Starting phenix.real_space_refine on Wed Feb 21 00:00:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v38_21029/02_2024/6v38_21029_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v38_21029/02_2024/6v38_21029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v38_21029/02_2024/6v38_21029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v38_21029/02_2024/6v38_21029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v38_21029/02_2024/6v38_21029_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v38_21029/02_2024/6v38_21029_updated.pdb" } resolution = 3.8 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= -0.002 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 8 9.91 5 P 28 5.49 5 Mg 4 5.21 5 S 180 5.16 5 C 19108 2.51 5 N 4564 2.21 5 O 5260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 153": "OD1" <-> "OD2" Residue "A ASP 186": "OD1" <-> "OD2" Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 432": "OD1" <-> "OD2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A ASP 482": "OD1" <-> "OD2" Residue "A TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 742": "NH1" <-> "NH2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A ASP 798": "OD1" <-> "OD2" Residue "A ASP 811": "OD1" <-> "OD2" Residue "A ASP 885": "OD1" <-> "OD2" Residue "A ASP 931": "OD1" <-> "OD2" Residue "A ARG 938": "NH1" <-> "NH2" Residue "A ASP 992": "OD1" <-> "OD2" Residue "A PHE 1000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1056": "OD1" <-> "OD2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 432": "OD1" <-> "OD2" Residue "B GLU 436": "OE1" <-> "OE2" Residue "B GLU 479": "OE1" <-> "OE2" Residue "B ASP 482": "OD1" <-> "OD2" Residue "B TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 742": "NH1" <-> "NH2" Residue "B GLU 761": "OE1" <-> "OE2" Residue "B ASP 798": "OD1" <-> "OD2" Residue "B ASP 811": "OD1" <-> "OD2" Residue "B ASP 885": "OD1" <-> "OD2" Residue "B ASP 931": "OD1" <-> "OD2" Residue "B ARG 938": "NH1" <-> "NH2" Residue "B ASP 992": "OD1" <-> "OD2" Residue "B PHE 1000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1056": "OD1" <-> "OD2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 329": "NH1" <-> "NH2" Residue "C ARG 368": "NH1" <-> "NH2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 432": "OD1" <-> "OD2" Residue "C GLU 436": "OE1" <-> "OE2" Residue "C GLU 479": "OE1" <-> "OE2" Residue "C ASP 482": "OD1" <-> "OD2" Residue "C TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 742": "NH1" <-> "NH2" Residue "C GLU 761": "OE1" <-> "OE2" Residue "C ASP 798": "OD1" <-> "OD2" Residue "C ASP 811": "OD1" <-> "OD2" Residue "C ASP 885": "OD1" <-> "OD2" Residue "C ASP 931": "OD1" <-> "OD2" Residue "C ARG 938": "NH1" <-> "NH2" Residue "C ASP 992": "OD1" <-> "OD2" Residue "C PHE 1000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1056": "OD1" <-> "OD2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 153": "OD1" <-> "OD2" Residue "D ASP 186": "OD1" <-> "OD2" Residue "D PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 329": "NH1" <-> "NH2" Residue "D ARG 368": "NH1" <-> "NH2" Residue "D PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 432": "OD1" <-> "OD2" Residue "D GLU 436": "OE1" <-> "OE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D ASP 482": "OD1" <-> "OD2" Residue "D TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 742": "NH1" <-> "NH2" Residue "D GLU 761": "OE1" <-> "OE2" Residue "D ASP 798": "OD1" <-> "OD2" Residue "D ASP 811": "OD1" <-> "OD2" Residue "D ASP 885": "OD1" <-> "OD2" Residue "D ASP 931": "OD1" <-> "OD2" Residue "D ARG 938": "NH1" <-> "NH2" Residue "D ASP 992": "OD1" <-> "OD2" Residue "D PHE 1000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1056": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29152 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 874, 6979 Classifications: {'peptide': 874} Link IDs: {'PTRANS': 27, 'TRANS': 846} Chain breaks: 5 Chain: "B" Number of atoms: 6979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 874, 6979 Classifications: {'peptide': 874} Link IDs: {'PTRANS': 27, 'TRANS': 846} Chain breaks: 5 Chain: "C" Number of atoms: 6979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 874, 6979 Classifications: {'peptide': 874} Link IDs: {'PTRANS': 27, 'TRANS': 846} Chain breaks: 5 Chain: "D" Number of atoms: 6979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 874, 6979 Classifications: {'peptide': 874} Link IDs: {'PTRANS': 27, 'TRANS': 846} Chain breaks: 5 Chain: "A" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 309 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 3, 'POV': 8} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 5} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 374 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 3, 'POV': 10} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 6} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 275 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 3, 'POV': 7} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 5} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 278 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 3, 'POV': 7} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 4} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 14.49, per 1000 atoms: 0.50 Number of scatterers: 29152 At special positions: 0 Unit cell: (144.3, 144.3, 127.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 8 19.99 S 180 16.00 P 28 15.00 Mg 4 11.99 O 5260 8.00 N 4564 7.00 C 19108 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: 11.41 Conformation dependent library (CDL) restraints added in 5.3 seconds 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6624 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 148 helices and 16 sheets defined 46.6% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.02 Creating SS restraints... Processing helix chain 'A' and resid 23 through 50 removed outlier: 5.206A pdb=" N LEU A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TRP A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 110 through 135 removed outlier: 4.410A pdb=" N SER A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 170 removed outlier: 3.849A pdb=" N ALA A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 181 through 199 removed outlier: 3.770A pdb=" N ASP A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) Proline residue: A 191 - end of helix removed outlier: 3.966A pdb=" N PHE A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 223 removed outlier: 3.675A pdb=" N GLN A 216 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER A 218 " --> pdb=" O ILE A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 258 Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 298 through 325 removed outlier: 4.014A pdb=" N LEU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLY A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.779A pdb=" N ASP A 362 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 435 through 450 Processing helix chain 'A' and resid 464 through 471 removed outlier: 3.573A pdb=" N HIS A 468 " --> pdb=" O HIS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 497 Processing helix chain 'A' and resid 503 through 510 removed outlier: 3.796A pdb=" N LEU A 510 " --> pdb=" O MET A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.553A pdb=" N GLY A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 546 No H-bonds generated for 'chain 'A' and resid 543 through 546' Processing helix chain 'A' and resid 550 through 554 Processing helix chain 'A' and resid 557 through 561 Processing helix chain 'A' and resid 602 through 605 No H-bonds generated for 'chain 'A' and resid 602 through 605' Processing helix chain 'A' and resid 700 through 703 No H-bonds generated for 'chain 'A' and resid 700 through 703' Processing helix chain 'A' and resid 707 through 712 Processing helix chain 'A' and resid 735 through 742 Proline residue: A 740 - end of helix Processing helix chain 'A' and resid 760 through 767 Processing helix chain 'A' and resid 786 through 791 Processing helix chain 'A' and resid 806 through 808 No H-bonds generated for 'chain 'A' and resid 806 through 808' Processing helix chain 'A' and resid 818 through 829 Processing helix chain 'A' and resid 885 through 890 removed