Starting phenix.real_space_refine on Tue Feb 20 03:10:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghg_40045/02_2024/8ghg_40045.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghg_40045/02_2024/8ghg_40045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghg_40045/02_2024/8ghg_40045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghg_40045/02_2024/8ghg_40045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghg_40045/02_2024/8ghg_40045.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghg_40045/02_2024/8ghg_40045.pdb" } resolution = 3.3 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= 0.016 sd= 0.061 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: 4 Type Number sf(0) Gaussians S 172 5.16 5 C 17307 2.51 5 N 4336 2.21 5 O 4844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 902": "OE1" <-> "OE2" Residue "C TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 362": "OD1" <-> "OD2" Residue "B TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 881": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26659 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6533 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 816, 6525 Classifications: {'peptide': 816} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 790} Chain breaks: 6 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 816, 6525 Classifications: {'peptide': 816} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 790} Chain breaks: 6 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 6664 Chain: "C" Number of atoms: 6802 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 853, 6794 Classifications: {'peptide': 853} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 825} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 853, 6794 Classifications: {'peptide': 853} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 825} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 6940 Chain: "B" Number of atoms: 6549 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 817, 6541 Classifications: {'peptide': 817} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 791} Chain breaks: 7 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 817, 6541 Classifications: {'peptide': 817} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 791} Chain breaks: 7 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 6681 Chain: "D" Number of atoms: 6775 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 849, 6767 Classifications: {'peptide': 849} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 821} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 849, 6767 Classifications: {'peptide': 849} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 821} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 6912 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AASN A 826 " occ=0.55 ... (14 atoms not shown) pdb=" ND2BASN A 826 " occ=0.45 residue: pdb=" N AASN C 826 " occ=0.59 ... (14 atoms not shown) pdb=" ND2BASN C 826 " occ=0.41 residue: pdb=" N AASN B 826 " occ=0.55 ... (14 atoms not shown) pdb=" ND2BASN B 826 " occ=0.45 residue: pdb=" N AASN D 826 " occ=0.59 ... (14 atoms not shown) pdb=" ND2BASN D 826 " occ=0.41 Time building chain proxies: 26.55, per 1000 atoms: 1.00 Number of scatterers: 26659 At special positions: 0 Unit cell: (147.96, 147.96, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 172 16.00 O 4844 8.00 N 4336 7.00 C 17307 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.46 Conformation dependent library (CDL) restraints added in 9.0 seconds 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6350 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 20 sheets defined 51.5% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'A' and resid 21 through 30 Processing helix chain 'A' and resid 108 through 128 removed outlier: 4.003A pdb=" N VAL A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 135 Processing helix chain 'A' and resid 149 through 170 removed outlier: 4.042A pdb=" N ASP A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 180 Processing helix chain 'A' and resid 180 through 199 Proline residue: A 191 - end of helix Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 229 through 260 removed outlier: 3.596A pdb=" N LYS A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 removed outlier: 3.727A pdb=" N CYS A 277 " --> pdb=" O THR A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 319 removed outlier: 4.050A pdb=" N PHE A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 328 removed outlier: 3.683A pdb=" N GLY A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 removed outlier: 3.947A pdb=" N ASP A 362 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 407 through 415 Processing helix chain 'A' and resid 432 through 451 removed outlier: 3.854A pdb=" N GLU A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 Processing helix chain 'A' and resid 485 through 500 removed outlier: 3.555A pdb=" N LEU A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 509 Processing helix chain 'A' and resid 523 through 533 removed outlier: 3.962A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 699 through 704 removed outlier: 3.791A pdb=" N VAL A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 742 Proline residue: A 740 - end of helix Processing helix chain 'A' and resid 747 through 751 Processing helix chain 'A' and resid 759 through 767 Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 785 through 792 removed outlier: 3.528A pdb=" N VAL A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 830 Processing helix chain 'A' and resid 872 through 876 removed outlier: 3.718A pdb=" N ASN A 875 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 892 removed outlier: 3.783A pdb=" N VAL A 888 " --> pdb=" O ASP A 885 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP A 892 " --> pdb=" O GLN A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.517A pdb=" N GLY A 912 " --> pdb=" O PHE A 909 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 913 " --> pdb=" O ALA A 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 909 through 913' Processing helix chain 'A' and resid 918 through 921 removed outlier: 3.789A pdb=" N ASP A 921 " --> pdb=" O SER A 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 918 through 921' Processing helix chain 'A' and resid 922 through 930 Processing helix chain 'A' and resid 932 through 942 Processing helix chain 'A' and resid 946 through 957 Processing helix chain 'A' and resid 996 through 1008 Processing helix chain 'C' and resid 118 through 136 removed outlier: 3.655A pdb=" N LEU C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL C 128 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE C 129 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE C 132 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN C 136 " --> pdb=" O ILE C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 170 removed outlier: 3.968A pdb=" N GLN C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 180 Processing helix chain 'C' and resid 180 through 200 Proline residue: C 191 - end of helix Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 232 through 260 Processing helix chain 'C' and resid 273 through 285 removed outlier: 4.026A pdb=" N TYR C 279 " --> pdb=" O TRP C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 297 through 310 removed outlier: 4.459A pdb=" N PHE C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 317 removed outlier: 3.949A pdb=" N SER C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 407 through 415 Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 432 through 451 removed outlier: 3.506A pdb=" N GLU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 464 No H-bonds generated for 'chain 'C' and resid 462 through 464' Processing helix chain 'C' and resid 465 through 471 Processing helix chain 'C' and resid 485 through 500 removed outlier: 3.506A pdb=" N