Starting phenix.real_space_refine on Sat Jan 20 02:20:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5v_10704/01_2024/6y5v_10704.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5v_10704/01_2024/6y5v_10704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5v_10704/01_2024/6y5v_10704.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5v_10704/01_2024/6y5v_10704.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5v_10704/01_2024/6y5v_10704.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5v_10704/01_2024/6y5v_10704.pdb" } resolution = 4.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 92 5.16 5 C 8728 2.51 5 N 2215 2.21 5 O 2365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 116": "OE1" <-> "OE2" Residue "A PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "A PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 917": "NH1" <-> "NH2" Residue "A GLU 1041": "OE1" <-> "OE2" Residue "A GLU 1065": "OE1" <-> "OE2" Residue "A GLU 1082": "OE1" <-> "OE2" Residue "B PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 497": "NH1" <-> "NH2" Residue "B GLU 580": "OE1" <-> "OE2" Residue "B GLU 768": "OE1" <-> "OE2" Residue "B ARG 891": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13400 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 879, 6641 Classifications: {'peptide': 879} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 32, 'TRANS': 846} Chain breaks: 4 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 106 Chain: "B" Number of atoms: 6653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 879, 6653 Classifications: {'peptide': 879} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 32, 'TRANS': 846} Chain breaks: 4 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 14, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 103 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.47, per 1000 atoms: 0.56 Number of scatterers: 13400 At special positions: 0 Unit cell: (149.4, 107.07, 94.62, 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 92 16.00 O 2365 8.00 N 2215 7.00 C 8728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 640 " distance=2.04 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 359 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 640 " distance=2.02 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 359 " - pdb=" SG CYS B 369 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A1204 " - " ASN A 377 " " NAG B1204 " - " ASN B 377 " " NAG C 1 " - " ASN A 328 " " NAG D 1 " - " ASN B 328 " Time building additional restraints: 5.66 Conformation dependent library (CDL) restraints added in 2.5 seconds 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3232 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 6 sheets defined 62.1% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 111 through 121 removed outlier: 3.536A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 156 through 193 removed outlier: 6.493A pdb=" N VAL A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N LEU A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 243 removed outlier: 3.651A pdb=" N MET A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 211 - end of helix Processing helix chain 'A' and resid 261 through 284 Processing helix chain 'A' and resid 285 through 314 removed outlier: 3.716A pdb=" N VAL A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N SER A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 removed outlier: 3.621A pdb=" N GLY A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.685A pdb=" N VAL A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N HIS A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 376' Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 433 through 442 removed outlier: 3.854A pdb=" N GLY A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 447 through 453 removed outlier: 3.650A pdb=" N SER A 452 " --> pdb=" O MET A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 491 Proline residue: A 466 - end of helix removed outlier: 3.836A pdb=" N VAL A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 513 removed outlier: 3.965A pdb=" N LEU A 513 " --> pdb=" O VAL A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 550 removed outlier: 4.277A pdb=" N ILE A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Proline residue: A 541 - end of helix removed outlier: 3.520A pdb=" N ASP A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 561 removed outlier: 3.872A pdb=" N VAL A 558 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 584 removed outlier: 3.577A pdb=" N LEU A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 616 Proline residue: A 593 - end of helix removed outlier: 3.745A pdb=" N CYS A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 675 removed outlier: 3.607A pdb=" N SER A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N TYR A 650 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N TYR A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 654 " --> pdb=" O TYR A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 696 removed outlier: 3.612A pdb=" N GLU A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 734 removed outlier: 4.186A pdb=" N LEU A 726 " --> pdb=" O HIS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 751 