outlier: 5.022A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 911 Processing helix chain 'A' and resid 917 through 929 removed outlier: 3.792A pdb=" N ASP A 921 " --> pdb=" O SER A 918 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER A 922 " --> pdb=" O VAL A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 941 removed outlier: 3.964A pdb=" N LEU A 934 " --> pdb=" O ASP A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 956 Processing helix chain 'A' and resid 966 through 969 No H-bonds generated for 'chain 'A' and resid 966 through 969' Processing helix chain 'A' and resid 996 through 1007 Processing helix chain 'A' and resid 1018 through 1021 removed outlier: 4.198A pdb=" N HIS A1021 " --> pdb=" O ARG A1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1018 through 1021' Processing helix chain 'B' and resid 23 through 50 removed outlier: 5.206A pdb=" N LEU B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N TRP B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 110 through 135 removed outlier: 4.410A pdb=" N SER B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 170 removed outlier: 3.850A pdb=" N ALA B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 181 through 199 removed outlier: 3.769A pdb=" N ASP B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) Proline residue: B 191 - end of helix removed outlier: 3.965A pdb=" N PHE B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 223 removed outlier: 3.674A pdb=" N GLN B 216 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER B 218 " --> pdb=" O ILE B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 258 Processing helix chain 'B' and resid 274 through 285 Processing helix chain 'B' and resid 298 through 325 removed outlier: 4.014A pdb=" N LEU B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLY B 310 " --> pdb=" O PHE B 306 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 353 through 363 removed outlier: 3.779A pdb=" N ASP B 362 " --> pdb=" O ASN B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 393 Processing helix chain 'B' and resid 408 through 414 Processing helix chain 'B' and resid 435 through 450 Processing helix chain 'B' and resid 464 through 471 removed outlier: 3.573A pdb=" N HIS B 468 " --> pdb=" O HIS B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 497 Processing helix chain 'B' and resid 503 through 510 removed outlier: 3.797A pdb=" N LEU B 510 " --> pdb=" O MET B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 532 removed outlier: 3.553A pdb=" N GLY B 531 " --> pdb=" O TYR B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 546 No H-bonds generated for 'chain 'B' and resid 543 through 546' Processing helix chain 'B' and resid 550 through 554 Processing helix chain 'B' and resid 557 through 561 Processing helix chain 'B' and resid 602 through 605 No H-bonds generated for 'chain 'B' and resid 602 through 605' Processing helix chain 'B' and resid 700 through 703 No H-bonds generated for 'chain 'B' and resid 700 through 703' Processing helix chain 'B' and resid 707 through 712 Processing helix chain 'B' and resid 735 through 742 Proline residue: B 740 - end of helix Processing helix chain 'B' and resid 760 through 767 Processing helix chain 'B' and resid 786 through 791 Processing helix chain 'B' and resid 806 through 808 No H-bonds generated for 'chain 'B' and resid 806 through 808' Processing helix chain 'B' and resid 818 through 829 Processing helix chain 'B' and resid 885 through 890 removed outlier: 5.022A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 911 Processing helix chain 'B' and resid 917 through 929 removed outlier: 3.793A pdb=" N ASP B 921 " --> pdb=" O SER B 918 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER B 922 " --> pdb=" O VAL B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 941 removed outlier: 3.965A pdb=" N LEU B 934 " --> pdb=" O ASP B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 956 Processing helix chain 'B' and resid 966 through 969 No H-bonds generated for 'chain 'B' and resid 966 through 969' Processing helix chain 'B' and resid 996 through 1007 Processing helix chain 'B' and resid 1018 through 1021 removed outlier: 4.198A pdb=" N HIS B1021 " --> pdb=" O ARG B1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1018 through 1021' Processing helix chain 'C' and resid 23 through 50 removed outlier: 5.206A pdb=" N LEU C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TRP C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 110 through 135 removed outlier: 4.410A pdb=" N SER C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 170 removed outlier: 3.850A pdb=" N ALA C 155 " --> pdb=" O GLN C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'C' and resid 181 through 199 removed outlier: 3.770A pdb=" N ASP C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) Proline residue: C 191 - end of helix removed outlier: 3.966A pdb=" N PHE C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 223 removed outlier: 3.674A pdb=" N GLN C 216 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER C 218 " --> pdb=" O ILE C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 258 Processing helix chain 'C' and resid 274 through 285 Processing helix chain 'C' and resid 298 through 325 removed outlier: 4.014A pdb=" N LEU C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLY C 310 " --> pdb=" O PHE C 306 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.779A pdb=" N ASP C 362 " --> pdb=" O ASN C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 393 Processing helix chain 'C' and resid 408 through 414 Processing helix chain 'C' and resid 435 through 450 Processing helix chain 'C' and resid 464 through 471 removed outlier: 3.573A pdb=" N HIS C 468 " --> pdb=" O HIS C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 497 Processing helix chain 'C' and resid 503 through 510 removed outlier: 3.796A pdb=" N LEU C 510 " --> pdb=" O MET C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 532 removed outlier: 3.553A pdb=" N GLY C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 546 No H-bonds generated for 'chain 'C' and resid 543 through 546' Processing helix chain 'C' and resid 550 through 554 Processing helix chain 'C' and resid 557 through 561 Processing helix chain 'C' and resid 602 through 605 No H-bonds generated for 'chain 'C' and resid 602 through 605' Processing helix chain 'C' and resid 700 through 703 No H-bonds generated for 'chain 'C' and resid 700 through 703' Processing helix chain 'C' and resid 707 through 712 Processing helix chain 'C' and resid 735 through 742 Proline residue: C 740 - end of helix Processing helix chain 'C' and resid 760 through 767 Processing helix chain 'C' and resid 786 through 791 Processing helix chain 'C' and resid 806 through 808 No H-bonds generated for 'chain 'C' and resid 806 through 808' Processing helix chain 'C' and resid 818 through 829 Processing helix chain 'C' and resid 885 through 890 removed outlier: 5.022A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 911 Processing helix chain 'C' and resid 917 through 929 removed outlier: 3.793A pdb=" N ASP C 921 " --> pdb=" O SER C 918 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER C 922 " --> pdb=" O VAL C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 931 through 941 removed outlier: 3.964A pdb=" N LEU C 934 " --> pdb=" O ASP C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 956 Processing helix chain 'C' and resid 966 through 969 No H-bonds generated for 'chain 'C' and resid 966 through 969' Processing helix chain 'C' and resid 996 through 1007 Processing helix chain 'C' and resid 1018 through 1021 removed outlier: 4.198A pdb=" N HIS C1021 " --> pdb=" O ARG C1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1018 through 1021' Processing helix chain 'D' and resid 23 through 50 removed outlier: 5.206A pdb=" N LEU D 49 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N TRP D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 105 Processing helix chain 'D' and resid 110 through 135 removed outlier: 4.410A pdb=" N SER D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 170 removed outlier: 3.850A pdb=" N ALA D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 181 through 199 removed outlier: 3.770A