LEU C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 509 Processing helix chain 'C' and resid 523 through 533 removed outlier: 4.079A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 562 Processing helix chain 'C' and resid 601 through 607 removed outlier: 3.626A pdb=" N VAL C 605 " --> pdb=" O ASP C 601 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG C 607 " --> pdb=" O LYS C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 703 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 733 through 739 removed outlier: 3.644A pdb=" N LEU C 737 " --> pdb=" O GLY C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 743 removed outlier: 3.879A pdb=" N ALA C 743 " --> pdb=" O PRO C 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 740 through 743' Processing helix chain 'C' and resid 747 through 751 Processing helix chain 'C' and resid 759 through 768 removed outlier: 4.235A pdb=" N ARG C 765 " --> pdb=" O GLU C 761 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU C 766 " --> pdb=" O TYR C 762 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 792 Processing helix chain 'C' and resid 817 through 830 Processing helix chain 'C' and resid 884 through 891 removed outlier: 3.589A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 905 removed outlier: 3.775A pdb=" N LEU C 905 " --> pdb=" O GLU C 902 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 902 through 905' Processing helix chain 'C' and resid 906 through 912 Processing helix chain 'C' and resid 918 through 921 removed outlier: 3.850A pdb=" N ASP C 921 " --> pdb=" O SER C 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 918 through 921' Processing helix chain 'C' and resid 922 through 930 Processing helix chain 'C' and resid 932 through 942 Processing helix chain 'C' and resid 946 through 957 Processing helix chain 'C' and resid 969 through 973 removed outlier: 3.719A pdb=" N ARG C 972 " --> pdb=" O LEU C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 992 removed outlier: 4.213A pdb=" N ASP C 989 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP C 992 " --> pdb=" O ASP C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1008 Processing helix chain 'B' and resid 24 through 30 Processing helix chain 'B' and resid 109 through 133 Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 147 through 170 removed outlier: 4.115A pdb=" N ILE B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 180 Processing helix chain 'B' and resid 180 through 200 Proline residue: B 191 - end of helix Processing helix chain 'B' and resid 207 through 215 removed outlier: 4.333A pdb=" N ARG B 210 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 212 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 215 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.676A pdb=" N ILE B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 260 removed outlier: 3.542A pdb=" N GLY B 260 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 297 through 319 removed outlier: 4.545A pdb=" N PHE B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 327 removed outlier: 4.789A pdb=" N ILE B 323 " --> pdb=" O PRO B 320 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLU B 324 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B 326 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 407 through 415 Processing helix chain 'B' and resid 432 through 451 removed outlier: 4.165A pdb=" N GLU B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.513A pdb=" N LEU B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE B 472 " --> pdb=" O HIS B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 500 removed outlier: 4.240A pdb=" N LEU B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 510 Processing helix chain 'B' and resid 523 through 533 removed outlier: 3.979A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 558 removed outlier: 4.276A pdb=" N VAL B 553 " --> pdb=" O SER B 549 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS B 554 " --> pdb=" O PHE B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 606 Processing helix chain 'B' and resid 607 through 609 No H-bonds generated for 'chain 'B' and resid 607 through 609' Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.706A pdb=" N VAL B 703 " --> pdb=" O GLU B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 742 Proline residue: B 740 - end of helix Processing helix chain 'B' and resid 759 through 767 Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing helix chain 'B' and resid 785 through 792 removed outlier: 3.625A pdb=" N VAL B 792 " --> pdb=" O ASP B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 797 Processing helix chain 'B' and resid 804 through 808 removed outlier: 3.863A pdb=" N GLN B 807 " --> pdb=" O SER B 804 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN B 808 " --> pdb=" O ALA B 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 804 through 808' Processing helix chain 'B' and resid 817 through 829 Processing helix chain 'B' and resid 872 through 876 removed outlier: 3.954A pdb=" N ASN B 875 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 892 removed outlier: 3.739A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP B 892 " --> pdb=" O GLN B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 912 Processing helix chain 'B' and resid 918 through 921 removed outlier: 3.647A pdb=" N ASP B 921 " --> pdb=" O SER B 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 918 through 921' Processing helix chain 'B' and resid 922 through 930 removed outlier: 3.759A pdb=" N PHE B 929 " --> pdb=" O SER B 925 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN B 930 " --> pdb=" O ALA B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 941 removed outlier: 4.175A pdb=" N THR B 935 " --> pdb=" O ASP B 931 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE B 937 " --> pdb=" O ILE B 933 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ARG B 938 " --> pdb=" O LEU B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 957 Processing helix chain 'B' and resid 996 through 1007 Processing helix chain 'D' and resid 24 through 33 removed outlier: 3.669A pdb=" N ALA D 27 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER D 29 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N MET D 30 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL D 31 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR D 32 " --> pdb=" O SER D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 116 Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 122 through 136 Processing helix chain 'D' and resid 150 through 171 removed outlier: 3.598A pdb=" N ALA D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 200 Proline residue: D 191 - end of helix Processing helix chain 'D' and resid 207 through 213 removed outlier: 3.610A pdb=" N LEU D 212 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ARG D 213 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 224 removed outlier: 4.246A pdb=" N SER D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU D 219 " --> pdb=" O ILE D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 260 removed outlier: 4.383A pdb=" N SER D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE D 241 " --> pdb=" O ASN D 237 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY D 260 " --> pdb=" O VAL D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 285 Processing helix chain 'D' and resid 297 through 318 removed outlier: 3.987A pdb=" N ALA D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 327 removed outlier: 4.059A pdb=" N ILE D 323 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 364 Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 407 through 415 Processing helix chain 'D' and resid 416 through 419 Processing helix chain 'D' and resid 432 through 451 removed outlier: 3.596A pdb=" N GLU D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 464 No H-bonds generated