Processing helix chain 'A' and resid 752 through 770 Processing helix chain 'A' and resid 783 through 795 removed outlier: 3.937A pdb=" N GLN A 793 " --> pdb=" O SER A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 835 Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 868 through 881 Proline residue: A 876 - end of helix Processing helix chain 'A' and resid 906 through 917 removed outlier: 3.745A pdb=" N PHE A 912 " --> pdb=" O ASP A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 931 No H-bonds generated for 'chain 'A' and resid 929 through 931' Processing helix chain 'A' and resid 932 through 946 removed outlier: 4.052A pdb=" N GLU A 938 " --> pdb=" O ALA A 934 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 946 " --> pdb=" O MET A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1048 Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1066 through 1078 Processing helix chain 'B' and resid 111 through 121 removed outlier: 3.567A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 149 removed outlier: 3.540A pdb=" N CYS B 144 " --> pdb=" O VAL B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 156 through 193 removed outlier: 6.320A pdb=" N VAL B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N LEU B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 243 removed outlier: 3.615A pdb=" N MET B 204 " --> pdb=" O GLY B 200 " (cutoff:3.500A) Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 261 through 284 Processing helix chain 'B' and resid 285 through 314 removed outlier: 3.712A pdb=" N VAL B 289 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N SER B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LEU B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 359 removed outlier: 3.530A pdb=" N GLY B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 376 removed outlier: 3.637A pdb=" N VAL B 374 " --> pdb=" O ASP B 370 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 433 through 442 removed outlier: 3.849A pdb=" N GLY B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 445 No H-bonds generated for 'chain 'B' and resid 443 through 445' Processing helix chain 'B' and resid 447 through 451 Processing helix chain 'B' and resid 460 through 489 Proline residue: B 466 - end of helix removed outlier: 3.667A pdb=" N VAL B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 517 through 550 removed outlier: 4.210A pdb=" N ILE B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Proline residue: B 541 - end of helix removed outlier: 3.502A pdb=" N ASP B 550 " --> pdb=" O ALA B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 561 removed outlier: 3.998A pdb=" N VAL B 558 " --> pdb=" O PHE B 555 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS B 561 " --> pdb=" O VAL B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 584 Processing helix chain 'B' and resid 587 through 616 Proline residue: B 593 - end of helix removed outlier: 3.728A pdb=" N CYS B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 675 removed outlier: 3.795A pdb=" N SER B 633 " --> pdb=" O HIS B 629 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N TYR B 650 " --> pdb=" O ILE B 646 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N TYR B 651 " --> pdb=" O SER B 647 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 654 " --> pdb=" O TYR B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 696 removed outlier: 3.669A pdb=" N GLU B 696 " --> pdb=" O LEU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 734 removed outlier: 3.996A pdb=" N LEU B 726 " --> pdb=" O HIS B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 751 Processing helix chain 'B' and resid 752 through 770 Processing helix chain 'B' and resid 783 through 795 removed outlier: 3.879A pdb=" N GLN B 793 " --> pdb=" O SER B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 835 removed outlier: 3.722A pdb=" N LYS B 823 " --> pdb=" O ALA B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 Processing helix chain 'B' and resid 868 through 881 removed outlier: 4.065A pdb=" N LEU B 872 " --> pdb=" O ASP B 868 " (cutoff:3.500A) Proline residue: B 876 - end of helix Processing helix chain 'B' and resid 884 through 886 No H-bonds generated for 'chain 'B' and resid 884 through 886' Processing helix chain 'B' and resid 906 through 917 removed outlier: 3.518A pdb=" N ALA B 910 " --> pdb=" O LYS B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 931 No H-bonds generated for 'chain 'B' and resid 929 through 931' Processing helix chain 'B' and resid 932 through 946 removed outlier: 3.954A pdb=" N GLU B 938 " --> pdb=" O ALA B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1048 Processing helix chain 'B' and resid 1066 through 1078 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA3, first strand: chain 'A' and resid 775 through 781 removed outlier: 6.463A pdb=" N LEU A 708 " --> pdb=" O ILE A 740 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLY A 742 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL A 710 " --> pdb=" O GLY A 742 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL A 744 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY A 808 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL A 805 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA A 