pdb=" N ASP D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) Proline residue: D 191 - end of helix removed outlier: 3.966A pdb=" N PHE D 194 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 223 removed outlier: 3.675A pdb=" N GLN D 216 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER D 218 " --> pdb=" O ILE D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 258 Processing helix chain 'D' and resid 274 through 285 Processing helix chain 'D' and resid 298 through 325 removed outlier: 4.014A pdb=" N LEU D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLY D 310 " --> pdb=" O PHE D 306 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 353 through 363 removed outlier: 3.779A pdb=" N ASP D 362 " --> pdb=" O ASN D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 393 Processing helix chain 'D' and resid 408 through 414 Processing helix chain 'D' and resid 435 through 450 Processing helix chain 'D' and resid 464 through 471 removed outlier: 3.573A pdb=" N HIS D 468 " --> pdb=" O HIS D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 497 Processing helix chain 'D' and resid 503 through 510 removed outlier: 3.797A pdb=" N LEU D 510 " --> pdb=" O MET D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 532 removed outlier: 3.553A pdb=" N GLY D 531 " --> pdb=" O TYR D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 546 No H-bonds generated for 'chain 'D' and resid 543 through 546' Processing helix chain 'D' and resid 550 through 554 Processing helix chain 'D' and resid 557 through 561 Processing helix chain 'D' and resid 602 through 605 No H-bonds generated for 'chain 'D' and resid 602 through 605' Processing helix chain 'D' and resid 700 through 703 No H-bonds generated for 'chain 'D' and resid 700 through 703' Processing helix chain 'D' and resid 707 through 712 Processing helix chain 'D' and resid 735 through 742 Proline residue: D 740 - end of helix Processing helix chain 'D' and resid 760 through 767 Processing helix chain 'D' and resid 786 through 791 Processing helix chain 'D' and resid 806 through 808 No H-bonds generated for 'chain 'D' and resid 806 through 808' Processing helix chain 'D' and resid 818 through 829 Processing helix chain 'D' and resid 885 through 890 removed outlier: 5.022A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 911 Processing helix chain 'D' and resid 917 through 929 removed outlier: 3.793A pdb=" N ASP D 921 " --> pdb=" O SER D 918 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER D 922 " --> pdb=" O VAL D 919 " (cutoff:3.500A) Processing helix chain 'D' and resid 931 through 941 removed outlier: 3.965A pdb=" N LEU D 934 " --> pdb=" O ASP D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 947 through 956 Processing helix chain 'D' and resid 966 through 969 No H-bonds generated for 'chain 'D' and resid 966 through 969' Processing helix chain 'D' and resid 996 through 1007 Processing helix chain 'D' and resid 1018 through 1021 removed outlier: 4.198A pdb=" N HIS D1021 " --> pdb=" O ARG D1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1018 through 1021' Processing sheet with id= A, first strand: chain 'A' and resid 374 through 377 removed outlier: 4.023A pdb=" N ALA A 421 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG A 455 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE A 424 " --> pdb=" O ARG A 455 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 457 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP A 482 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N MET A 460 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE A 484 " --> pdb=" O MET A 460 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 537 through 540 Processing sheet with id= C, first strand: chain 'A' and resid 914 through 916 removed outlier: 7.991A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR A 880 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 977 through 981 removed outlier: 3.705A pdb=" N LEU A1048 " --> pdb=" O TYR A1015 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY A1013 " --> pdb=" O PHE A1050 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU A1052 " --> pdb=" O CYS A1011 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N CYS A1011 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 374 through 377 removed outlier: 4.023A pdb=" N ALA B 421 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG B 455 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE B 424 " --> pdb=" O ARG B 455 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 457 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP B 482 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N MET B 460 " --> pdb=" O ASP B 482 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 484 " --> pdb=" O MET B 460 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 537 through 540 Processing sheet with id= G, first strand: chain 'B' and resid 914 through 916 removed outlier: 7.991A pdb=" N PHE B 915 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR B 880 " --> pdb=" O PHE B 915 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N CYS B 800 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLU B 881 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE B 802 " --> pdb=" O GLU B 881 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 977 through 981 removed outlier: 3.704A pdb=" N LEU B1048 " --> pdb=" O TYR B1015 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY B1013 " --> pdb=" O PHE B1050 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU B1052 " --> pdb=" O CYS B1011 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N CYS B1011 " --> pdb=" O LEU B1052 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 374 through 377 removed outlier: 4.023A pdb=" N ALA C 421 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG C 455 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE C 424 " --> pdb=" O ARG C 455 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE C 457 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP C 482 " --> pdb=" O THR C 458 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N MET C 460 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE C 484 " --> pdb=" O MET C 460 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 537 through 540 Processing sheet with id= K, first strand: chain 'C' and resid 914 through 916 removed outlier: 7.991A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 977 through 981 removed outlier: 3.705A pdb=" N LEU C1048 " --> pdb=" O TYR C1015 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU C1052 " --> pdb=" O CYS C1011 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N CYS C1011 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 374 through 377 removed outlier: 4.024A pdb=" N ALA D 421 " --> pdb=" O HIS D 344 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG D 455 " --> pdb=" O CYS D 422 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE D 424 " --> pdb=" O ARG D 455 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE D 457 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP D 482 " --> pdb=" O THR D 458 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N MET D 460 " --> pdb=" O ASP D 482 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE D 484 " --> pdb=" O MET D 460 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 537 through 540 Processing sheet with id= O, first strand: chain 'D' and resid 914 through 916 removed outlier: 7.991A pdb=" N PHE D 915 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR D 880 " --> pdb=" O PHE D 915 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N CYS D 800 " --> pdb=" O ILE D 879 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLU D 881 " --> pdb=" O CYS D 800 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE D 802 " --> pdb=" O GLU D 881 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 977 through 981 removed outlier: 3.705A pdb=" N LEU D1048 " --> pdb=" O TYR D1015 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY D1013 " --> pdb=" O PHE D1050 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU D1052 " --> pdb=" O CYS D1011 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N CYS D1011 " --> pdb=" O LEU D1052 " (cutoff:3.500A) 1080 hydrogen bonds defined for protein. 