for 'chain 'D' and resid 462 through 464' Processing helix chain 'D' and resid 465 through 471 removed outlier: 3.570A pdb=" N ASN D 471 " --> pdb=" O ALA D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 500 Processing helix chain 'D' and resid 502 through 509 Processing helix chain 'D' and resid 523 through 533 removed outlier: 4.139A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 562 Processing helix chain 'D' and resid 601 through 606 Processing helix chain 'D' and resid 607 through 609 No H-bonds generated for 'chain 'D' and resid 607 through 609' Processing helix chain 'D' and resid 699 through 703 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 733 through 739 removed outlier: 3.633A pdb=" N LEU D 737 " --> pdb=" O GLY D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 743 removed outlier: 3.563A pdb=" N ALA D 743 " --> pdb=" O PRO D 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 740 through 743' Processing helix chain 'D' and resid 747 through 751 Processing helix chain 'D' and resid 759 through 767 removed outlier: 3.653A pdb=" N LEU D 763 " --> pdb=" O SER D 759 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 770 No H-bonds generated for 'chain 'D' and resid 768 through 770' Processing helix chain 'D' and resid 785 through 792 Processing helix chain 'D' and resid 817 through 830 Processing helix chain 'D' and resid 884 through 892 removed outlier: 3.695A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP D 892 " --> pdb=" O GLN D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 905 Processing helix chain 'D' and resid 906 through 912 Processing helix chain 'D' and resid 918 through 920 No H-bonds generated for 'chain 'D' and resid 918 through 920' Processing helix chain 'D' and resid 921 through 930 removed outlier: 4.436A pdb=" N SER D 925 " --> pdb=" O ASP D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 932 through 942 Processing helix chain 'D' and resid 946 through 957 Processing helix chain 'D' and resid 969 through 974 removed outlier: 3.697A pdb=" N ARG D 972 " --> pdb=" O LEU D 969 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG D 974 " --> pdb=" O ASN D 971 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 989 removed outlier: 4.202A pdb=" N ASP D 989 " --> pdb=" O PRO D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1008 Processing helix chain 'D' and resid 1019 through 1021 No H-bonds generated for 'chain 'D' and resid 1019 through 1021' Processing sheet with id=AA1, first strand: chain 'A' and resid 398 through 400 removed outlier: 6.446A pdb=" N ILE A 375 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY A 349 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N HIS A 344 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N LEU A 423 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A 482 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 458 " --> pdb=" O ASP A 482 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 540 removed outlier: 4.245A pdb=" N LEU A 564 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.690A pdb=" N ILE A 754 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU A 779 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N PHE A 756 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 719 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL A 757 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A 721 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 720 " --> pdb=" O MET A 799 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1014 through 1017 Processing sheet with id=AA5, first strand: chain 'C' and resid 398 through 399 removed outlier: 6.550A pdb=" N ILE C 375 " --> pdb=" O GLU C 399 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY C 349 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N HIS C 344 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N LEU C 423 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP C 482 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR C 458 " --> pdb=" O ASP C 482 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 535 through 538 removed outlier: 3.914A pdb=" N ILE C 598 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU C 564 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 568 through 569 Processing sheet with id=AA8, first strand: chain 'C' and resid 776 through 780 removed outlier: 6.547A pdb=" N ILE C 754 " --> pdb=" O SER C 777 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU C 779 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N PHE C 756 " --> pdb=" O LEU C 779 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL C 719 " --> pdb=" O VAL C 755 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N VAL C 757 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL C 721 " --> pdb=" O VAL C 757 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 976 through 981 removed outlier: 3.810A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU C1052 " --> pdb=" O CYS C1011 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N CYS C1011 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 140 through 141 removed outlier: 3.612A pdb=" N SER B 140 " --> pdb=" O SER B 202 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 398 through 402 removed outlier: 6.150A pdb=" N ILE B 375 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N TYR B 401 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N PHE B 377 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY B 349 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N HIS B 344 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N LEU B 423 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL B 346 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU B 425 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N CYS B 348 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 535 through 540 removed outlier: 7.048A pdb=" N LEU B 594 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE B 568 " --> pdb=" O LEU B 594 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE B 596 " --> pdb=" O ILE B 566 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 564 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 776 through 780 removed outlier: 6.669A pdb=" N ILE B 754 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU B 779 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE B 756 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL B 719 " --> pdb=" O VAL B 755 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL B 757 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL B 721 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 720 " --> pdb=" O MET B 799 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N CYS B 800 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N GLU B 881 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE B 802 " --> pdb=" O GLU B 881 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 975 through 976 Processing sheet with id=AB6, first strand: chain 'B' and resid 1014 through 1017 Processing sheet with id=AB7, first strand: chain 'D' and resid 398 through 402 removed outlier: 8.719A pdb=" N GLU D 399 " --> pdb=" O VAL D 373 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE D 375 " --> pdb=" O GLU D 399 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N TYR D 401 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE D 377 " --> pdb=" O TYR D 401 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS D 343 " --> pdb=" O GLU D 374 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL D 376 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE D 345 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N LEU D 378 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL D 347 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N LEU D 423 " --> pdb=" O HIS D 344 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL D 346 