842 " --> pdb=" O VAL A 805 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET A 807 " --> pdb=" O ALA A 842 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL A1053 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL A1087 " --> pdb=" O VAL A1053 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU A1055 " --> pdb=" O VAL A1087 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU A1054 " --> pdb=" O ASN A 859 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASP A 861 " --> pdb=" O LEU A1054 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ASN A1056 " --> pdb=" O ASP A 861 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N TRP A 863 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 921 " --> pdb=" O ILE A 890 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AA5, first strand: chain 'B' and resid 342 through 345 Processing sheet with id=AA6, first strand: chain 'B' and resid 775 through 781 removed outlier: 6.534A pdb=" N LEU B 708 " --> pdb=" O ILE B 740 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLY B 742 " --> pdb=" O LEU B 708 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL B 710 " --> pdb=" O GLY B 742 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N VAL B 744 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLY B 808 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL B 805 " --> pdb=" O LEU B 840 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ALA B 842 " --> pdb=" O VAL B 805 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N MET B 807 " --> pdb=" O ALA B 842 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B1084 " --> pdb=" O LYS B 843 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B1053 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL B1087 " --> pdb=" O VAL B1053 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU B1055 " --> pdb=" O VAL B1087 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU B1054 " --> pdb=" O ASN B 859 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP B 861 " --> pdb=" O LEU B1054 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASN B1056 " --> pdb=" O ASP B 861 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N TRP B 863 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N GLU B 921 " --> pdb=" O CYS B 888 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE B 890 " --> pdb=" O GLU B 921 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLU B 923 " --> pdb=" O ILE B 890 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE B 892 " --> pdb=" O GLU B 923 " (cutoff:3.500A) 799 hydrogen bonds defined for protein. 2307 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.48 Time building geometry restraints manager: 6.03 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: 4188 1.35 - 1.47: 3417 1.47 - 1.59: 5955 1.59 - 1.71: 0 1.71 - 1.83: 146 Bond restraints: 13706 Sorted by residual: bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" C1 NAG A1204 " pdb=" O5 NAG A1204 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.51e+00 bond pdb=" C1 NAG B1204 " pdb=" O5 NAG B1204 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" CG1 ILE B 473 " pdb=" CD1 ILE B 473 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.12e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.06e+00 ... (remaining 13701 not shown) Histogram of bond angle deviations from ideal: 98.90 - 105.93: 288 105.93 - 112.97: 7632 112.97 - 120.01: 4730 120.01 - 127.04: 5823 127.04 - 134.08: 179 Bond angle restraints: 18652 Sorted by residual: angle pdb=" N TRP A 864 " pdb=" CA TRP A 864 " pdb=" C TRP A 864 " ideal model delta sigma weight residual 108.23 116.47 -8.24 1.72e+00 3.38e-01 2.30e+01 angle pdb=" C ILE B 639 " pdb=" N CYS B 640 " pdb=" CA CYS B 640 " ideal model delta sigma weight residual 122.38 115.97 6.41 1.81e+00 3.05e-01 1.26e+01 angle pdb=" C VAL A 866 " pdb=" N HIS A 867 " pdb=" CA HIS A 867 " ideal model delta sigma weight residual 122.59 117.57 5.02 1.57e+00 4.06e-01 1.02e+01 angle pdb=" N PHE B 442 " pdb=" CA PHE B 442 " pdb=" C PHE B 442 " ideal model delta sigma weight residual 109.81 116.76 -6.95 2.21e+00 2.05e-01 9.88e+00 angle pdb=" N VAL B 866 " pdb=" CA VAL B 866 " pdb=" C VAL B 866 " ideal model delta sigma weight residual 109.34 115.77 -6.43 2.08e+00 2.31e-01 9.55e+00 ... (remaining 18647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.80: 7721 21.80 - 43.59: 324 43.59 - 65.39: 32 65.39 - 87.19: 14 87.19 - 108.99: 8 Dihedral angle restraints: 8099 sinusoidal: 3068 harmonic: 5031 Sorted by residual: dihedral pdb=" CA CYS B 640 " pdb=" C CYS B 640 " pdb=" N LEU B 641 " pdb=" CA LEU B 641 " ideal model delta harmonic sigma weight residual 180.00 155.11 24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ILE B 865 " pdb=" C ILE B 865 " pdb=" N VAL B 866 " pdb=" CA VAL B 866 " ideal model delta harmonic sigma weight residual 180.00 -156.41 -23.59 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLN B 707 " pdb=" C GLN B 707 " pdb=" N LEU B 708 " pdb=" CA LEU B 708 " ideal model delta harmonic sigma weight residual -180.00 -156.60 -23.40 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 8096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1778 0.055 - 0.110: 389 0.110 - 0.165: 54 0.165 - 0.219: 1 0.219 - 0.274: 2 Chirality