2868 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: 10.55 Time building geometry restraints manager: 12.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4532 1.31 - 1.44: 8103 1.44 - 1.57: 16665 1.57 - 1.70: 212 1.70 - 1.83: 284 Bond restraints: 29796 Sorted by residual: bond pdb=" C5 CLR C1111 " pdb=" C6 CLR C1111 " ideal model delta sigma weight residual 1.332 1.575 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CLR A1109 " pdb=" C6 CLR A1109 " ideal model delta sigma weight residual 1.332 1.574 -0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CLR D1111 " pdb=" C6 CLR D1111 " ideal model delta sigma weight residual 1.332 1.574 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C5 CLR B1114 " pdb=" C6 CLR B1114 " ideal model delta sigma weight residual 1.332 1.574 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C5 CLR D1112 " pdb=" C6 CLR D1112 " ideal model delta sigma weight residual 1.332 1.573 -0.241 2.00e-02 2.50e+03 1.45e+02 ... (remaining 29791 not shown) Histogram of bond angle deviations from ideal: 97.29 - 104.72: 469 104.72 - 112.15: 15168 112.15 - 119.58: 10848 119.58 - 127.01: 13596 127.01 - 134.44: 319 Bond angle restraints: 40400 Sorted by residual: angle pdb=" O13 POV D1107 " pdb=" P POV D1107 " pdb=" O14 POV D1107 " ideal model delta sigma weight residual 121.11 100.87 20.24 3.00e+00 1.11e-01 4.55e+01 angle pdb=" O13 POV A1113 " pdb=" P POV A1113 " pdb=" O14 POV A1113 " ideal model delta sigma weight residual 121.11 100.90 20.21 3.00e+00 1.11e-01 4.54e+01 angle pdb=" O13 POV B1109 " pdb=" P POV B1109 " pdb=" O14 POV B1109 " ideal model delta sigma weight residual 121.11 100.92 20.19 3.00e+00 1.11e-01 4.53e+01 angle pdb=" O13 POV A1105 " pdb=" P POV A1105 " pdb=" O14 POV A1105 " ideal model delta sigma weight residual 121.11 100.92 20.19 3.00e+00 1.11e-01 4.53e+01 angle pdb=" O13 POV B1102 " pdb=" P POV B1102 " pdb=" O14 POV B1102 " ideal model delta sigma weight residual 121.11 100.92 20.19 3.00e+00 1.11e-01 4.53e+01 ... (remaining 40395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 17396 35.16 - 70.31: 704 70.31 - 105.47: 88 105.47 - 140.63: 20 140.63 - 175.78: 16 Dihedral angle restraints: 18224 sinusoidal: 8000 harmonic: 10224 Sorted by residual: dihedral pdb=" C29 POV C1101 " pdb="C210 POV C1101 " pdb="C211 POV C1101 " pdb="C212 POV C1101 " ideal model delta sinusoidal sigma weight residual 112.25 -71.97 -175.78 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C29 POV D1102 " pdb="C210 POV D1102 " pdb="C211 POV D1102 " pdb="C212 POV D1102 " ideal model delta sinusoidal sigma weight residual 112.25 -71.97 -175.78 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C29 POV B1103 " pdb="C210 POV B1103 " pdb="C211 POV B1103 " pdb="C212 POV B1103 " ideal model delta sinusoidal sigma weight residual 112.25 -71.97 -175.78 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 18221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3730 0.088 - 0.176: 694 0.176 - 0.264: 116 0.264 - 0.352: 4 0.352 - 0.440: 20 Chirality restraints: 4564 Sorted by residual: chirality pdb=" C13 CLR D1112 " pdb=" C12 CLR D1112 " pdb=" C14 CLR D1112 " pdb=" C17 CLR D1112 " both_signs ideal model delta sigma weight residual False -2.93 -2.49 -0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" C13 CLR C1112 " pdb=" C12 CLR C1112 " pdb=" C14 CLR C1112 " pdb=" C17 CLR C1112 " both_signs ideal model delta sigma weight residual False -2.93 -2.49 -0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" C13 CLR A1110 " pdb=" C12 CLR A1110 " pdb=" C14 CLR A1110 " pdb=" C17 CLR A1110 " both_signs ideal model delta sigma weight residual False -2.93 -2.49 -0.44 2.00e-01 2.50e+01 4.77e+00 ... (remaining 4561 not shown) Planarity restraints: 4904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B1103 " 0.367 2.00e-02 2.50e+03 3.38e-01 1.14e+03 pdb=" C29 POV B1103 " -0.465 2.00e-02 2.50e+03 pdb="C210 POV B1103 " -0.176 2.00e-02 2.50e+03 pdb="C211 POV B1103 " 0.273 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A1114 " -0.367 2.00e-02 2.50e+03 3.38e-01 1.14e+03 pdb=" C29 POV A1114 " 0.461 2.00e-02 2.50e+03 pdb="C210 POV A1114 " 0.182 2.00e-02 2.50e+03 pdb="C211 POV A1114 " -0.276 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C1101 " 0.367 2.00e-02 2.50e+03 3.38e-01 1.14e+03 pdb=" C29 POV C1101 " -0.463 2.00e-02 2.50e+03 pdb="C210 POV C1101 " -0.178 2.00e-02 2.50e+03 pdb="C211 POV C1101 " 0.274 2.00e-02 2.50e+03 ... (remaining 4901 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 7167 2.78 - 3.31: 28326 3.31 - 3.84: 50751 3.84 - 4.37: 57978 4.37 - 4.90: 95766 Nonbonded interactions: 239988 Sorted by model distance: nonbonded pdb=" N ASN C 143 " pdb=" OD1 ASN C 143 " model vdw 2.255 2.520 nonbonded pdb=" N ASN B 143 " pdb=" OD1 ASN B 143 " model vdw 2.255 2.520 nonbonded pdb=" N ASN A 143 " pdb=" OD1 ASN A 143 " model vdw 2.256 2.520 nonbonded pdb=" N ASN D 143 " pdb=" OD1 ASN D 143 " model vdw 2.256 2.520 nonbonded pdb=" O LYS D1002 " pdb=" OG1 THR D1006 " model vdw 2.272 2.440 ... (remaining 239983 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 1056) selection = (chain 'B' and resid 19 through 1056) selection = (chain 'C' and resid 19 through 1056) selection = (chain 'D' and resid 19 through 1056) } 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: 0.720 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: 5.080 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 76.090 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.160 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 : 0.014 0.243 29796 Z= 0.899 Angle : 1.470 20.241 40400 Z= 0.737 Chirality : 0.073 0.440 4564 Planarity : 0.018 0.338 4904 Dihedral : 19.779 175.783 11600 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.55 % Allowed : 8.73 % Favored : 86.72 % 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: -2.89 (0.12), residues: 3448 helix: -1.56 (0.10), residues: 1764 sheet: -2.10 (0.26), residues: 324 loop : -2.17 (0.15), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 767 HIS 0.006 0.002 HIS B 753 PHE 0.047 0.003 PHE D1000 TYR 0.017 0.002 TYR A 463 ARG 0.006 0.001 ARG B 742 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 400 time to evaluate : 3.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9201 (mmm) cc_final: 0.8863 (mpp) REVERT: A 304 MET cc_start: 0.9371 (mmm) cc_final: 0.9056 (mmm) REVERT: A 371 VAL cc_start: 0.8094 (OUTLIER) cc_final: 0.7864 (m) REVERT: A 387 LEU cc_start: 0.9636 (tp) cc_final: 0.9347 (tp) REVERT: A 491 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8692 (mt) REVERT: A 825 LEU cc_start: 0.9445 (mt) cc_final: 0.9244 (mm) REVERT: A 924 MET cc_start: 0.8921 (mmm) cc_final: 0.8716 (mmt) REVERT: B 104 MET cc_start: 0.9111 (mmm) cc_final: 0.8862 (mmm) REVERT: B 152 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8615 (mp) REVERT: B 218 SER cc_start: 0.9333 (OUTLIER) cc_final: 0.9055 (p) REVERT: B 304 MET cc_start: 0.9357 (mmm) cc_final: 0.9072 (mmm) REVERT: B 387 LEU cc_start: 0.9667 (tp) cc_final: 0.9376 (tp) REVERT: B 471 ASN cc_start: 0.8364 (m110) cc_final: 0.7801 (m-40) REVERT: B 513 MET cc_start: 0.7801 (mmt) cc_final: 0.7540 (mmm) REVERT: B 597 PHE cc_start: 0.7806 (m-10) cc_final: 0.7561 (m-10) REVERT: B 878 ILE cc_start: 0.9280 (pt) cc_final: 0.8945 (pt) REVERT: B 879 ILE cc_start: 0.9012 (mt) cc_final: 0.8807 (tt) REVERT: B 924 MET cc_start: 0.9031 (mmm) cc_final: 0.8757 (mmt) REVERT: C 30 MET cc_start: 0.8581 (tpp) cc_final: 0.8193 (tpp) REVERT: C 104 MET cc_start: 0.9270 (mmm) cc_final: 0.8947 (mpp) REVERT: C 321 GLU cc_start: 0.8892 (tt0) cc_final: 0.8594 (mt-10) REVERT: C 371 VAL cc_start: 0.8006 (OUTLIER) cc_final: 0.7740 (m) REVERT: C 372 ASN cc_start: 0.7760 (m-40) cc_final: 0.7429 (p0) REVERT: C 387 LEU cc_start: 0.9641 (tp) cc_final: 0.9287 (tp) REVERT: C 471 ASN cc_start: 0.8365 (m110) cc_final: 0.7796 (m-40) REVERT: C 506 MET cc_start: 0.8832 (tpt) cc_final: 0.8517 (tpp) REVERT: C 565 MET cc_start: 0.6970 (tpt) cc_final: 0.6667 (tpt) REVERT: C 825 LEU cc_start: 0.9546 (mt) cc_final: 0.9341 (mm) REVERT: C 924 MET cc_start: 0.9023 (mmm) cc_final: 0.8641 (mmt) REVERT: D 30 MET cc_start: 0.8604 (tpp) cc_final: 0.8168 (tpp) REVERT: D 104 MET cc_start: 0.9250 (mmm) cc_final: 0.8922 (mpp) REVERT: D 321 GLU cc_start: 0.8795 (tt0) cc_final: 0.8491 (mt-10) REVERT: D 371 VAL cc_start: 0.7973 (OUTLIER) cc_final: 0.7705 (m) REVERT: D 372 ASN cc_start: 0.7701 (m-40) cc_final: 0.7407 (p0) REVERT: D 387 LEU cc_start: 0.9620 (tp) cc_final: 0.9259 (tp) REVERT: D 506 MET cc_start: 0.8800 (tpt) cc_final: 0.8558 (tpt) REVERT: D 565 MET cc_start: 0.6968 (tpt) cc_final: 0.6659 (tpt) REVERT: D 825 LEU cc_start: 0.9541 (mt) cc_final: 0.9325 (mm) REVERT: D 924 MET cc_start: 0.9004 (mmm) cc_final: 0.8636 (mmt) outliers start: 140 outliers final: 29 residues processed: 502 average time/residue: 0.3556 time to fit residues: 296.3259 Evaluate side-chains 282 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 247 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 809 ASN Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 809 ASN Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 809 ASN Chi-restraints excluded: chain D residue 815 LEU Chi-restraints excluded: chain D residue 885 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 146 optimal weight: 0.0470 chunk 90 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 272 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 316 optimal weight: 4.