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU D 425 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N CYS D 348 " --> pdb=" O LEU D 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 458 through 460 Processing sheet with id=AB9, first strand: chain 'D' and resid 535 through 539 removed outlier: 4.019A pdb=" N ALA D 567 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE D 598 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N MET D 565 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 776 through 780 removed outlier: 6.520A pdb=" N ILE D 754 " --> pdb=" O SER D 777 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU D 779 " --> pdb=" O ILE D 754 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N PHE D 756 " --> pdb=" O LEU D 779 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL D 719 " --> pdb=" O VAL D 755 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL D 757 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL D 721 " --> pdb=" O VAL D 757 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 976 through 981 removed outlier: 3.523A pdb=" N MET D1053 " --> pdb=" O ARG D 976 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY D1013 " --> pdb=" O PHE D1050 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU D1052 " --> pdb=" O CYS D1011 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N CYS D1011 " --> pdb=" O LEU D1052 " (cutoff:3.500A) 1082 hydrogen bonds defined for protein. 3049 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: 8.78 Time building geometry restraints manager: 10.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8413 1.35 - 1.47: 6806 1.47 - 1.59: 11794 1.59 - 1.72: 0 1.72 - 1.84: 256 Bond restraints: 27269 Sorted by residual: bond pdb=" C PRO D 191 " pdb=" N PRO D 192 " ideal model delta sigma weight residual 1.335 1.375 -0.039 1.30e-02 5.92e+03 9.19e+00 bond pdb=" CG MET B 282 " pdb=" SD MET B 282 " ideal model delta sigma weight residual 1.803 1.842 -0.039 2.50e-02 1.60e+03 2.48e+00 bond pdb=" C VAL A 319 " pdb=" N PRO A 320 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.11e+00 bond pdb=" CA ASN B 225 " pdb=" CB ASN B 225 " ideal model delta sigma weight residual 1.530 1.552 -0.022 1.69e-02 3.50e+03 1.63e+00 bond pdb=" N MET B 282 " pdb=" CA MET B 282 " ideal model delta sigma weight residual 1.459 1.474 -0.015 1.23e-02 6.61e+03 1.58e+00 ... (remaining 27264 not shown) Histogram of bond angle deviations from ideal: 98.55 - 105.67: 426 105.67 - 112.79: 14361 112.79 - 119.91: 9505 119.91 - 127.03: 12415 127.03 - 134.15: 287 Bond angle restraints: 36994 Sorted by residual: angle pdb=" CB MET B 30 " pdb=" CG MET B 30 " pdb=" SD MET B 30 " ideal model delta sigma weight residual 112.70 128.15 -15.45 3.00e+00 1.11e-01 2.65e+01 angle pdb=" CG MET B 282 " pdb=" SD MET B 282 " pdb=" CE MET B 282 " ideal model delta sigma weight residual 100.90 112.12 -11.22 2.20e+00 2.07e-01 2.60e+01 angle pdb=" N PHE C 307 " pdb=" CA PHE C 307 " pdb=" CB PHE C 307 " ideal model delta sigma weight residual 110.12 116.17 -6.05 1.47e+00 4.63e-01 1.69e+01 angle pdb=" C LEU B 224 " pdb=" N ASN B 225 " pdb=" CA ASN B 225 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.69e+01 angle pdb=" C VAL B 119 " pdb=" N PHE B 120 " pdb=" CA PHE B 120 " ideal model delta sigma weight residual 121.14 114.13 7.01 1.75e+00 3.27e-01 1.60e+01 ... (remaining 36989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 14513 17.66 - 35.32: 1321 35.32 - 52.98: 205 52.98 - 70.65: 27 70.65 - 88.31: 14 Dihedral angle restraints: 16080 sinusoidal: 6288 harmonic: 9792 Sorted by residual: dihedral pdb=" CA LEU B 281 " pdb=" C LEU B 281 " pdb=" N MET B 282 " pdb=" CA MET B 282 " ideal model delta harmonic sigma weight residual 180.00 153.30 26.70 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA LEU D 238 " pdb=" C LEU D 238 " pdb=" N LEU D 239 " pdb=" CA LEU D 239 " ideal model delta harmonic sigma weight residual -180.00 -157.58 -22.42 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PHE C 303 " pdb=" C PHE C 303 " pdb=" N MET C 304 " pdb=" CA MET C 304 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 16077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2908 0.042 - 0.084: 1003 0.084 - 0.125: 295 0.125 - 0.167: 26 0.167 - 0.209: 5 Chirality restraints: 4237 Sorted by residual: chirality pdb=" CB VAL A 371 " pdb=" CA VAL A 371 " pdb=" CG1 VAL A 371 " pdb=" CG2 VAL A 371 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CG LEU A 272 " pdb=" CB LEU A 272 " pdb=" CD1 LEU A 272 " pdb=" CD2 LEU A 272 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CA ASN B 225 " pdb=" N ASN B 225 " pdb=" C ASN B 225 " pdb=" CB ASN B 225 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 4234 not shown) Planarity restraints: 4650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 178 " -0.027 2.00e-02 2.50e+03 2.79e-02 1.95e+01 pdb=" CG TRP B 178 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP B 178 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP B 178 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 178 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 178 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 178 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 178 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 178 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 178 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 307 " -0.029 2.00e-02 2.50e+03 2.38e-02 9.90e+00 pdb=" CG PHE C 307 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE C 307 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 307 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 307 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 307 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 307 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 191 " 0.040 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO A 192 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " 0.034 5.00e-02 4.00e+02 ... (remaining 4647 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 925 2.71 - 3.26: 27975 3.26 - 3.81: 43500 3.81 - 4.35: 52369 4.35 - 4.90: 86040 Nonbonded interactions: 210809 Sorted by model distance: nonbonded pdb=" O PHE A 177 " pdb=" OG SER A 183 " model vdw 2.168 2.440 nonbonded pdb=" O MET B 691 " pdb=" OG SER B 744 " model vdw 2.229 2.440 nonbonded pdb=" OG1 THR B 273 " pdb=" OE1 GLU B 276 " model vdw 2.230 2.440 nonbonded pdb=" OG1 THR C 965 " pdb=" O GLN C 967 " model vdw 2.251 2.440 nonbonded pdb=" O MET B 282 " pdb=" OG SER B 286 " model vdw 2.257 2.440 ... (remaining 210804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 33 or resid 111 through 368 or resid 371 throug \ h 825 or resid 827 through 1056)) selection = (chain 'B' and (resid 19 through 33 or resid 111 through 368 or resid 371 throug \ h 825 or resid 827 through 976 or resid 995 through 1056)) selection = (chain 'C' and (resid 19 through 33 or resid 111 through 368 or resid 371 throug \ h 570 or resid 591 through 825 or resid 827 through 958 or resid 964 through 976 \ or resid 995 through 1056)) selection = (chain 'D' and (resid 19 through 33 or resid 111 through 570 or resid 591 throug \ h 825 or resid 827 through 958 or resid 964 through 976 or resid 995 through 105 \ 6)) } 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=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.020 Extract box with map and model: 5.210 Check model and map are aligned: 0.390 Set scattering table: 0.260 Process input model: 86.480 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 : 0.003 0.047 27269 Z= 0.175 Angle : 0.696 15.454 36994 Z= 0.346 Chirality : 0.044 0.209 4237 Planarity : 0.004 0.060 4650 Dihedral : 13.544 88.307 9730 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.10 % Allowed : 0.37 % Favored : 99.52 % 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: -0.96 (0.14), residues: 3295 helix: -0.45 (0.13), residues: 1534 sheet: 0.95 (0.30), residues: 338 loop : -1.15 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.001 TRP B 178 HIS 0.004 0.001 HIS C 586 PHE 0.053 0.001 PHE C 307 TYR 0.023 0.001 TYR B1015 ARG 0.014 0.000 ARG A 974 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 178 time to evaluate : 2.977 Fit side-chains revert: symmetry clash REVERT: A 188 PHE cc_start: 0.9058 (m-10) cc_final: 0.8848 (m-80) REVERT: A 242 PHE cc_start: 0.9559 (t80) cc_final: 0.9194 (t80) REVERT: A 252 PHE cc_start: 0.9330 (t80) cc_final: 0.8826 (t80) REVERT: A 285 MET cc_start: 0.9138 (mpp) cc_final: 0.8896 (mpp) REVERT: A 307 PHE cc_start: 0.8943 (m-10) cc_final: 0.8537 (m-80) REVERT: A 314 MET cc_start: 0.9140 (tmm) cc_final: 0.8790 (tmm) REVERT: A 881 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8121 (tm-30) REVERT: C 30 MET cc_start: 0.9346 (pmm) cc_final: 0.9107 (pmm) REVERT: C 34 PHE cc_start: 0.6851 (m-80) cc_final: 0.6426 (m-80) REVERT: C 285 MET cc_start: 0.9174 (mpp) cc_final: 0.8772 (mpp) REVERT: C 304 MET cc_start: 0.9499 (mmp) cc_final: 0.8975 (mmm) REVERT: C 312 LEU cc_start: 0.9239 (mm) cc_final: 0.8936 (mm) REVERT: C 314 MET cc_start: 0.8695 (tpt) cc_final: 0.8296 (tpp) REVERT: C 460 MET cc_start: 0.7837 (mmm) cc_final: 0.7574 (mmm) REVERT: C 1009 MET cc_start: 0.8808 (tpp) cc_final: 0.8525 (tpp) REVERT: B 120 PHE cc_start: 0.8643 (p90) cc_final: 0.8179 (p90) REVERT: B 154 MET cc_start: 0.7766 (mmp) cc_final: 0.7533 (mmm) REVERT: B 558 PHE cc_start: 0.7180 (t80) cc_final: 0.6918 (t80) REVERT: B 1009 MET cc_start: 0.7909 (pmm) cc_final: 0.7322 (pmm) REVERT: D 284 THR cc_start: 0.9321 (m) cc_final: 0.9100 (m) REVERT: D 302 LEU cc_start: 0.9801 (mt) cc_final: 0.9572 (mt) REVERT: D 303 PHE cc_start: 0.9333 (m-10) cc_final: 0.9050 (m-80) REVERT: D 306 PHE cc_start: 0.9476 (m-80) cc_final: 0.9116 (m-80) REVERT: D 1009 MET cc_start: 0.8976 (mmp) cc_final: 0.8732 (mmp) outliers start: 3 outliers final: 3 residues processed: 181 average time/residue: 0.3466 time to fit residues: 106.2785 Evaluate side-chains 153 residues out of total 2948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 150 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain B residue 329 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 279 optimal weight: 4.9990 chunk 250 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 85 optimal weight: 50.0000 chunk 169 optimal weight: 50.0000 chunk 134 optimal weight: 6.9990 chunk 259 optimal weight: 40.0000 chunk 100 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 300 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN A 749 HIS A 771 HIS A 816 GLN A 893 GLN A 930 ASN A 967 GLN C 379 HIS C 402 GLN C 464 HIS C 534 ASN C 736 ASN C 749 HIS C 808 ASN ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN B 344 HIS B 465 ASN B 496 GLN B 509 ASN ** B 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 GLN D 225 ASN D 344 HIS D 534 ASN D 693 HIS ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 HIS ** D 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 932 ASN D 971 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27269 Z= 0.265 Angle : 0.601 10.543 36994 Z= 0.306 Chirality : 0.042 0.166 4237 Planarity : 0.004 0.058 4650 Dihedral : 4.416 36.354 3568 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.51 % Favored : 94.46 % Rotamer: Outliers : 0.51 % Allowed : 6.07 % Favored : 93.42 % 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: -0.57 (0.15), residues: 3295 helix: -0.07 (0.13), residues: 1528 sheet: 0.89 (0.29), residues: 360 loop : -0.96 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 178 HIS 0.003 0.001 HIS B 753 PHE 0.041 0.001 PHE C 307 TYR 0.031 0.001 TYR C 163 ARG 0.004 0.000 ARG A 974 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 163 time to evaluate : 3.313 Fit side-chains revert: symmetry clash REVERT: A 242 PHE cc_start: 0.9527 (t80) cc_final: 0.9231 (t80) REVERT: A 252 PHE cc_start: 0.9346 (t80) cc_final: 0.9019 (t80) REVERT: A 285 MET cc_start: 0.9221 (mpp) cc_final: 0.8944 (mpp) REVERT: A 307 PHE cc_start: 0.8935 (m-10) cc_final: 0.8388 (m-80) REVERT: A 314 MET cc_start: 0.9126 (tmm) cc_final: 0.8729 (tmm) REVERT: A 881 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8182 (tm-30) REVERT: C 30 MET cc_start: 0.9302 (pmm) cc_final: 0.9064 (pmm) REVERT: C 34 PHE cc_start: 0.6869 (m-80) cc_final: 0.6409 (m-80) REVERT: C 282 MET cc_start: 0.9379 (mmm) cc_final: 0.9072 (tpp) REVERT: C 285 MET cc_start: 0.9172 (mpp) cc_final: 0.8671 (mpp) REVERT: C 304 MET cc_start: 0.9585 (mmp) cc_final: 0.8942 (mmm) REVERT: C 307 PHE cc_start: 0.8440 (m-80) cc_final: 0.7946 (m-80) REVERT: C 312 LEU cc_start: 0.9235 (mm) cc_final: 0.8684 (mt) REVERT: C 314 MET cc_start: 0.8775 (tpt) cc_final: 0.8374 (tpp) REVERT: C 565 MET cc_start: 0.8690 (mmp) cc_final: 0.8358 (mmp) REVERT: C 1009 MET cc_start: 0.8897 (tpp) cc_final: 0.8651 (tpp) REVERT: B 285 MET cc_start: 0.9383 (mmm) cc_final: 0.9148 (mmm) REVERT: B 304 MET cc_start: 0.9586 (ptm) cc_final: 0.9209 (ppp) REVERT: B 799 MET cc_start: 0.7587 (tmm) cc_final: 0.7381 (tmm) REVERT: B 830 MET cc_start: 0.8701 (tpp) cc_final: 0.8170 (tpp) REVERT: B 1009 MET cc_start: 0.8305 (pmm) cc_final: 0.7714 (pmm) REVERT: D 302 LEU cc_start: 0.9788 (mt) cc_final: 0.9447 (mt) REVERT: D 306 PHE cc_start: 0.9484 (m-80) cc_final: 0.9145 (m-80) REVERT: D 881 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7572 (tm-30) outliers start: 15 outliers final: 13 residues processed: 168 average time/residue: 0.3592 time to fit residues: 103.7393 Evaluate side-chains 160 residues out of total 2948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 885 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 167 optimal weight: 0.0050 chunk 93 optimal weight: 0.6980 chunk 250 optimal weight: 9.9990 chunk 204 optimal weight: 8.9990 chunk 82 optimal weight: 40.0000 chunk 301 optimal weight: 6.9990 chunk 325 optimal weight: 20.0000 chunk 268 optimal weight: 8.9990 chunk 298 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 241 optimal weight: 10.0000 overall best weight: 2.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS A 930 ASN A1008 ASN C 496 GLN ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 771 HIS ** B 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 ASN ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27269 Z= 0.185 Angle : 0.563 10.292 36994 Z= 0.283 Chirality : 0.041 0.256 4237 Planarity : 0.004 0.057 4650 Dihedral : 4.294 36.111 3567 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.30 % Favored : 94.67 % Rotamer: Outliers : 0.71 % Allowed : 7.94 % Favored : 91.35 % 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: -0.44 (0.15), residues: 3295 helix: 0.06 (0.13), residues: 1522 sheet: 0.91 (0.29), residues: 353 loop : -0.90 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 178 HIS 0.006 0.001 HIS A 749 PHE 0.047 0.001 PHE C 306 TYR 0.041 0.001 TYR B 279 ARG 0.005 0.000 ARG A 974 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 3.