restraints: 2224 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB ILE B 865 " pdb=" CA ILE B 865 " pdb=" CG1 ILE B 865 " pdb=" CG2 ILE B 865 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 2221 not shown) Planarity restraints: 2309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B1034 " 0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C HIS B1034 " -0.073 2.00e-02 2.50e+03 pdb=" O HIS B1034 " 0.027 2.00e-02 2.50e+03 pdb=" N THR B1035 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 536 " -0.020 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C SER A 536 " 0.071 2.00e-02 2.50e+03 pdb=" O SER A 536 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU A 537 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 536 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.17e+01 pdb=" C SER B 536 " 0.059 2.00e-02 2.50e+03 pdb=" O SER B 536 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU B 537 " -0.020 2.00e-02 2.50e+03 ... (remaining 2306 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2441 2.77 - 3.30: 13570 3.30 - 3.83: 22102 3.83 - 4.37: 25069 4.37 - 4.90: 43729 Nonbonded interactions: 106911 Sorted by model distance: nonbonded pdb=" O PRO A1058 " pdb=" OH TYR A1070 " model vdw 2.232 2.440 nonbonded pdb=" NH1 ARG A 680 " pdb=" O PRO B 698 " model vdw 2.241 2.520 nonbonded pdb=" OD1 ASN B 859 " pdb=" OG SER B 889 " model vdw 2.277 2.440 nonbonded pdb=" O SER A 789 " pdb=" NE2 GLN A 793 " model vdw 2.313 2.520 nonbonded pdb=" O PHE B 825 " pdb=" OG1 THR B 828 " model vdw 2.313 2.440 ... (remaining 106906 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 102 through 312 or (resid 313 and (name N or name CA or na \ me C or name O or name CB )) or resid 314 through 341 or (resid 342 and (name N \ or name CA or name C or name O or name CB )) or resid 343 through 393 or (resid \ 394 and (name N or name CA or name C or name O or name CB )) or resid 395 throug \ h 491 or (resid 492 and (name N or name CA or name C or name O or name CB )) or \ resid 493 through 504 or (resid 505 and (name N or name CA or name C or name O o \ r name CB )) or resid 506 through 715 or (resid 716 and (name N or name CA or na \ me C or name O or name CB )) or resid 717 through 772 or (resid 773 and (name N \ or name CA or name C or name O or name CB )) or resid 774 through 856 or (resid \ 857 and (name N or name CA or name C or name O or name CB )) or resid 858 throug \ h 872 or (resid 873 and (name N or name CA or name C or name O or name CB )) or \ resid 874 through 882 or (resid 883 and (name N or name CA or name C or name O o \ r name CB )) or resid 884 through 913 or (resid 914 and (name N or name CA or na \ me C or name O or name CB )) or resid 915 through 918 or (resid 919 through 920 \ and (name N or name CA or name C or name O or name CB )) or resid 921 through 92 \ 6 or (resid 927 and (name N or name CA or name C or name O or name CB )) or resi \ d 928 through 937 or (resid 938 through 946 and (name N or name CA or name C or \ name O or name CB )) or resid 1028 or (resid 1029 and (name N or name CA or name \ C or name O or name CB )) or resid 1030 through 1045 or (resid 1046 and (name N \ or name CA or name C or name O or name CB )) or resid 1047 through 1078 or (res \ id 1079 and (name N or name CA or name C or name O or name CB )) or resid 1080 t \ hrough 1081 or (resid 1082 and (name N or name CA or name C or name O or name CB \ )) or resid 1083 through 1093 or resid 1204)) selection = (chain 'B' and (resid 102 through 112 or (resid 113 through 114 and (name N or n \ ame CA or name C or name O or name CB )) or resid 115 through 116 or (resid 117 \ through 121 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 3 through 211 or (resid 212 and (name N or name CA or name C or name O or name C \ B )) or resid 213 through 286 or (resid 287 and (name N or name CA or name C or \ name O or name CB )) or resid 288 through 290 or (resid 291 and (name N or name \ CA or name C or name O or name CB )) or resid 292 through 346 or (resid 347 thro \ ugh 348 and (name N or name CA or name C or name O or name CB )) or resid 349 th \ rough 364 or (resid 365 through 367 and (name N or name CA or name C or name O o \ r name CB )) or resid 368 through 417 or (resid 418 and (name N or name CA or na \ me C or name O or name CB )) or resid 419 through 420 or (resid 421 and (name N \ or name CA or name C or name O or name CB )) or resid 422 through 462 or (resid \ 463 and (name N or name CA or name C or name O or name CB )) or resid 464 throug \ h 616 or (resid 617 and (name N or name CA or name C or name O or name CB )) or \ resid 618 through 634 or (resid 635 and (name N or name CA or name C or name O o \ r name CB )) or resid 636 through 694 or (resid 695 and (name N or name CA or na \ me C or name O or name CB )) or resid 696 through 886 or (resid 887 and (name N \ or name CA or name C or name O or name CB )) or resid 888 through 896 or (resid \ 905 through 907 and (name N or name CA or name C or name O or name CB )) or resi \ d 908 through 939 or (resid 940 through 946 and (name N or name CA or name C or \ name O or name CB )) or resid 1028 through 1093 or resid 1204)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.350 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 39.050 