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN A 265 ASN A 344 HIS A 372 ASN ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 GLN A 462 GLN ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** A 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN B 265 ASN B 372 ASN B 379 HIS B 459 GLN B 462 GLN ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 ASN B 501 GLN ** B 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 ASN ** B 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 GLN C 143 ASN C 200 ASN C 258 ASN C 265 ASN C 344 HIS C 379 HIS C 459 GLN C 462 GLN ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 ASN ** C 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN D 143 ASN D 200 ASN D 258 ASN D 265 ASN D 344 HIS D 379 HIS D 459 GLN D 462 GLN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29796 Z= 0.199 Angle : 0.609 13.137 40400 Z= 0.304 Chirality : 0.042 0.210 4564 Planarity : 0.004 0.044 4904 Dihedral : 15.743 179.762 5232 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.24 % Allowed : 14.09 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.13), residues: 3448 helix: -0.59 (0.11), residues: 1796 sheet: -1.45 (0.27), residues: 364 loop : -1.91 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 477 HIS 0.003 0.001 HIS B 693 PHE 0.031 0.002 PHE B1000 TYR 0.012 0.001 TYR D 130 ARG 0.011 0.000 ARG B 786 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 289 time to evaluate : 3.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9101 (mmm) cc_final: 0.8865 (mpp) REVERT: A 314 MET cc_start: 0.9388 (ttp) cc_final: 0.9098 (ttp) REVERT: A 373 VAL cc_start: 0.9119 (OUTLIER) cc_final: 0.8844 (p) REVERT: A 387 LEU cc_start: 0.9640 (tp) cc_final: 0.9329 (tp) REVERT: A 712 MET cc_start: 0.8411 (ptm) cc_final: 0.7899 (ppp) REVERT: A 722 CYS cc_start: 0.8963 (m) cc_final: 0.8576 (p) REVERT: B 314 MET cc_start: 0.9373 (ttp) cc_final: 0.9061 (ttp) REVERT: B 387 LEU cc_start: 0.9704 (tp) cc_final: 0.9364 (tp) REVERT: B 471 ASN cc_start: 0.8500 (m-40) cc_final: 0.8226 (m110) REVERT: B 712 MET cc_start: 0.8287 (ptp) cc_final: 0.8029 (ptp) REVERT: B 924 MET cc_start: 0.8909 (mmm) cc_final: 0.8333 (mmt) REVERT: C 30 MET cc_start: 0.8595 (tpp) cc_final: 0.8170 (mmt) REVERT: C 34 PHE cc_start: 0.8909 (m-80) cc_final: 0.8303 (m-80) REVERT: C 104 MET cc_start: 0.9206 (mmm) cc_final: 0.8975 (mpp) REVERT: C 321 GLU cc_start: 0.8958 (tt0) cc_final: 0.8662 (mt-10) REVERT: C 387 LEU cc_start: 0.9649 (tp) cc_final: 0.9292 (tp) REVERT: C 459 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.9146 (pt0) REVERT: C 722 CYS cc_start: 0.8936 (m) cc_final: 0.8517 (p) REVERT: D 30 MET cc_start: 0.8609 (tpp) cc_final: 0.8192 (mmt) REVERT: D 34 PHE cc_start: 0.8959 (m-80) cc_final: 0.8493 (m-80) REVERT: D 104 MET cc_start: 0.9196 (mmm) cc_final: 0.8950 (mpp) REVERT: D 321 GLU cc_start: 0.8882 (tt0) cc_final: 0.8595 (mt-10) REVERT: D 387 LEU cc_start: 0.9643 (tp) cc_final: 0.9290 (tp) REVERT: D 459 GLN cc_start: 0.9356 (OUTLIER) cc_final: 0.9144 (pt0) REVERT: D 506 MET cc_start: 0.8764 (tpt) cc_final: 0.8563 (tpt) REVERT: D 712 MET cc_start: 0.8434 (ptm) cc_final: 0.7991 (ppp) REVERT: D 722 CYS cc_start: 0.8973 (m) cc_final: 0.8534 (p) outliers start: 69 outliers final: 47 residues processed: 331 average time/residue: 0.3309 time to fit residues: 188.3696 Evaluate side-chains 289 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 239 time to evaluate : 3.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 372 ASN Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 809 ASN Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 809 ASN Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 459 GLN Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 809 ASN Chi-restraints excluded: chain D residue 813 THR Chi-restraints excluded: chain D residue 815 LEU Chi-restraints excluded: chain D residue 885 ASP Chi-restraints excluded: chain D residue 935 THR Chi-restraints excluded: chain D residue 1014 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 263 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 316 optimal weight: 7.9990 chunk 342 optimal weight: 7.9990 chunk 281 optimal weight: 7.9990 chunk 313 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 253 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 ASN ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN A 379 HIS A 451 HIS A 464 HIS ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 ASN A 749 HIS ** A 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN B 451 HIS B 459 GLN B 464 HIS ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 ASN B 749 HIS ** B 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 ASN C 182 ASN C 451 HIS C 464 HIS ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 ASN C 749 HIS ** C 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN D 182 ASN D 451 HIS D 464 HIS ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 ASN D 749 HIS ** D 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 29796 Z= 0.550 Angle : 0.826 12.347 40400 Z= 0.418 Chirality : 0.047 0.194 4564 Planarity : 0.005 0.043 4904 Dihedral : 15.185 175.673 5194 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.19 % Allowed : 16.27 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.14), residues: 3448 helix: -0.55 (0.12), residues: 1760 sheet: -1.57 (0.25), residues: 412 loop : -1.68 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 23 HIS 0.009 0.002 HIS A 451 PHE 0.029 0.003 PHE B1000 TYR 0.026 0.003 TYR B 540 ARG 0.009 0.001 ARG B 786 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 216 time to evaluate : 3.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8372 (tpp) cc_final: 0.8111 (tpp) REVERT: A 50 TRP cc_start: 0.6342 (t60) cc_final: 0.4939 (p-90) REVERT: A 263 TRP cc_start: 0.6941 (OUTLIER) cc_final: 0.6633 (p90) REVERT: A 712 MET cc_start: 0.8540 (ptm) cc_final: 0.8101 (ppp) REVERT: A 822 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9119 (mm) REVERT: B 214 LEU cc_start: 0.9558 (mt) cc_final: 0.9279 (mp) REVERT: B 263 TRP cc_start: 0.6660 (OUTLIER) cc_final: 0.6302 (p90) REVERT: B 314 MET cc_start: 0.9474 (ttp) cc_final: 0.9226 (ttp) REVERT: B 471 ASN cc_start: 0.8482 (m-40) cc_final: 0.8230 (m110) REVERT: B 513 MET cc_start: 0.8499 (mmm) cc_final: 0.8214 (mmm) REVERT: B 564 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7906 (tt) REVERT: B 712 MET cc_start: 0.8397 (ptp) cc_final: 0.8171 (ptp) REVERT: B 799 MET cc_start: 0.8536 (tpp) cc_final: 0.8186 (tpp) REVERT: B 822 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9041 (mm) REVERT: B 894 ASP cc_start: 0.9230 (OUTLIER) cc_final: 0.8851 (p0) REVERT: C 50 TRP cc_start: 0.6469 (t60) cc_final: 0.5389 (p-90) REVERT: C 263 TRP cc_start: 0.6913 (OUTLIER) cc_final: 0.6367 (p90) REVERT: C 712 MET cc_start: 0.8237 (ptp) cc_final: 0.7992 (ppp) REVERT: C 822 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9120 (mm) REVERT: C 1053 MET cc_start: 0.8966 (ptp) cc_final: 0.8542 (mtm) REVERT: D 21 MET cc_start: 0.8384 (mmm) cc_final: 0.8048 (tpt) REVERT: D 50 TRP cc_start: 0.6299 (t60) cc_final: 0.5231 (p-90) REVERT: D 263 TRP