001 TYR B 121 ARG 0.008 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 9 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 137 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 1.316 Fit side-chains REVERT: A 206 ASP cc_start: 0.7431 (m-30) cc_final: 0.7003 (m-30) REVERT: A 271 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7586 (ttt90) REVERT: A 514 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: A 1000 MET cc_start: 0.8026 (tmm) cc_final: 0.7661 (ttp) REVERT: A 1064 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6307 (mt-10) REVERT: A 1215 ARG cc_start: 0.7866 (ptm160) cc_final: 0.7576 (ptp90) REVERT: B 242 MET cc_start: 0.8528 (mpp) cc_final: 0.7862 (mpp) outliers start: 22 outliers final: 18 residues processed: 132 average time/residue: 0.2416 time to fit residues: 46.6630 Evaluate side-chains 132 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 TYR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1025 ASP Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 90 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 HIS ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN B 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12117 Z= 0.154 Angle : 0.499 7.157 16438 Z= 0.252 Chirality : 0.043 0.567 1841 Planarity : 0.003 0.045 2064 Dihedral : 9.177 103.767 1963 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.34 % Allowed : 14.00 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.23), residues: 1427 helix: 1.95 (0.22), residues: 637 sheet: 0.90 (0.37), residues: 204 loop : -0.85 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 281 HIS 0.002 0.001 HIS A 359 PHE 0.013 0.001 PHE A 955 TYR 0.012 0.001 TYR B 121 ARG 0.009 0.000 ARG A 166 ********************** REFINEMENT MACRO_CYCLE 10 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: 17 poor density : 122 time to evaluate : 1.273 Fit side-chains REVERT: A 206 ASP cc_start: 0.7392 (m-30) cc_final: 0.6984 (m-30) REVERT: A 271 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7557 (ttt90) REVERT: A 514 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: A 1000 MET cc_start: 0.7975 (tmm) cc_final: 0.7677 (ttp) REVERT: A 1215 ARG cc_start: 0.7834 (ptm160) cc_final: 0.7537 (ptp90) REVERT: B 224 GLU cc_start: 0.7838 (tp30) cc_final: 0.7353 (tp30) REVERT: B 242 MET cc_start: 0.8508 (mpp) cc_final: 0.7847 (mpp) outliers start: 17 outliers final: 13 residues processed: 135 average time/residue: 0.2425 time to fit residues: 48.3191 Evaluate side-chains 132 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 TYR Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1025 ASP Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 0.0370 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.0370 chunk 99 optimal weight: 3.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 479 HIS ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.163381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.121775 restraints weight = 13828.703| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.15 r_work: 0.3436 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12117 Z= 0.175 Angle : 0.504 6.949 16438 Z= 0.256 Chirality : 0.043 0.525 1841 Planarity : 0.003 0.049 2064 Dihedral : 9.108 103.402 1963 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.42 % Allowed : 14.48 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.23), residues: 1427 helix: 1.95 (0.21), residues: 640 sheet: 0.92 (0.37), residues: 204 loop : -0.84 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 317 HIS 0.002 0.001 HIS A 449 PHE 0.013 0.001 PHE A 527 TYR 0.012 0.001 TYR B 121 ARG 0.008 0.000 ARG A 631 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2777.59 seconds wall clock time: 51 minutes 30.60 seconds (3090.60 seconds total)