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13706 Z= 0.270 Angle : 0.681 8.244 18652 Z= 0.375 Chirality : 0.046 0.274 2224 Planarity : 0.005 0.042 2305 Dihedral : 12.747 108.986 4849 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.29 % Allowed : 2.96 % Favored : 96.75 % 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: -2.25 (0.18), residues: 1738 helix: -0.66 (0.15), residues: 932 sheet: -2.03 (0.42), residues: 100 loop : -2.51 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 570 HIS 0.011 0.001 HIS A 867 PHE 0.017 0.001 PHE B 847 TYR 0.020 0.002 TYR A 935 ARG 0.003 0.000 ARG A1083 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 421 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ILE cc_start: 0.9185 (mt) cc_final: 0.8981 (tt) REVERT: A 303 SER cc_start: 0.9185 (m) cc_final: 0.8975 (p) REVERT: A 334 ARG cc_start: 0.7112 (mtt180) cc_final: 0.6742 (mtt180) REVERT: A 360 ASN cc_start: 0.7688 (m-40) cc_final: 0.7405 (p0) REVERT: A 536 SER cc_start: 0.9398 (m) cc_final: 0.9131 (t) REVERT: A 551 ASN cc_start: 0.8103 (m-40) cc_final: 0.7552 (t0) REVERT: A 590 LEU cc_start: 0.8761 (mt) cc_final: 0.8494 (mt) REVERT: A 601 MET cc_start: 0.8868 (tpp) cc_final: 0.8661 (tpp) REVERT: A 628 TYR cc_start: 0.8229 (t80) cc_final: 0.8023 (t80) REVERT: A 707 GLN cc_start: 0.9296 (mm-40) cc_final: 0.9017 (mm110) REVERT: B 278 MET cc_start: 0.8579 (mmp) cc_final: 0.8098 (mmp) REVERT: B 372 TYR cc_start: 0.8182 (t80) cc_final: 0.7648 (t80) REVERT: B 381 ILE cc_start: 0.7907 (mt) cc_final: 0.7454 (mm) REVERT: B 445 VAL cc_start: 0.9489 (m) cc_final: 0.9222 (t) REVERT: B 523 ILE cc_start: 0.9220 (pt) cc_final: 0.8747 (tp) REVERT: B 536 SER cc_start: 0.9471 (m) cc_final: 0.9205 (p) REVERT: B 562 SER cc_start: 0.8845 (m) cc_final: 0.8573 (t) REVERT: B 573 LEU cc_start: 0.8858 (tp) cc_final: 0.8574 (mm) REVERT: B 590 LEU cc_start: 0.8560 (mt) cc_final: 0.8277 (mt) REVERT: B 601 MET cc_start: 0.8589 (tpp) cc_final: 0.8290 (tpp) REVERT: B 863 TRP cc_start: 0.8545 (m100) cc_final: 0.8007 (m100) REVERT: B 886 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.8023 (ttm-80) REVERT: B 892 ILE cc_start: 0.9177 (mm) cc_final: 0.8925 (mp) outliers start: 4 outliers final: 2 residues processed: 424 average time/residue: 0.2477 time to fit residues: 151.8377 Evaluate side-chains 269 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 267 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 136 optimal weight: 0.1980 chunk 52 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 158 optimal weight: 0.5980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 346 ASN A 882 HIS A1040 ASN B 133 GLN B 483 ASN B 613 GLN ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 ASN B 867 HIS B 881 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13706 Z= 0.222 Angle : 0.590 9.364 18652 Z= 0.302 Chirality : 0.043 0.257 2224 Planarity : 0.004 0.046 2305 Dihedral : 7.301 69.446 2021 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.60 % 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: -0.49 (0.20), residues: 1738 helix: 0.88 (0.16), residues: 956 sheet: -2.24 (0.40), residues: 136 loop : -1.70 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 809 HIS 0.005 0.001 HIS B 802 PHE 0.017 0.001 PHE A1073 TYR 0.019 0.001 TYR A 935 ARG 0.007 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 337 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 VAL cc_start: 0.8939 (t) cc_final: 0.8707 (t) REVERT: A 360 ASN cc_start: 0.7510 (m-40) cc_final: 0.7296 (p0) REVERT: A 505 LYS cc_start: 0.8486 (mmmt) cc_final: 0.7907 (ptmt) REVERT: A 536 SER cc_start: 0.9336 (m) cc_final: 0.9098 (t) REVERT: A 590 LEU cc_start: 0.8736 (mt) cc_final: 0.8521 (mt) REVERT: A 601 MET cc_start: 0.9108 (tpp) cc_final: 0.8335 (tpp) REVERT: A 628 TYR cc_start: 0.8173 (t80) cc_final: 0.7860 (t80) REVERT: A 861 ASP cc_start: 0.7095 (m-30) cc_final: 0.6779 (m-30) REVERT: A 1038 LYS cc_start: 0.9288 (tttt) cc_final: 0.9039 (ttmt) REVERT: B 278 MET cc_start: 0.8543 (mmp) cc_final: 0.8042 (mmp) REVERT: B 372 TYR cc_start: 0.8213 (t80) cc_final: 0.7684 (t80) REVERT: B 381 ILE cc_start: 0.7478 (mt) cc_final: 0.7066 (mm) REVERT: B 397 TRP cc_start: 0.8316 (m100) cc_final: 0.8114 (m100) REVERT: B 523 ILE cc_start: 0.9181 (pt) cc_final: 0.8767 (tp) REVERT: B 536 SER cc_start: 0.9477 (m) cc_final: 0.9067 (p) REVERT: B 573 LEU cc_start: 0.8877 (tp) cc_final: 0.8492 (mm) REVERT: B 597 MET cc_start: 0.9337 (tpp) cc_final: 0.9055 (tpp) REVERT: B 707 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7876 (mp10) REVERT: B 867 HIS cc_start: 0.6618 (OUTLIER) cc_final: 0.6396 (t-170) REVERT: B 886 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.7962 (ttm-80) REVERT: B 892 ILE cc_start: 0.9225 (mm) cc_final: 0.9003 (mp) outliers start: 1 outliers final: 0 residues processed: 337 average time/residue: 0.2201 time to fit residues: 111.6562 Evaluate side-chains 250 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 249 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 43 optimal weight: 0.0170 chunk 158 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN A 613 GLN ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 HIS B 915 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13706 Z= 0.308 Angle : 0.627 10.489 