cc_start: 0.6957 (OUTLIER) cc_final: 0.5117 (p90) REVERT: D 264 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6610 (mm-30) REVERT: D 506 MET cc_start: 0.8883 (tpt) cc_final: 0.8663 (tpt) REVERT: D 712 MET cc_start: 0.8487 (ptm) cc_final: 0.8270 (ppp) REVERT: D 822 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9142 (mm) REVERT: D 1053 MET cc_start: 0.8973 (ptp) cc_final: 0.8553 (mtm) outliers start: 129 outliers final: 95 residues processed: 318 average time/residue: 0.3430 time to fit residues: 188.0127 Evaluate side-chains 298 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 193 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 989 ASP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 263 TRP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 760 ILE Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 809 ASN Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 894 ASP Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 263 TRP Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 579 ILE Chi-restraints excluded: chain C residue 736 ASN Chi-restraints excluded: chain C residue 760 ILE Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 809 ASN Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 894 ASP Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 989 ASP Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 263 TRP Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 736 ASN Chi-restraints excluded: chain D residue 760 ILE Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 794 ILE Chi-restraints excluded: chain D residue 809 ASN Chi-restraints excluded: chain D residue 813 THR Chi-restraints excluded: chain D residue 815 LEU Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain D residue 885 ASP Chi-restraints excluded: chain D residue 894 ASP Chi-restraints excluded: chain D residue 927 THR Chi-restraints excluded: chain D residue 935 THR Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 989 ASP Chi-restraints excluded: chain D residue 1014 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 9.9990 chunk 238 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 212 optimal weight: 0.8980 chunk 317 optimal weight: 4.9990 chunk 336 optimal weight: 2.9990 chunk 165 optimal weight: 0.0020 chunk 301 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN A 468 HIS ** A 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 ASN ** C 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN D 459 GLN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 932 ASN ** D 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1054 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29796 Z= 0.177 Angle : 0.560 11.251 40400 Z= 0.281 Chirality : 0.041 0.263 4564 Planarity : 0.004 0.038 4904 Dihedral : 13.999 150.560 5194 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.44 % Allowed : 18.80 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.14), residues: 3448 helix: -0.25 (0.12), residues: 1796 sheet: -1.43 (0.27), residues: 392 loop : -1.62 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 767 HIS 0.005 0.001 HIS B 254 PHE 0.030 0.001 PHE C1000 TYR 0.013 0.001 TYR A 130 ARG 0.003 0.000 ARG A 974 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 239 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.8881 (tt0) cc_final: 0.8670 (mt-10) REVERT: A 387 LEU cc_start: 0.9669 (tp) cc_final: 0.9362 (tp) REVERT: A 564 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7892 (tt) REVERT: A 712 MET cc_start: 0.8426 (ptm) cc_final: 0.7898 (ppp) REVERT: B 214 LEU cc_start: 0.9468 (mt) cc_final: 0.9259 (mt) REVERT: B 314 MET cc_start: 0.9347 (ttp) cc_final: 0.9073 (ttp) REVERT: B 321 GLU cc_start: 0.8876 (tt0) cc_final: 0.8659 (mt-10) REVERT: B 387 LEU cc_start: 0.9697 (tp) cc_final: 0.9387 (tp) REVERT: B 513 MET cc_start: 0.8517 (mmm) cc_final: 0.8311 (mmm) REVERT: B 564 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7732 (tt) REVERT: B 712 MET cc_start: 0.8425 (ptp) cc_final: 0.8155 (ptp) REVERT: B 799 MET cc_start: 0.8555 (tpp) cc_final: 0.8163 (tpp) REVERT: C 50 TRP cc_start: 0.6621 (t60) cc_final: 0.5408 (p-90) REVERT: C 214 LEU cc_start: 0.9576 (mt) cc_final: 0.9338 (mp) REVERT: C 264 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6683 (mm-30) REVERT: C 321 GLU cc_start: 0.8889 (tt0) cc_final: 0.8650 (mt-10) REVERT: C 387 LEU cc_start: 0.9660 (tp) cc_final: 0.9334 (tp) REVERT: C 564 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7818 (tt) REVERT: C 712 MET cc_start: 0.8218 (ptp) cc_final: 0.7876 (ppp) REVERT: C 822 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9055 (mm) REVERT: D 50 TRP cc_start: 0.6666 (t60) cc_final: 0.5225 (p-90) REVERT: D 264 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6736 (mm-30) REVERT: D 321 GLU cc_start: 0.8878 (tt0) cc_final: 0.8639 (mt-10) REVERT: D 387 LEU cc_start: 0.9648 (tp) cc_final: 0.9321 (tp) REVERT: D 564 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7811 (tt) REVERT: D 712 MET cc_start: 0.8414 (ptm) cc_final: 0.7904 (ppp) outliers start: 75 outliers final: 56 residues processed: 298 average time/residue: 0.3491 time to fit residues: 179.3157 Evaluate side-chains 279 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 218 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 760 ILE Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 809 ASN Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 736 ASN Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 760 ILE Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 809 ASN Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 736 ASN Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 809 ASN Chi-restraints excluded: chain D residue 885 ASP Chi-restraints excluded: chain D residue 1014 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 250 optimal weight: 0.4980 chunk 138 optimal weight: 10.0000 chunk 287 optimal weight: 0.0980 chunk 232 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 chunk 301 optimal weight: 0.0980 chunk 84 optimal weight: 0.8980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A 372 ASN ** A 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 ASN ** C 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 GLN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29796 Z= 0.138 Angle : 0.524 10.568 40400 Z= 0.261 Chirality : 0.040 0.200 4564 Planarity : 0.003 0.038 4904 Dihedral : 12.931 126.074 5186 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.08 % Allowed : 19.45 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3448 helix: -0.02 (0.12), residues: 1792 sheet: -1.27 (0.27), residues: 392 loop : -1.43 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 767 HIS 0.007 0.001 HIS B 468 PHE 0.028 0.001 PHE D1000 TYR 0.022 0.001 TYR D 130 ARG 0.006 0.000 ARG B 976 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 252 time to evaluate : 3.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.8862 (tt0) cc_final: 0.8630 (mt-10) REVERT: A 372 ASN cc_start: 0.7424 (OUTLIER) cc_final: 0.6917 (t0) REVERT: A 712 MET cc_start: 0.8408 (ptm) cc_final: 0.7878 (ppp) REVERT: A 830 MET cc_start: 0.9128 (mtm) cc_final: 0.8900 (mtm) REVERT: B 173 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7665 (p0) REVERT: B 214 LEU cc_start: 0.9529 (mt) cc_final: 0.9291 (mp) REVERT: B 264 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6466 (mm-30) REVERT: B 314 MET cc_start: 0.9321 (ttp) cc_final: 0.9023 (ttp) REVERT: B 321 GLU cc_start: 0.8853 (tt0) cc_final: 0.8627 (mt-10) REVERT: B 799 MET cc_start: 0.8656 (tpp) cc_final: 0.8334 (tpp) REVERT: C 30 MET cc_start: 0.8464 (tpp) cc_final: 0.8192 (mmt) REVERT: C 34 PHE cc_start: 0.8969 (m-80) cc_final: 0.8677 (m-80) REVERT: C 50 TRP cc_start: 0.6674 (t60) cc_final: 0.5402 (p-90) REVERT: C 214 LEU cc_start: 0.9576 (mt) cc_final: 0.9363 (mp) REVERT: C 264 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6676 (mm-30) REVERT: C 387 LEU cc_start: 0.9657 (tp) cc_final: 0.9306 (tp) REVERT: C 564 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7804 (tt) REVERT: C 712 MET cc_start: 0.8252 (ptp) cc_final: 0.7901 (ppp) REVERT: D 30 MET cc_start: 0.8469 (tpp) cc_final: 0.8201 (mmt) REVERT: D 34 PHE cc_start: 0.8987 (m-80) cc_final: 0.8726 (m-80) REVERT: D 50 TRP cc_start: 0.6624 (t60) cc_final: 0.5092 (p-90) REVERT: D 214 LEU cc_start: 0.9597 (mt) cc_final: 0.9383 (mp) REVERT: D 264 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6734 (mm-30) REVERT: D 321 GLU cc_start: 0.8875 (tt0) cc_final: 0.8672 (mt-10) REVERT: D 387 LEU cc_start: 0.9648 (tp) cc_final: 0.9296 (tp) REVERT: D 564 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7798 (tt) REVERT: D 830 MET cc_start: 0.9043 (mtm) cc_final: 0.8828 (mtm) outliers start: 64 outliers final: 45 residues processed: 299 average time/residue: 0.3346 time to fit residues: 173.0974 Evaluate side-chains 277 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 228 time to evaluate : 3.