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.9338 (t80) cc_final: 0.8756 (t80) REVERT: A 285 MET cc_start: 0.9217 (mpp) cc_final: 0.8898 (mmt) REVERT: A 303 PHE cc_start: 0.9292 (m-80) cc_final: 0.8738 (t80) REVERT: A 307 PHE cc_start: 0.9041 (m-10) cc_final: 0.8470 (m-80) REVERT: A 881 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8180 (tm-30) REVERT: C 282 MET cc_start: 0.9427 (mmm) cc_final: 0.9066 (tpp) REVERT: C 285 MET cc_start: 0.9256 (mpp) cc_final: 0.8764 (mpp) REVERT: C 304 MET cc_start: 0.9592 (mmp) cc_final: 0.9275 (mmm) REVERT: C 307 PHE cc_start: 0.8241 (m-80) cc_final: 0.7719 (m-80) REVERT: C 312 LEU cc_start: 0.9274 (mm) cc_final: 0.8900 (mm) REVERT: C 314 MET cc_start: 0.8782 (tpt) cc_final: 0.8368 (tpp) REVERT: C 565 MET cc_start: 0.8834 (mmp) cc_final: 0.8378 (mmp) REVERT: C 1009 MET cc_start: 0.8915 (tpp) cc_final: 0.8653 (tpp) REVERT: B 154 MET cc_start: 0.8032 (mmm) cc_final: 0.7783 (mmm) REVERT: B 282 MET cc_start: 0.9534 (tpt) cc_final: 0.9306 (tpp) REVERT: B 304 MET cc_start: 0.9543 (ptm) cc_final: 0.9256 (ppp) REVERT: B 739 MET cc_start: 0.8941 (tpt) cc_final: 0.8739 (tpt) REVERT: B 799 MET cc_start: 0.7739 (tmm) cc_final: 0.7490 (tmm) REVERT: B 830 MET cc_start: 0.8720 (tpp) cc_final: 0.8158 (tpp) REVERT: B 1009 MET cc_start: 0.8174 (pmm) cc_final: 0.7541 (pmm) REVERT: D 302 LEU cc_start: 0.9699 (mt) cc_final: 0.9354 (mt) REVERT: D 306 PHE cc_start: 0.9418 (m-80) cc_final: 0.9065 (m-80) REVERT: D 881 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7569 (tm-30) REVERT: D 1009 MET cc_start: 0.9018 (mmp) cc_final: 0.8733 (mmp) outliers start: 21 outliers final: 16 residues processed: 168 average time/residue: 0.3377 time to fit residues: 98.5572 Evaluate side-chains 166 residues out of total 2948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 150 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 885 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 297 optimal weight: 9.9990 chunk 226 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 302 optimal weight: 10.0000 chunk 319 optimal weight: 3.9990 chunk 157 optimal weight: 0.4980 chunk 286 optimal weight: 1.9990 chunk 86 optimal weight: 50.0000 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 GLN ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27269 Z= 0.204 Angle : 0.569 11.841 36994 Z= 0.286 Chirality : 0.041 0.308 4237 Planarity : 0.004 0.056 4650 Dihedral : 4.260 37.358 3566 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.73 % Favored : 94.24 % Rotamer: Outliers : 0.92 % Allowed : 9.47 % Favored : 89.62 % 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: -0.38 (0.15), residues: 3295 helix: 0.12 (0.13), residues: 1521 sheet: 0.91 (0.29), residues: 365 loop : -0.89 (0.17), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 178 HIS 0.006 0.001 HIS A 749 PHE 0.036 0.001 PHE C 307 TYR 0.028 0.001 TYR B 279 ARG 0.004 0.000 ARG C 301 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 3.252 Fit side-chains revert: symmetry clash REVERT: A 252 PHE cc_start: 0.9315 (t80) cc_final: 0.8705 (t80) REVERT: A 285 MET cc_start: 0.9244 (mpp) cc_final: 0.8996 (mpp) REVERT: A 303 PHE cc_start: 0.9319 (m-80) cc_final: 0.8772 (t80) REVERT: A 307 PHE cc_start: 0.9071 (m-10) cc_final: 0.8545 (m-80) REVERT: A 881 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8191 (tm-30) REVERT: C 34 PHE cc_start: 0.6943 (m-80) cc_final: 0.6457 (m-80) REVERT: C 282 MET cc_start: 0.9434 (mmm) cc_final: 0.9180 (tpp) REVERT: C 285 MET cc_start: 0.9265 (mpp) cc_final: 0.8802 (mpp) REVERT: C 304 MET cc_start: 0.9613 (mmp) cc_final: 0.8829 (mmm) REVERT: C 307 PHE cc_start: 0.8264 (m-80) cc_final: 0.7942 (m-80) REVERT: C 312 LEU cc_start: 0.9237 (mm) cc_final: 0.8838 (mm) REVERT: C 314 MET cc_start: 0.8806 (tpt) cc_final: 0.8391 (tpp) REVERT: C 496 GLN cc_start: 0.9523 (OUTLIER) cc_final: 0.9291 (mm-40) REVERT: C 565 MET cc_start: 0.8902 (mmp) cc_final: 0.8502 (mmp) REVERT: C 1009 MET cc_start: 0.8957 (tpp) cc_final: 0.8688 (tpp) REVERT: B 154 MET cc_start: 0.8058 (mmm) cc_final: 0.7803 (mmm) REVERT: B 304 MET cc_start: 0.9546 (ptm) cc_final: 0.9244 (ppp) REVERT: B 830 MET cc_start: 0.8735 (tpp) cc_final: 0.8132 (tpp) REVERT: B 1009 MET cc_start: 0.8255 (pmm) cc_final: 0.7617 (pmm) REVERT: D 30 MET cc_start: 0.8164 (tpp) cc_final: 0.7859 (tpp) REVERT: D 302 LEU cc_start: 0.9659 (mt) cc_final: 0.9279 (mt) REVERT: D 303 PHE cc_start: 0.9291 (m-10) cc_final: 0.9063 (m-10) REVERT: D 306 PHE cc_start: 0.9440 (m-80) cc_final: 0.9085 (m-80) REVERT: D 881 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7600 (tm-30) REVERT: D 1009 MET cc_start: 0.9003 (mmp) cc_final: 0.8671 (mmp) outliers start: 27 outliers final: 22 residues processed: 164 average time/residue: 0.3353 time to fit residues: 94.1970 Evaluate side-chains 167 residues out of total 2948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 144 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 885 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 266 optimal weight: 8.9990 chunk 181 optimal weight: 7.9990 chunk 4 optimal weight: 30.0000 chunk 238 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 273 optimal weight: 5.9990 chunk 221 optimal weight: 8.9990 chunk 0 optimal weight: 60.0000 chunk 163 optimal weight: 4.9990 chunk 287 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN C 771 HIS ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 749 HIS ** D 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 27269 Z= 0.303 Angle : 0.618 11.595 36994 Z= 0.311 Chirality : 0.042 0.296 4237 Planarity : 0.004 0.056 4650 Dihedral : 4.387 39.856 3566 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.18 % Favored : 93.79 % Rotamer: Outliers : 0.95 % Allowed : 11.27 % Favored : 87.78 % 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: -0.44 (0.15), residues: 3295 helix: 0.08 (0.13), residues: 1536 sheet: 0.80 (0.29), residues: 365 loop : -0.91 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 178 HIS 0.007 0.001 HIS A 749 PHE 0.038 0.001 PHE C 303 TYR 0.021 0.001 TYR C 163 ARG 0.003 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 2.936 Fit side-chains revert: symmetry clash REVERT: A 252 PHE cc_start: 0.9330 (t80) cc_final: 0.8606 (t80) REVERT: A 285 MET cc_start: 0.9320 (mpp) cc_final: 0.9069 (mpp) REVERT: A 303 PHE cc_start: 0.9366 (m-80) cc_final: 0.8910 (t80) REVERT: A 307 PHE cc_start: 0.9131 (m-10) cc_final: 0.8421 (m-80) REVERT: A 881 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8229 (tm-30) REVERT: A 1049 ILE cc_start: 0.1388 (OUTLIER) cc_final: 0.0282 (tp) REVERT: C 30 MET cc_start: 0.9418 (pmm) cc_final: 0.9204 (pmm) REVERT: C 34 PHE cc_start: 0.6957 (m-80) cc_final: 0.6514 (m-80) REVERT: C 285 MET cc_start: 0.9287 (mpp) cc_final: 0.8921 (mpp) REVERT: C 304 MET cc_start: 0.9620 (mmp) cc_final: 0.9287 (mmm) REVERT: C 307 PHE cc_start: 0.8232 (m-80) cc_final: 0.7662 (m-80) REVERT: C 314 MET cc_start: 0.8836 (tpt) cc_final: 0.8305 (tmm) REVERT: C 513 MET cc_start: 0.8776 (tpt) cc_final: 0.8313 (tpt) REVERT: C 565 MET cc_start: 0.8911 (mmp) cc_final: 0.8594 (mmp) REVERT: C 1009 MET cc_start: 0.8990 (tpp) cc_final: 0.8734 (tpp) REVERT: B 154 MET cc_start: 0.8142 (mmm) cc_final: 0.7870 (mmm) REVERT: B 304 MET cc_start: 0.9527 (ptm) cc_final: 0.9218 (ppp) REVERT: B 442 MET cc_start: 0.9506 (mmm) cc_final: 0.9282 (mmm) REVERT: B 830 MET cc_start: 0.8825 (tpp) cc_final: 0.8164 (tpp) REVERT: B 881 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8155 (tm-30) REVERT: B 1009 MET cc_start: 0.8576 (pmm) cc_final: 0.7922 (pmm) REVERT: D 306 PHE cc_start: 0.9448 (m-80) cc_final: 0.9086 (m-80) REVERT: D 881 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7551 (tm-30) REVERT: D 1009 MET cc_start: 0.9009 (mmp) cc_final: 0.8754 (mmp) outliers start: 28 outliers final: 24 residues processed: 162 average time/residue: 0.3410 time to fit residues: 94.6149 Evaluate side-chains 167 residues out of total 2948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 2.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 950 GLU Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 885 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 107 optimal weight: 0.9980 chunk 288 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 320 optimal weight: 4.9990 chunk 265 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27269 Z= 0.210 Angle : 0.588 12.334 36994 Z= 0.293 Chirality : 0.042 0.317 4237 Planarity : 0.004 0.055 4650 Dihedral : 4.320 41.162 3566 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.88 % Favored : 94.09 % Rotamer: Outliers : 1.05 % Allowed : 12.01 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 3295 helix: 0.15 (0.13), residues: 1526 sheet: 0.80 (0.29), residues: 365 loop : -0.87 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 178 HIS 0.005 0.001 HIS A 749 PHE 0.034 0.001 PHE C 303 TYR 0.032 0.001 TYR B 279 ARG 0.004 0.000 ARG A 974 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 149 time to evaluate : 2.