18652 Z= 0.320 Chirality : 0.044 0.199 2224 Planarity : 0.004 0.039 2305 Dihedral : 5.938 48.738 2021 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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: 0.02 (0.21), residues: 1738 helix: 1.30 (0.17), residues: 958 sheet: -2.12 (0.41), residues: 136 loop : -1.47 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 864 HIS 0.009 0.001 HIS B 790 PHE 0.023 0.002 PHE B 775 TYR 0.012 0.001 TYR B 753 ARG 0.007 0.000 ARG A 891 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 SER cc_start: 0.8684 (t) cc_final: 0.8305 (p) REVERT: A 360 ASN cc_start: 0.7472 (m-40) cc_final: 0.7251 (p0) REVERT: A 505 LYS cc_start: 0.8520 (mmmt) cc_final: 0.7939 (ptmt) REVERT: A 590 LEU cc_start: 0.8752 (mt) cc_final: 0.8542 (mt) REVERT: A 601 MET cc_start: 0.9173 (tpp) cc_final: 0.8854 (tpp) REVERT: A 628 TYR cc_start: 0.8382 (t80) cc_final: 0.7998 (t80) REVERT: A 637 MET cc_start: 0.9158 (ttm) cc_final: 0.8058 (tmm) REVERT: A 822 TRP cc_start: 0.8529 (p-90) cc_final: 0.8123 (p-90) REVERT: A 880 LYS cc_start: 0.7406 (tttp) cc_final: 0.7147 (ttmt) REVERT: A 1071 MET cc_start: 0.8372 (tpt) cc_final: 0.7961 (tpp) REVERT: B 312 ILE cc_start: 0.8650 (mm) cc_final: 0.8445 (pt) REVERT: B 314 SER cc_start: 0.8987 (t) cc_final: 0.8718 (p) REVERT: B 358 PHE cc_start: 0.7988 (m-80) cc_final: 0.7700 (m-80) REVERT: B 397 TRP cc_start: 0.8349 (m100) cc_final: 0.8103 (m100) REVERT: B 436 LEU cc_start: 0.9086 (tp) cc_final: 0.8874 (tp) REVERT: B 523 ILE cc_start: 0.9184 (pt) cc_final: 0.8831 (tp) REVERT: B 536 SER cc_start: 0.9486 (m) cc_final: 0.8981 (p) REVERT: B 573 LEU cc_start: 0.8877 (tp) cc_final: 0.8504 (mm) REVERT: B 590 LEU cc_start: 0.8537 (mt) cc_final: 0.8279 (mt) REVERT: B 597 MET cc_start: 0.9162 (tpp) cc_final: 0.8691 (tpt) REVERT: B 886 ARG cc_start: 0.8126 (ttm-80) cc_final: 0.7868 (ttm-80) REVERT: B 892 ILE cc_start: 0.9248 (mm) cc_final: 0.9041 (mp) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.2105 time to fit residues: 103.2960 Evaluate side-chains 242 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.0970 chunk 119 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 106 optimal weight: 0.0970 chunk 158 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 790 HIS B 867 HIS ** B1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13706 Z= 0.171 Angle : 0.559 9.001 18652 Z= 0.283 Chirality : 0.042 0.217 2224 Planarity : 0.003 0.036 2305 Dihedral : 4.777 28.968 2021 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.07 % Allowed : 2.75 % Favored : 97.18 % 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: 0.50 (0.21), residues: 1738 helix: 1.67 (0.17), residues: 962 sheet: -1.75 (0.42), residues: 136 loop : -1.27 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 630 HIS 0.006 0.001 HIS A 915 PHE 0.018 0.001 PHE B 775 TYR 0.014 0.001 TYR B1070 ARG 0.008 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 322 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 SER cc_start: 0.8632 (t) cc_final: 0.8287 (p) REVERT: A 360 ASN cc_start: 0.7520 (m-40) cc_final: 0.7244 (p0) REVERT: A 505 LYS cc_start: 0.8505 (mmmt) cc_final: 0.7929 (ptmt) REVERT: A 597 MET cc_start: 0.8945 (tpp) cc_final: 0.8512 (tpp) REVERT: A 601 MET cc_start: 0.9130 (tpp) cc_final: 0.8704 (tpp) REVERT: A 628 TYR cc_start: 0.8229 (t80) cc_final: 0.7962 (t80) REVERT: A 637 MET cc_start: 0.9163 (ttm) cc_final: 0.8005 (tmm) REVERT: A 644 MET cc_start: 0.9088 (mtm) cc_final: 0.8235 (ttm) REVERT: A 803 ASN cc_start: 0.8855 (p0) cc_final: 0.8112 (p0) REVERT: A 822 TRP cc_start: 0.8472 (p-90) cc_final: 0.8070 (p-90) REVERT: A 880 LYS cc_start: 0.7371 (tttp) cc_final: 0.7102 (ttmt) REVERT: A 1071 MET cc_start: 0.8267 (tpt) cc_final: 0.7875 (tpp) REVERT: B 301 ILE cc_start: 0.9158 (mm) cc_final: 0.8956 (mm) REVERT: B 355 TRP cc_start: 0.6444 (t-100) cc_final: 0.6209 (t-100) REVERT: B 381 ILE cc_start: 0.7811 (mm) cc_final: 0.7416 (mm) REVERT: B 397 TRP cc_start: 0.8295 (m100) cc_final: 0.8037 (m100) REVERT: B 523 ILE cc_start: 0.9149 (pt) cc_final: 0.8772 (tp) REVERT: B 536 SER cc_start: 0.9488 (m) cc_final: 0.8926 (p) REVERT: B 573 LEU cc_start: 0.8803 (tp) cc_final: 0.8423 (mm) REVERT: B 590 LEU cc_start: 0.8440 (mt) cc_final: 0.8197 (mt) REVERT: B 597 MET cc_start: 0.9172 (tpp) cc_final: 0.8948 (tpp) REVERT: B 863 TRP cc_start: 0.8657 (m100) cc_final: 0.8312 (m100) REVERT: B 867 HIS cc_start: 0.6726 (OUTLIER) cc_final: 0.6506 (t-170) REVERT: B 886 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7680 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 323 average time/residue: 0.2538 time to fit residues: 123.8380 Evaluate side-chains 238 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN B 867 HIS ** B1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13706 Z= 0.254 Angle : 0.585 8.905 18652 Z= 0.296 Chirality : 0.043 0.189 2224 Planarity : 0.003 0.032 2305 Dihedral : 4.403 22.670 2021 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % 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: 0.48 (0.21), residues: 1738 helix: 1.57 (0.17), residues: 978 sheet: -1.49 (0.43), residues: 132 loop : -1.28 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 630 HIS 0.005 0.001 HIS A 802 PHE 0.021 0.001 PHE B1073 TYR 0.011 0.001 TYR B 753 ARG 0.006 