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 736 ASN Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 1014 ILE Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 736 ASN Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 885 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 7.9990 chunk 302 optimal weight: 0.1980 chunk 66 optimal weight: 0.0000 chunk 197 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 336 optimal weight: 0.9980 chunk 279 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29796 Z= 0.132 Angle : 0.514 10.355 40400 Z= 0.255 Chirality : 0.040 0.205 4564 Planarity : 0.003 0.037 4904 Dihedral : 12.160 100.635 5180 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.82 % Allowed : 20.06 % Favored : 78.12 % 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: -0.88 (0.14), residues: 3448 helix: 0.11 (0.12), residues: 1796 sheet: -1.05 (0.28), residues: 392 loop : -1.30 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 203 HIS 0.005 0.001 HIS B 254 PHE 0.026 0.001 PHE B1000 TYR 0.026 0.001 TYR B 130 ARG 0.005 0.000 ARG B 974 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 247 time to evaluate : 3.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6602 (mm-30) REVERT: A 321 GLU cc_start: 0.8871 (tt0) cc_final: 0.8624 (mt-10) REVERT: A 712 MET cc_start: 0.8418 (ptm) cc_final: 0.7876 (ppp) REVERT: B 264 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6516 (mm-30) REVERT: B 314 MET cc_start: 0.9313 (ttp) cc_final: 0.8999 (ttp) REVERT: B 321 GLU cc_start: 0.8865 (tt0) cc_final: 0.8649 (mt-10) REVERT: B 564 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7675 (tt) REVERT: B 799 MET cc_start: 0.8658 (tpp) cc_final: 0.8330 (tpp) REVERT: C 34 PHE cc_start: 0.9019 (m-80) cc_final: 0.8817 (m-80) REVERT: C 50 TRP cc_start: 0.6633 (t60) cc_final: 0.5137 (p-90) REVERT: C 264 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6778 (mm-30) REVERT: C 564 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7810 (tt) REVERT: C 712 MET cc_start: 0.8271 (ptp) cc_final: 0.7944 (ppp) REVERT: D 34 PHE cc_start: 0.9018 (m-80) cc_final: 0.8809 (m-80) REVERT: D 50 TRP cc_start: 0.6753 (t60) cc_final: 0.5110 (p-90) REVERT: D 264 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6769 (mm-30) REVERT: D 321 GLU cc_start: 0.8877 (tt0) cc_final: 0.8657 (mt-10) REVERT: D 564 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7817 (tt) outliers start: 56 outliers final: 45 residues processed: 287 average time/residue: 0.3485 time to fit residues: 170.6648 Evaluate side-chains 272 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 224 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 736 ASN Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 736 ASN Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 885 ASP Chi-restraints excluded: chain D residue 932 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 191 optimal weight: 1.9990 chunk 245 optimal weight: 0.1980 chunk 190 optimal weight: 2.9990 chunk 283 optimal weight: 5.9990 chunk 188 optimal weight: 0.7980 chunk 335 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 204 optimal weight: 0.0060 chunk 154 optimal weight: 0.8980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 979 GLN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 29796 Z= 0.135 Angle : 0.509 9.811 40400 Z= 0.252 Chirality : 0.040 0.219 4564 Planarity : 0.003 0.037 4904 Dihedral : 11.595 89.691 5176 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.95 % Allowed : 20.42 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.15), residues: 3448 helix: 0.25 (0.12), residues: 1772 sheet: -0.86 (0.29), residues: 392 loop : -1.03 (0.18), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 477 HIS 0.006 0.001 HIS C 254 PHE 0.026 0.001 PHE D1000 TYR 0.026 0.001 TYR A 130 ARG 0.002 0.000 ARG C 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 245 time to evaluate : 3.239 Fit side-chains revert: symmetry clash REVERT: A 264 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6679 (mm-30) REVERT: A 321 GLU cc_start: 0.8876 (tt0) cc_final: 0.8596 (mt-10) REVERT: B 264 GLU cc_start: 0.6937 (mm-30) cc_final: 0.6549 (mm-30) REVERT: B 314 MET cc_start: 0.9306 (ttp) cc_final: 0.9001 (ttp) REVERT: B 321 GLU cc_start: 0.8876 (tt0) cc_final: 0.8657 (mt-10) REVERT: B 564 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7880 (tt) REVERT: B 799 MET cc_start: 0.8624 (tpp) cc_final: 0.8345 (tpp) REVERT: C 30 MET cc_start: 0.8840 (mmt) cc_final: 0.8640 (tpp) REVERT: C 50 TRP cc_start: 0.6642 (t60) cc_final: 0.5025 (p-90) REVERT: C 173 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7816 (p0) REVERT: C 264 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6802 (mm-30) REVERT: C 564 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7814 (tt) REVERT: C 712 MET cc_start: 0.8190 (ptp) cc_final: 0.7917 (ppp) REVERT: C 925 SER cc_start: 0.8630 (p) cc_final: 0.8367 (p) REVERT: D 50 TRP cc_start: 0.6540 (t60) cc_final: 0.4945 (p-90) REVERT: D 264 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6874 (mm-30) REVERT: D 321 GLU cc_start: 0.8882 (tt0) cc_final: 0.8629 (mt-10) REVERT: D 564 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7821 (tt) REVERT: D 712 MET cc_start: 0.8441 (ptm) cc_final: 0.8213 (ppp) outliers start: 60 outliers final: 49 residues processed: 291 average time/residue: 0.3458 time to fit residues: 172.8784 Evaluate side-chains 280 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 227 time to evaluate : 3.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 736 ASN Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 932 ASN Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 736 ASN Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 885 ASP Chi-restraints excluded: chain D residue 932 ASN Chi-restraints excluded: chain D residue 946 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 ASN ** A 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 HIS ** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN C 459 GLN ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS ** C 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 979 GLN D 459 GLN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 HIS ** D 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 29796 Z= 0.359 Angle : 0.642 10.877 40400 Z= 0.323 Chirality : 0.043 0.207 4564 Planarity : 0.004 0.035 4904 Dihedral : 12.201 89.996 5176 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.31 % Allowed : 20.84 % Favored : 76.85 % 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: -0.67 (0.15), residues: 3448 helix: 0.09 (0.12), residues: 1740 sheet: -0.89 (0.28), residues: 408 loop : -0.86 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 475 HIS 0.006 0.001 HIS D 254 PHE 0.034 0.002 PHE A 217 TYR 0.030 0.002 TYR A 130 ARG 0.007 0.001 ARG A 974 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 206 time to evaluate : 3.