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 252 PHE cc_start: 0.9341 (t80) cc_final: 0.8642 (t80) REVERT: A 285 MET cc_start: 0.9308 (mpp) cc_final: 0.9057 (mpp) REVERT: A 303 PHE cc_start: 0.9363 (m-80) cc_final: 0.8768 (t80) REVERT: A 307 PHE cc_start: 0.9115 (m-10) cc_final: 0.8555 (m-80) REVERT: A 881 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8197 (tm-30) REVERT: C 30 MET cc_start: 0.9419 (pmm) cc_final: 0.9168 (pmm) REVERT: C 34 PHE cc_start: 0.6962 (m-80) cc_final: 0.6509 (m-80) REVERT: C 282 MET cc_start: 0.9470 (tpp) cc_final: 0.9116 (tpt) REVERT: C 285 MET cc_start: 0.9248 (mpp) cc_final: 0.8775 (mpp) REVERT: C 304 MET cc_start: 0.9624 (mmp) cc_final: 0.8779 (mmm) REVERT: C 307 PHE cc_start: 0.8277 (m-80) cc_final: 0.7850 (m-80) REVERT: C 312 LEU cc_start: 0.9180 (mm) cc_final: 0.8663 (mm) REVERT: C 314 MET cc_start: 0.8824 (tpt) cc_final: 0.8303 (tmm) REVERT: C 460 MET cc_start: 0.8131 (mmm) cc_final: 0.7900 (mmm) REVERT: C 513 MET cc_start: 0.8788 (tpt) cc_final: 0.8370 (tpt) REVERT: C 565 MET cc_start: 0.8889 (mmp) cc_final: 0.8568 (mmp) REVERT: C 1009 MET cc_start: 0.8969 (tpp) cc_final: 0.8720 (tpp) REVERT: B 154 MET cc_start: 0.8230 (mmm) cc_final: 0.7969 (mmm) REVERT: B 304 MET cc_start: 0.9526 (ptm) cc_final: 0.9217 (ppp) REVERT: B 442 MET cc_start: 0.9486 (mmm) cc_final: 0.9274 (mmm) REVERT: B 830 MET cc_start: 0.8769 (tpp) cc_final: 0.8079 (tpp) REVERT: B 881 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8163 (tm-30) REVERT: B 1009 MET cc_start: 0.8407 (pmm) cc_final: 0.7715 (pmm) REVERT: D 30 MET cc_start: 0.8089 (tpp) cc_final: 0.7875 (tpp) REVERT: D 306 PHE cc_start: 0.9393 (m-80) cc_final: 0.9047 (m-80) REVERT: D 881 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7550 (tm-30) REVERT: D 1009 MET cc_start: 0.9009 (mmp) cc_final: 0.8774 (mmp) outliers start: 31 outliers final: 23 residues processed: 166 average time/residue: 0.3368 time to fit residues: 96.8710 Evaluate side-chains 170 residues out of total 2948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 147 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 950 GLU Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 885 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 308 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 233 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 chunk 269 optimal weight: 0.5980 chunk 178 optimal weight: 8.9990 chunk 319 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 GLN C 397 GLN ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27269 Z= 0.188 Angle : 0.590 14.266 36994 Z= 0.291 Chirality : 0.041 0.309 4237 Planarity : 0.003 0.056 4650 Dihedral : 4.259 42.267 3566 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.82 % Favored : 94.15 % Rotamer: Outliers : 0.95 % Allowed : 12.66 % Favored : 86.39 % 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: -0.30 (0.15), residues: 3295 helix: 0.20 (0.14), residues: 1521 sheet: 0.83 (0.29), residues: 365 loop : -0.83 (0.17), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 178 HIS 0.005 0.001 HIS A 749 PHE 0.035 0.001 PHE C 303 TYR 0.021 0.001 TYR A 279 ARG 0.003 0.000 ARG C 301 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 3.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.9540 (t80) cc_final: 0.9304 (m-80) REVERT: A 252 PHE cc_start: 0.9328 (t80) cc_final: 0.8652 (t80) REVERT: A 303 PHE cc_start: 0.9349 (m-80) cc_final: 0.8755 (t80) REVERT: A 307 PHE cc_start: 0.9118 (m-10) cc_final: 0.8626 (m-80) REVERT: A 881 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8188 (tm-30) REVERT: A 1049 ILE cc_start: 0.1105 (OUTLIER) cc_final: 0.0062 (tp) REVERT: C 285 MET cc_start: 0.9236 (mpp) cc_final: 0.8722 (mpp) REVERT: C 304 MET cc_start: 0.9635 (mmp) cc_final: 0.8944 (mmm) REVERT: C 307 PHE cc_start: 0.8277 (m-80) cc_final: 0.7864 (m-80) REVERT: C 312 LEU cc_start: 0.9256 (mm) cc_final: 0.8759 (mm) REVERT: C 314 MET cc_start: 0.8851 (tpt) cc_final: 0.8363 (tpp) REVERT: C 460 MET cc_start: 0.8135 (mmm) cc_final: 0.7887 (mmm) REVERT: C 513 MET cc_start: 0.8785 (tpt) cc_final: 0.8497 (tpt) REVERT: C 565 MET cc_start: 0.8878 (mmp) cc_final: 0.8606 (mmp) REVERT: C 1009 MET cc_start: 0.8991 (tpp) cc_final: 0.8765 (tpp) REVERT: B 154 MET cc_start: 0.8267 (mmm) cc_final: 0.7999 (mmm) REVERT: B 304 MET cc_start: 0.9511 (ptm) cc_final: 0.9170 (ppp) REVERT: B 442 MET cc_start: 0.9481 (mmm) cc_final: 0.9263 (mmm) REVERT: B 830 MET cc_start: 0.8754 (tpp) cc_final: 0.7778 (tpp) REVERT: B 881 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8191 (tm-30) REVERT: B 1009 MET cc_start: 0.8437 (pmm) cc_final: 0.7716 (pmm) REVERT: D 30 MET cc_start: 0.8132 (tpp) cc_final: 0.7791 (tpp) REVERT: D 306 PHE cc_start: 0.9372 (m-80) cc_final: 0.8931 (m-80) REVERT: D 881 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7561 (tm-30) REVERT: D 1009 MET cc_start: 0.9005 (mmp) cc_final: 0.8769 (mmp) outliers start: 28 outliers final: 24 residues processed: 168 average time/residue: 0.3336 time to fit residues: 96.5154 Evaluate side-chains 169 residues out of total 2948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 3.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 950 GLU Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 885 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 202 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 250 optimal weight: 10.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27269 Z= 0.252 Angle : 0.613 13.642 36994 Z= 0.304 Chirality : 0.042 0.324 4237 Planarity : 0.004 0.055 4650 Dihedral : 4.322 44.283 3566 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.24 % Favored : 93.73 % Rotamer: Outliers : 1.09 % Allowed : 13.06 % Favored : 85.85 % 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: -0.37 (0.15), residues: 3295 helix: 0.15 (0.13), residues: 1536 sheet: 0.77 (0.29), residues: 365 loop : -0.88 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 178 HIS 0.005 0.001 HIS A 749 PHE 0.037 0.001 PHE C 303 TYR 0.034 0.001 TYR B 279 ARG 0.003 0.000 ARG C 301 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 146 time to evaluate : 3.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.9536 (t80) cc_final: 0.9306 (m-80) REVERT: A 252 PHE cc_start: 0.9335 (t80) cc_final: 0.8603 (t80) REVERT: A 303 PHE cc_start: 0.9373 (m-80) cc_final: 0.8910 (t80) REVERT: A 307 PHE cc_start: 0.9143 (m-10) cc_final: 0.8544 (m-80) REVERT: A 536 MET cc_start: 0.8792 (tpp) cc_final: 0.8518 (tpp) REVERT: A 881 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8203 (tm-30) REVERT: A 1049 ILE cc_start: 0.1261 (OUTLIER) cc_final: 0.0169 (pt) REVERT: C 282 MET cc_start: 0.9500 (tpp) cc_final: 0.9019 (tpp) REVERT: C 285 MET cc_start: 0.9256 (mpp) cc_final: 0.8756 (mpp) REVERT: C 307 PHE cc_start: 0.8360 (m-80) cc_final: 0.7910 (m-80) REVERT: C 312 LEU cc_start: 0.9239 (mm) cc_final: 0.8746 (mm) REVERT: C 314 MET cc_start: 0.8877 (tpt) cc_final: 0.8419 (tpp) REVERT: C 513 MET cc_start: 0.8827 (tpt) cc_final: 0.8530 (tpt) REVERT: C 565 MET cc_start: 0.8910 (mmp) cc_final: 0.8665 (mmp) REVERT: C 1009 MET cc_start: 0.9012 (tpp) cc_final: 0.8798 (tpp) REVERT: B 304 MET cc_start: 0.9515 (ptm) cc_final: 0.9171 (ppp) REVERT: B 442 MET cc_start: 0.9496 (mmm) cc_final: 0.9283 (mmm) REVERT: B 830 MET cc_start: 0.8841 (tpp) cc_final: 0.7868 (tpp) REVERT: B 881 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8211 (tm-30) REVERT: B 1009 MET cc_start: 0.8530 (pmm) cc_final: 0.7827 (pmm) REVERT: D 30 MET cc_start: 0.8206 (tpp) cc_final: 0.7977 (tpp) REVERT: D 306 PHE cc_start: 0.9345 (m-80) cc_final: 0.8888 (m-80) REVERT: D 881 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7560 (tm-30) REVERT: D 1009 MET cc_start: 0.9014 (mmp) cc_final: 0.8786 (mmp) outliers start: 32 outliers final: 29 residues processed: 162 average time/residue: 0.3340 time to fit residues: 93.4202 Evaluate side-chains 175 residues out of total 2948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 3.