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 ARG cc_start: 0.7113 (mtt-85) cc_final: 0.6570 (mtt180) REVERT: A 360 ASN cc_start: 0.7462 (m-40) cc_final: 0.7205 (p0) REVERT: A 505 LYS cc_start: 0.8558 (mmmt) cc_final: 0.8059 (pttt) REVERT: A 601 MET cc_start: 0.9150 (tpp) cc_final: 0.8744 (tpp) REVERT: A 628 TYR cc_start: 0.8460 (t80) cc_final: 0.8036 (t80) REVERT: A 822 TRP cc_start: 0.8548 (p-90) cc_final: 0.7570 (p-90) REVERT: A 880 LYS cc_start: 0.7480 (tttp) cc_final: 0.7157 (ttmt) REVERT: A 1071 MET cc_start: 0.8274 (tpt) cc_final: 0.7965 (tpp) REVERT: B 314 SER cc_start: 0.8990 (t) cc_final: 0.8703 (p) REVERT: B 326 LEU cc_start: 0.8318 (tt) cc_final: 0.7835 (tt) REVERT: B 372 TYR cc_start: 0.7724 (t80) cc_final: 0.7302 (t80) REVERT: B 381 ILE cc_start: 0.7787 (mm) cc_final: 0.7472 (mm) REVERT: B 397 TRP cc_start: 0.8311 (m100) cc_final: 0.8036 (m100) REVERT: B 436 LEU cc_start: 0.9054 (tp) cc_final: 0.8813 (tt) REVERT: B 470 ILE cc_start: 0.9110 (mt) cc_final: 0.8905 (mt) REVERT: B 523 ILE cc_start: 0.9230 (pt) cc_final: 0.8851 (tp) REVERT: B 536 SER cc_start: 0.9510 (m) cc_final: 0.8940 (p) REVERT: B 573 LEU cc_start: 0.8843 (tp) cc_final: 0.8487 (mm) REVERT: B 590 LEU cc_start: 0.8473 (mt) cc_final: 0.8241 (mt) REVERT: B 661 MET cc_start: 0.6929 (tmm) cc_final: 0.6623 (tmm) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.2366 time to fit residues: 111.9115 Evaluate side-chains 233 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 700 HIS A 915 HIS B 867 HIS ** B1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13706 Z= 0.201 Angle : 0.575 8.312 18652 Z= 0.293 Chirality : 0.042 0.202 2224 Planarity : 0.003 0.033 2305 Dihedral : 4.292 22.041 2021 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.07 % Allowed : 2.17 % Favored : 97.76 % 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: 0.58 (0.21), residues: 1738 helix: 1.66 (0.17), residues: 976 sheet: -1.28 (0.42), residues: 142 loop : -1.29 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 630 HIS 0.006 0.001 HIS A 700 PHE 0.021 0.001 PHE B 775 TYR 0.011 0.001 TYR B 650 ARG 0.005 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 309 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.8635 (mp) cc_final: 0.8421 (mp) REVERT: A 187 MET cc_start: 0.8262 (ttp) cc_final: 0.7978 (ttm) REVERT: A 314 SER cc_start: 0.8069 (p) cc_final: 0.7866 (p) REVERT: A 360 ASN cc_start: 0.7423 (m-40) cc_final: 0.7169 (p0) REVERT: A 453 ASN cc_start: 0.8661 (t0) cc_final: 0.8356 (t0) REVERT: A 505 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8093 (pttt) REVERT: A 601 MET cc_start: 0.9113 (tpp) cc_final: 0.8720 (tpp) REVERT: A 628 TYR cc_start: 0.8404 (t80) cc_final: 0.7985 (t80) REVERT: A 637 MET cc_start: 0.9023 (ttm) cc_final: 0.7956 (tmm) REVERT: A 644 MET cc_start: 0.9066 (mtm) cc_final: 0.8503 (ttm) REVERT: A 724 ARG cc_start: 0.8254 (mmp-170) cc_final: 0.8027 (mmp-170) REVERT: A 803 ASN cc_start: 0.8985 (p0) cc_final: 0.8295 (p0) REVERT: A 822 TRP cc_start: 0.8065 (p-90) cc_final: 0.7648 (p-90) REVERT: A 1067 ASP cc_start: 0.8522 (p0) cc_final: 0.8263 (p0) REVERT: B 314 SER cc_start: 0.8983 (t) cc_final: 0.8698 (p) REVERT: B 381 ILE cc_start: 0.7712 (mm) cc_final: 0.7504 (mm) REVERT: B 397 TRP cc_start: 0.8281 (m100) cc_final: 0.8023 (m100) REVERT: B 436 LEU cc_start: 0.9022 (tp) cc_final: 0.8814 (tt) REVERT: B 470 ILE cc_start: 0.9140 (mt) cc_final: 0.8911 (mt) REVERT: B 523 ILE cc_start: 0.9212 (pt) cc_final: 0.8845 (tp) REVERT: B 536 SER cc_start: 0.9495 (m) cc_final: 0.8935 (p) REVERT: B 573 LEU cc_start: 0.8817 (tp) cc_final: 0.8433 (mm) REVERT: B 590 LEU cc_start: 0.8441 (mt) cc_final: 0.8217 (mt) REVERT: B 661 MET cc_start: 0.7028 (tmm) cc_final: 0.6625 (tmm) REVERT: B 863 TRP cc_start: 0.8689 (m100) cc_final: 0.8415 (m100) outliers start: 1 outliers final: 0 residues processed: 310 average time/residue: 0.2135 time to fit residues: 102.4893 Evaluate side-chains 235 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 104 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 915 HIS ** B1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13706 Z= 0.168 Angle : 0.561 8.188 18652 Z= 0.285 Chirality : 0.041 0.219 2224 Planarity : 0.003 0.032 2305 Dihedral : 4.127 21.065 2021 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: 0.81 (0.21), residues: 1738 helix: 1.79 (0.17), residues: 980 sheet: -0.93 (0.43), residues: 142 loop : -1.16 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 630 HIS 0.006 0.001 HIS A 915 PHE 0.020 0.001 PHE B1073 TYR 0.010 0.001 TYR A 425 ARG 0.005 0.000 ARG B 886 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 360 ASN cc_start: 0.7387 (m-40) cc_final: 0.7124 (p0) REVERT: A 449 MET cc_start: 0.8436 (mmp) cc_final: 0.7265 (mmp) REVERT: A 481 LEU cc_start: 0.8611 (mt) cc_final: 0.8401 (mt) REVERT: A 505 LYS cc_start: 0.8624 (mmmt) cc_final: 0.8053 (ptmt) REVERT: A 597 MET cc_start: 0.8945 (mmm) cc_final: 0.8409 (tpp) REVERT: A 601 MET cc_start: 0.9094 (tpp) cc_final: 0.8661 (tpp) REVERT: A 628 TYR cc_start: 0.8426 (t80) cc_final: 0.8078 (t80) REVERT: A 637 MET cc_start: 0.8996 (ttm) cc_final: 0.7934 (tmm) REVERT: A 644 MET cc_start: 0.9020 (mtm) cc_final: 0.8604 (ttm) REVERT: A 803 ASN cc_start: 0.8916 (p0) cc_final: 0.8181 (p0) REVERT: A 822 TRP cc_start: 