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8388 (tpp) cc_final: 0.7850 (tpp) REVERT: A 264 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6614 (mm-30) REVERT: A 513 MET cc_start: 0.8677 (mmp) cc_final: 0.8470 (mmm) REVERT: B 264 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6730 (mm-30) REVERT: B 314 MET cc_start: 0.9394 (ttp) cc_final: 0.9130 (ttp) REVERT: B 513 MET cc_start: 0.8687 (mmp) cc_final: 0.8475 (mmm) REVERT: B 564 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7907 (tt) REVERT: B 691 MET cc_start: 0.5784 (tpp) cc_final: 0.5365 (tpp) REVERT: B 712 MET cc_start: 0.7942 (ptp) cc_final: 0.7655 (pmm) REVERT: B 799 MET cc_start: 0.8645 (tpp) cc_final: 0.8386 (tpp) REVERT: C 21 MET cc_start: 0.8572 (tpp) cc_final: 0.8036 (tpp) REVERT: C 173 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7862 (p0) REVERT: C 513 MET cc_start: 0.8707 (mmp) cc_final: 0.8497 (mmm) REVERT: C 564 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7903 (tt) REVERT: C 712 MET cc_start: 0.8235 (ptp) cc_final: 0.7956 (ppp) REVERT: C 925 SER cc_start: 0.8861 (p) cc_final: 0.8534 (p) REVERT: D 50 TRP cc_start: 0.6825 (t60) cc_final: 0.5382 (p90) REVERT: D 173 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7855 (p0) REVERT: D 513 MET cc_start: 0.8711 (mmp) cc_final: 0.8498 (mmm) REVERT: D 564 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7904 (tt) REVERT: D 925 SER cc_start: 0.8767 (p) cc_final: 0.8461 (p) outliers start: 71 outliers final: 60 residues processed: 262 average time/residue: 0.3484 time to fit residues: 157.8199 Evaluate side-chains 260 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 195 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 1053 MET Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 736 ASN Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 932 ASN Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 1053 MET Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 736 ASN Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 885 ASP Chi-restraints excluded: chain D residue 932 ASN Chi-restraints excluded: chain D residue 946 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 2.9990 chunk 321 optimal weight: 7.9990 chunk 293 optimal weight: 1.9990 chunk 312 optimal weight: 5.9990 chunk 188 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 chunk 295 optimal weight: 0.9990 chunk 311 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 979 GLN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29796 Z= 0.188 Angle : 0.541 11.315 40400 Z= 0.269 Chirality : 0.041 0.229 4564 Planarity : 0.003 0.037 4904 Dihedral : 11.851 89.994 5176 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.18 % Allowed : 21.43 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.15), residues: 3448 helix: 0.16 (0.12), residues: 1768 sheet: -0.70 (0.29), residues: 360 loop : -0.95 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 477 HIS 0.006 0.001 HIS C 254 PHE 0.026 0.001 PHE D1000 TYR 0.034 0.001 TYR B 130 ARG 0.004 0.000 ARG A 974 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 211 time to evaluate : 3.342 Fit side-chains REVERT: A 264 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6736 (mm-30) REVERT: B 30 MET cc_start: 0.8738 (tpp) cc_final: 0.8362 (tpp) REVERT: B 314 MET cc_start: 0.9347 (ttp) cc_final: 0.9079 (ttp) REVERT: B 564 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7917 (tt) REVERT: B 691 MET cc_start: 0.5841 (tpp) cc_final: 0.5606 (tpp) REVERT: B 712 MET cc_start: 0.7871 (ptp) cc_final: 0.7664 (pmm) REVERT: B 799 MET cc_start: 0.8630 (tpp) cc_final: 0.8391 (tpp) REVERT: C 173 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7867 (p0) REVERT: C 564 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7880 (tt) REVERT: C 712 MET cc_start: 0.8223 (ptp) cc_final: 0.7912 (ppp) REVERT: C 925 SER cc_start: 0.8797 (p) cc_final: 0.8482 (p) REVERT: D 173 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7858 (p0) REVERT: D 564 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7883 (tt) REVERT: D 925 SER cc_start: 0.8695 (p) cc_final: 0.8402 (p) outliers start: 67 outliers final: 61 residues processed: 263 average time/residue: 0.3457 time to fit residues: 155.6999 Evaluate side-chains 265 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 199 time to evaluate : 3.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 736 ASN Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 932 ASN Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 1053 MET Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 736 ASN Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 885 ASP Chi-restraints excluded: chain D residue 932 ASN Chi-restraints excluded: chain D residue 946 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 4.9990 chunk 330 optimal weight: 3.9990 chunk 201 optimal weight: 10.0000 chunk 156 optimal weight: 0.0980 chunk 229 optimal weight: 7.9990 chunk 346 optimal weight: 8.9990 chunk 319 optimal weight: 3.9990 chunk 276 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 213 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 ASN ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 979 GLN D 182 ASN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29796 Z= 0.294 Angle : 0.611 12.129 40400 Z= 0.304 Chirality : 0.042 0.218 4564 Planarity : 0.004 0.036 4904 Dihedral : 12.098 89.795 5176 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.27 % Allowed : 21.36 % Favored : 76.36 % 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: -0.71 (0.15), residues: 3448 helix: 0.08 (0.12), residues: 1740 sheet: -0.83 (0.28), residues: 400 loop : -0.93 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 477 HIS 0.005 0.001 HIS C 254 PHE 0.038 0.002 PHE D 217 TYR 0.035 0.002 TYR C 130 ARG 0.007 0.000 ARG A 974 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 201 time to evaluate : 3.562 Fit side-chains REVERT: B 30 MET cc_start: 0.8724 (tpp) cc_final: 0.8456 (tpp) REVERT: B 314 MET cc_start: 0.9397 (ttp) cc_final: 0.9133 (ttp) REVERT: B 712 MET cc_start: 0.7926 (ptp) cc_final: 0.7685 (pmm) REVERT: B 799 MET cc_start: 0.8637 (tpp) cc_final: 0.8406 (tpp) REVERT: C 173 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7847 (p0) REVERT: C 564 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7903 (tt) REVERT: C 712 MET cc_start: 0.8252 (ptp) cc_final: 0.7921 (ppp) REVERT: C 925 SER cc_start: 0.8714 (p) cc_final: 0.8485 (p) REVERT: D 173 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7839 (p0) REVERT: D 564 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7899 (tt) REVERT: D 712 MET cc_start: 0.8520 (ptm) cc_final: 0.8254 (ppp) REVERT: D 925 SER cc_start: 0.8799 (p) cc_final: 0.8553 (p) outliers start: 70 outliers final: 62 residues processed: 254 average time/residue: 0.3362 time to fit residues: 147.2429 Evaluate side-chains 261 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 195 time to evaluate : 3.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 885 ASP Chi-restraints excluded: chain B residue 935 THR Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 736 ASN Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 932 ASN Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 1053 MET Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 736 ASN Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 778 ILE Chi-restraints excluded: chain D residue 885 ASP Chi-restraints excluded: chain D residue 932 ASN Chi-restraints excluded: chain D residue 946 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 8.9990 chunk 294 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 254 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 276 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 283 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 50 optimal weight: 0.0010 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN ** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 979 GLN D 182 ASN ** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.085797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.071208 restraints weight = 105490.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.073206 restraints weight = 57337.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.074616 restraints weight = 38108.049| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29796 Z= 0.136 Angle : 0.538 11.917 40400 Z= 0.264 Chirality : 0.040 0.235 4564 Planarity : 0.003 0.037 4904 Dihedral : 11.566 88.569 5176 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.98 % Allowed : 21.75 % Favored : 76.27 % 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: -0.53 (0.15), residues: 3448 helix: 0.27 (0.13), residues: 1744 sheet: -0.71 (0.29), residues: 372 loop : -0.93 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 477 HIS 0.006 0.001 HIS C 254 PHE 0.034 0.001 PHE D 217 TYR 0.033 0.001 TYR C 130 ARG 0.003 0.000 ARG A 974 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4708.91 seconds wall clock time: 88 minutes 29.53 seconds (5309.53 seconds total)