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 950 GLU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain A residue 1051 CYS Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 885 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 290 optimal weight: 10.0000 chunk 305 optimal weight: 10.0000 chunk 278 optimal weight: 1.9990 chunk 297 optimal weight: 0.0980 chunk 178 optimal weight: 20.0000 chunk 129 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 268 optimal weight: 5.9990 chunk 281 optimal weight: 0.9980 chunk 296 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN B 451 HIS ** B 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27269 Z= 0.169 Angle : 0.596 13.692 36994 Z= 0.292 Chirality : 0.042 0.328 4237 Planarity : 0.003 0.056 4650 Dihedral : 4.244 45.213 3566 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.98 % Allowed : 13.27 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 3295 helix: 0.21 (0.14), residues: 1523 sheet: 0.81 (0.29), residues: 365 loop : -0.83 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 178 HIS 0.004 0.001 HIS A 749 PHE 0.034 0.001 PHE C 303 TYR 0.017 0.001 TYR C 163 ARG 0.002 0.000 ARG C 301 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 153 time to evaluate : 2.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.9533 (t80) cc_final: 0.9306 (m-80) REVERT: A 252 PHE cc_start: 0.9336 (t80) cc_final: 0.8811 (t80) REVERT: A 303 PHE cc_start: 0.9339 (m-80) cc_final: 0.8889 (t80) REVERT: A 307 PHE cc_start: 0.9128 (m-10) cc_final: 0.8609 (m-80) REVERT: A 881 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8193 (tm-30) REVERT: C 252 PHE cc_start: 0.9471 (t80) cc_final: 0.9253 (t80) REVERT: C 282 MET cc_start: 0.9514 (tpp) cc_final: 0.9089 (tpp) REVERT: C 285 MET cc_start: 0.9275 (mpp) cc_final: 0.8804 (mpp) REVERT: C 303 PHE cc_start: 0.9239 (t80) cc_final: 0.8579 (t80) REVERT: C 307 PHE cc_start: 0.8211 (m-80) cc_final: 0.7322 (m-80) REVERT: C 312 LEU cc_start: 0.9282 (mm) cc_final: 0.8798 (mm) REVERT: C 314 MET cc_start: 0.8871 (tpt) cc_final: 0.8409 (tpp) REVERT: C 460 MET cc_start: 0.8153 (mmm) cc_final: 0.7917 (mmm) REVERT: C 565 MET cc_start: 0.8879 (mmp) cc_final: 0.8632 (mmp) REVERT: B 304 MET cc_start: 0.9503 (ptm) cc_final: 0.9167 (ppp) REVERT: B 436 GLU cc_start: 0.8973 (mp0) cc_final: 0.8338 (mp0) REVERT: B 830 MET cc_start: 0.8753 (tpp) cc_final: 0.7765 (tpp) REVERT: B 881 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8240 (tm-30) REVERT: B 1009 MET cc_start: 0.8406 (pmm) cc_final: 0.7665 (pmm) REVERT: D 30 MET cc_start: 0.8283 (tpp) cc_final: 0.8062 (tpp) REVERT: D 306 PHE cc_start: 0.9319 (m-80) cc_final: 0.8850 (m-80) REVERT: D 739 MET cc_start: 0.9219 (tpt) cc_final: 0.9014 (tpt) REVERT: D 881 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7540 (tm-30) REVERT: D 1009 MET cc_start: 0.9013 (mmp) cc_final: 0.8782 (mmp) outliers start: 29 outliers final: 24 residues processed: 170 average time/residue: 0.3350 time to fit residues: 98.5572 Evaluate side-chains 172 residues out of total 2948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 950 GLU Chi-restraints excluded: chain A residue 1051 CYS Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 885 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 195 optimal weight: 5.9990 chunk 314 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 218 optimal weight: 7.9990 chunk 329 optimal weight: 4.9990 chunk 303 optimal weight: 0.0370 chunk 262 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 202 optimal weight: 6.9990 chunk 161 optimal weight: 0.9980 overall best weight: 3.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27269 Z= 0.205 Angle : 0.616 15.707 36994 Z= 0.301 Chirality : 0.042 0.337 4237 Planarity : 0.003 0.055 4650 Dihedral : 4.261 46.124 3566 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.85 % Allowed : 13.37 % Favored : 85.78 % 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: -0.29 (0.15), residues: 3295 helix: 0.21 (0.14), residues: 1519 sheet: 0.82 (0.29), residues: 365 loop : -0.82 (0.17), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 178 HIS 0.005 0.001 HIS A 749 PHE 0.033 0.001 PHE C 303 TYR 0.033 0.001 TYR B 279 ARG 0.002 0.000 ARG A 207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6590 Ramachandran restraints generated. 3295 Oldfield, 0 Emsley, 3295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 3.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.9528 (t80) cc_final: 0.9303 (m-80) REVERT: A 252 PHE cc_start: 0.9303 (t80) cc_final: 0.8501 (t80) REVERT: A 303 PHE cc_start: 0.9342 (m-80) cc_final: 0.8763 (t80) REVERT: A 307 PHE cc_start: 0.9129 (m-10) cc_final: 0.8615 (m-80) REVERT: A 881 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8200 (tm-30) REVERT: A 1009 MET cc_start: 0.8518 (tpt) cc_final: 0.8233 (tpt) REVERT: C 282 MET cc_start: 0.9517 (tpp) cc_final: 0.9080 (tpp) REVERT: C 285 MET cc_start: 0.9251 (mpp) cc_final: 0.8732 (mpp) REVERT: C 303 PHE cc_start: 0.9223 (t80) cc_final: 0.8226 (t80) REVERT: C 307 PHE cc_start: 0.8196 (m-80) cc_final: 0.7284 (m-80) REVERT: C 312 LEU cc_start: 0.9270 (mm) cc_final: 0.8787 (mm) REVERT: C 314 MET cc_start: 0.8875 (tpt) cc_final: 0.8374 (tpp) REVERT: C 460 MET cc_start: 0.8256 (mmm) cc_final: 0.8050 (mmm) REVERT: C 565 MET cc_start: 0.8862 (mmp) cc_final: 0.8628 (mmp) REVERT: C 1009 MET cc_start: 0.9091 (tpp) cc_final: 0.8785 (tpp) REVERT: B 282 MET cc_start: 0.9510 (tpt) cc_final: 0.9240 (tpp) REVERT: B 304 MET cc_start: 0.9517 (ptm) cc_final: 0.9175 (ppp) REVERT: B 436 GLU cc_start: 0.8962 (mp0) cc_final: 0.8449 (mp0) REVERT: B 830 MET cc_start: 0.8796 (tpp) cc_final: 0.7803 (tpp) REVERT: B 881 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8253 (tm-30) REVERT: B 1009 MET cc_start: 0.8473 (pmm) cc_final: 0.7721 (pmm) REVERT: D 306 PHE cc_start: 0.9326 (m-80) cc_final: 0.8855 (m-80) REVERT: D 739 MET cc_start: 0.9227 (tpt) cc_final: 0.8984 (tpt) REVERT: D 881 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7561 (tm-30) REVERT: D 1009 MET cc_start: 0.9018 (mmp) cc_final: 0.8789 (mmp) outliers start: 25 outliers final: 25 residues processed: 164 average time/residue: 0.3373 time to fit residues: 95.5560 Evaluate side-chains 172 residues out of total 2948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 950 GLU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1051 CYS Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 923 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 817 ASP Chi-restraints excluded: chain D residue 885 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 208 optimal weight: 6.9990 chunk 279 optimal weight: 10.0000 chunk 80 optimal weight: 0.0000 chunk 242 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 263 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 270 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.069365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.046333 restraints weight = 246852.615| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 7.05 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27269 Z= 0.197 Angle : 0.619 15.222 36994 Z= 0.302 Chirality : 0.042 0.323 4237 Planarity : 0.003 0.055 4650 Dihedral : 4.252 47.102 3566 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.88 % Allowed : 13.40 % Favored : 85.71 % 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: -0.30 (0.15), residues: 3295 helix: 0.21 (0.14), residues: 1519 sheet: 0.81 (0.29), residues: 365 loop : -0.82 (0.17), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 178 HIS 0.005 0.001 HIS A 749 PHE 0.040 0.001 PHE C 307 TYR 0.031 0.001 TYR B 279 ARG 0.002 0.000 ARG A 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4509.91 seconds wall clock time: 84 minutes 4.66 seconds (5044.66 seconds total)