0.8042 (p-90) cc_final: 0.7708 (p-90) REVERT: B 314 SER cc_start: 0.9003 (t) cc_final: 0.8703 (p) REVERT: B 355 TRP cc_start: 0.6533 (t-100) cc_final: 0.6251 (t-100) REVERT: B 397 TRP cc_start: 0.8271 (m100) cc_final: 0.7992 (m100) REVERT: B 436 LEU cc_start: 0.8962 (tp) cc_final: 0.8728 (tp) REVERT: B 470 ILE cc_start: 0.9139 (mt) cc_final: 0.8915 (mt) REVERT: B 523 ILE cc_start: 0.9220 (pt) cc_final: 0.8821 (tp) REVERT: B 536 SER cc_start: 0.9497 (m) cc_final: 0.8893 (p) REVERT: B 573 LEU cc_start: 0.8777 (tp) cc_final: 0.8395 (mm) REVERT: B 590 LEU cc_start: 0.8371 (mt) cc_final: 0.8148 (mt) REVERT: B 661 MET cc_start: 0.7059 (tmm) cc_final: 0.6681 (tmm) REVERT: B 863 TRP cc_start: 0.8738 (m100) cc_final: 0.8357 (m100) REVERT: B 864 TRP cc_start: 0.8203 (t60) cc_final: 0.7473 (t60) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.2059 time to fit residues: 98.2736 Evaluate side-chains 233 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 915 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 HIS ** B1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13706 Z= 0.205 Angle : 0.587 9.575 18652 Z= 0.298 Chirality : 0.042 0.189 2224 Planarity : 0.003 0.034 2305 Dihedral : 4.149 21.436 2021 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.07 % Allowed : 0.87 % Favored : 99.06 % 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: 0.81 (0.21), residues: 1738 helix: 1.77 (0.17), residues: 980 sheet: -0.88 (0.43), residues: 142 loop : -1.14 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 630 HIS 0.006 0.001 HIS A 915 PHE 0.030 0.001 PHE A 605 TYR 0.010 0.001 TYR A 935 ARG 0.007 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 299 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.8543 (tpp) cc_final: 0.8305 (tpp) REVERT: A 360 ASN cc_start: 0.7416 (m-40) cc_final: 0.7069 (p0) REVERT: A 487 PHE cc_start: 0.8317 (m-10) cc_final: 0.7980 (m-80) REVERT: A 505 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8038 (ptmt) REVERT: A 601 MET cc_start: 0.9065 (tpp) cc_final: 0.8595 (tpp) REVERT: A 628 TYR cc_start: 0.8477 (t80) cc_final: 0.8088 (t80) REVERT: A 644 MET cc_start: 0.9064 (mtm) cc_final: 0.8514 (ttm) REVERT: A 803 ASN cc_start: 0.9001 (p0) cc_final: 0.8290 (p0) REVERT: A 1067 ASP cc_start: 0.8503 (p0) cc_final: 0.8193 (p0) REVERT: B 397 TRP cc_start: 0.8249 (m100) cc_final: 0.7977 (m100) REVERT: B 436 LEU cc_start: 0.8973 (tp) cc_final: 0.8672 (tp) REVERT: B 523 ILE cc_start: 0.9195 (pt) cc_final: 0.8861 (tp) REVERT: B 536 SER cc_start: 0.9500 (m) cc_final: 0.8890 (p) REVERT: B 573 LEU cc_start: 0.8793 (tp) cc_final: 0.8400 (mm) REVERT: B 590 LEU cc_start: 0.8423 (mt) cc_final: 0.8211 (mt) REVERT: B 863 TRP cc_start: 0.8712 (m100) cc_final: 0.8217 (m100) REVERT: B 864 TRP cc_start: 0.8188 (t60) cc_final: 0.7449 (t60) outliers start: 1 outliers final: 0 residues processed: 300 average time/residue: 0.2020 time to fit residues: 94.5677 Evaluate side-chains 231 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 0.0370 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 141 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 165 optimal weight: 7.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 915 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN ** B1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13706 Z= 0.160 Angle : 0.574 13.295 18652 Z= 0.287 Chirality : 0.041 0.183 2224 Planarity : 0.003 0.037 2305 Dihedral : 4.060 19.437 2021 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.07 % Allowed : 0.43 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.21), residues: 1738 helix: 1.87 (0.17), residues: 982 sheet: -0.79 (0.44), residues: 142 loop : -1.13 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 630 HIS 0.006 0.001 HIS A 915 PHE 0.025 0.001 PHE A 221 TYR 0.015 0.001 TYR B 372 ARG 0.004 0.000 ARG B 886 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 308 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 ASN cc_start: 0.7403 (m-40) cc_final: 0.7062 (p0) REVERT: A 487 PHE cc_start: 0.8265 (m-10) cc_final: 0.7956 (m-80) REVERT: A 505 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8055 (ptmt) REVERT: A 601 MET cc_start: 0.8970 (tpp) cc_final: 0.8539 (tpp) REVERT: A 628 TYR cc_start: 0.8434 (t80) cc_final: 0.8041 (t80) REVERT: A 644 MET cc_start: 0.8970 (mtm) cc_final: 0.8485 (ttm) REVERT: A 672 GLU cc_start: 0.8156 (tt0) cc_final: 0.7821 (tm-30) REVERT: A 803 ASN cc_start: 0.8943 (p0) cc_final: 0.8198 (p0) REVERT: A 1067 ASP cc_start: 0.8485 (p0) cc_final: 0.8180 (p0) REVERT: B 523 ILE cc_start: 0.9177 (pt) cc_final: 0.8818 (tp) REVERT: B 573 LEU cc_start: 0.8760 (tp) cc_final: 0.8368 (mm) REVERT: B 590 LEU cc_start: 0.8385 (mt) cc_final: 0.8138 (mt) REVERT: B 661 MET cc_start: 0.6944 (tmm) cc_final: 0.6686 (tmm) REVERT: B 864 TRP cc_start: 0.8154 (t60) cc_final: 0.7468 (t60) outliers start: 1 outliers final: 0 residues processed: 309 average time/residue: 0.2212 time to fit residues: 106.0683 Evaluate side-chains 240 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 147 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 915 HIS ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 HIS ** B1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3912 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: