Starting phenix.real_space_refine on Sat Mar 16 10:25:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq8_17108/03_2024/8oq8_17108_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq8_17108/03_2024/8oq8_17108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq8_17108/03_2024/8oq8_17108.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq8_17108/03_2024/8oq8_17108.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq8_17108/03_2024/8oq8_17108_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq8_17108/03_2024/8oq8_17108_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 9428 2.51 5 N 2248 2.21 5 O 2681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14432 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2765 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2757 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2768 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2761 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2778 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Chain: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 111 Unusual residues: {'D10': 2, 'D12': 2, 'HEX': 3, 'NAG': 2, 'RI5': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 90 Unusual residues: {'D10': 2, 'D12': 2, 'HEX': 3, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 90 Unusual residues: {'D10': 2, 'D12': 2, 'HEX': 3, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 90 Unusual residues: {'D10': 2, 'D12': 2, 'HEX': 3, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 90 Unusual residues: {'D10': 2, 'D12': 2, 'HEX': 3, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Time building chain proxies: 8.05, per 1000 atoms: 0.56 Number of scatterers: 14432 At special positions: 0 Unit cell: (93.4775, 95.495, 140.553, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 2681 8.00 N 2248 7.00 C 9428 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 Atom "HETATM13855 O5 NAG A 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM14142 O5 NAG D 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM14052 O5 NAG C 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM14232 O5 NAG E 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM13841 O5 NAG A 501 .*. O " rejected from bonding due to valence issues. Atom "HETATM13962 O5 NAG B 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM14066 O5 NAG C 503 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 140 " " NAG A 502 " - " ASN A 234 " " NAG B 502 " - " ASN B 140 " " NAG B 503 " - " ASN B 234 " " NAG C 502 " - " ASN C 140 " " NAG C 503 " - " ASN C 234 " " NAG D 502 " - " ASN D 140 " " NAG D 503 " - " ASN D 234 " " NAG E 502 " - " ASN E 140 " " NAG E 503 " - " ASN E 234 " Time building additional restraints: 5.36 Conformation dependent library (CDL) restraints added in 2.4 seconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 30 sheets defined 37.1% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.973A pdb=" N LYS A 151 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 236 removed outlier: 3.596A pdb=" N SER A 236 " --> pdb=" O GLY A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 236' Processing helix chain 'A' and resid 281 through 304 removed outlier: 4.384A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 3.603A pdb=" N TRP A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N PHE A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP A 304 " --> pdb=" O TRP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 334 Proline residue: A 315 - end of helix removed outlier: 3.511A pdb=" N SER A 334 " --> pdb=" O GLY A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 379 removed outlier: 3.604A pdb=" N TYR A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A 359 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 477 removed outlier: 3.999A pdb=" N ILE A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Proline residue: A 464 - end of helix Processing helix chain 'B' and resid 75 through 78 No H-bonds generated for 'chain 'B' and resid 75 through 78' Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 281 through 304 removed outlier: 4.544A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 3.641A pdb=" N TRP B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N SER B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N PHE B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TRP B 304 " --> pdb=" O TRP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 334 Proline residue: B 315 - end of helix removed outlier: 3.630A pdb=" N SER B 334 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 379 removed outlier: 3.731A pdb=" N TYR B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 359 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 360 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 477 removed outlier: 3.926A pdb=" N ILE B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Proline residue: B 464 - end of helix Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 81 through 83 No H-bonds generated for 'chain 'C' and resid 81 through 83' Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 147 through 152 removed outlier: 4.322A pdb=" N LYS C 151 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 236 removed outlier: 3.590A pdb=" N SER C 236 " --> pdb=" O GLY C 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 233 through 236' Processing helix chain 'C' and resid 281 through 304 removed outlier: 4.519A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Proline residue: C 291 - end of helix removed outlier: 3.693A pdb=" N TRP C 300 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL C 301 " --> pdb=" O MET C 297 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER C 302 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N PHE C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TRP C 304 " --> pdb=" O TRP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 334 Proline residue: C 315 - end of helix Processing helix chain 'C' and resid 343 through 379 removed outlier: 3.631A pdb=" N TYR C 347 " --> pdb=" O ALA C 343 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL C 359 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 360 " --> pdb=" O PHE C 356 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR C 362 " --> pdb=" O SER C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 477 removed outlier: 4.039A pdb=" N ILE C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Proline residue: C 464 - end of helix Processing helix chain 'D' and resid 75 through 78 No H-bonds generated for 'chain 'D' and resid 75 through 78' Processing helix chain 'D' and resid 131 through 133 No H-bonds generated for 'chain 'D' and resid 131 through 133' Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 233 through 236 removed outlier: 3.598A pdb=" N SER D 236 " --> pdb=" O GLY D 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 233 through 236' Processing helix chain 'D' and resid 281 through 304 removed outlier: 4.456A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Proline residue: D 291 - end of helix removed outlier: 3.644A pdb=" N TRP D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL D 301 " --> pdb=" O MET D 297 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER D 302 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N PHE D 303 " --> pdb=" O SER D 299 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TRP D 304 " --> pdb=" O TRP D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 334 Proline residue: D 315 - end of helix removed outlier: 3.666A pdb=" N SER D 334 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 379 removed outlier: 3.601A pdb=" N TYR D 347 " --> pdb=" O ALA D 343 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL D 359 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 360 " --> pdb=" O PHE D 356 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR D 362 " --> pdb=" O SER D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 477 removed outlier: 3.917A pdb=" N ILE D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) Proline residue: D 464 - end of helix Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 131 through 133 No H-bonds generated for 'chain 'E' and resid 131 through 133' Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 233 through 236 removed outlier: 3.678A pdb=" N SER E 236 " --> pdb=" O GLY E 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 233 through 236' Processing helix chain 'E' and resid 281 through 304 removed outlier: 4.477A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Proline residue: E 291 - end of helix removed outlier: 3.712A pdb=" N TRP E 300 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL E 301 " --> pdb=" O MET E 297 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N PHE E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TRP E 304 " --> pdb=" O TRP E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 334 Proline residue: E 315 - end of helix removed outlier: 3.644A pdb=" N SER E 334 " --> pdb=" O GLY E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 379 removed outlier: 3.710A pdb=" N TYR E 347 " --> pdb=" O ALA E 343 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL E 359 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU E 360 " --> pdb=" O PHE E 356 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR E 362 " --> pdb=" O SER E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 477 removed outlier: 3.966A pdb=" N ILE E 461 " --> pdb=" O LYS E 457 " (cutoff:3.500A) Proline residue: E 464 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 226 through 230 removed outlier: 6.368A pdb=" N ILE A 97 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N TYR A 229 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL A 99 " --> pdb=" O TYR A 229 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LYS A 129 " --> pdb=" O PRO A 98 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR A 121 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU A 108 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR A 119 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 103 through 105 Processing sheet with id= C, first strand: chain 'A' and resid 110 through 112 removed outlier: 3.941A pdb=" N SER A 110 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.732A pdb=" N GLU A 215 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 254 through 262 removed outlier: 3.504A pdb=" N THR A 256 " --> pdb=" O TYR A 272 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 163 through 168 removed outlier: 6.911A pdb=" N THR A 195 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER A 166 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR A 193 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 226 through 230 removed outlier: 6.422A pdb=" N ILE B 97 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N TYR B 229 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL B 99 " --> pdb=" O TYR B 229 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LYS B 129 " --> pdb=" O PRO B 98 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR B 121 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LEU B 108 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR B 119 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= I, first strand: chain 'B' and resid 110 through 112 removed outlier: 3.991A pdb=" N SER B 110 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 158 through 161 removed outlier: 4.704A pdb=" N GLU B 215 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 254 through 262 Processing sheet with id= L, first strand: chain 'B' and resid 163 through 168 removed outlier: 6.906A pdb=" N THR B 195 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER B 166 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR B 193 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 226 through 230 removed outlier: 6.408A pdb=" N ILE C 97 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR C 229 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL C 99 " --> pdb=" O TYR C 229 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LYS C 129 " --> pdb=" O PRO C 98 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR C 121 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU C 108 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR C 119 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 103 through 105 Processing sheet with id= O, first strand: chain 'C' and resid 110 through 112 removed outlier: 3.878A pdb=" N SER C 110 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 158 through 161 removed outlier: 4.692A pdb=" N GLU C 215 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 254 through 262 Processing sheet with id= R, first strand: chain 'C' and resid 163 through 168 removed outlier: 6.851A pdb=" N THR C 195 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER C 166 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR C 193 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 226 through 230 removed outlier: 6.343A pdb=" N ILE D 97 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N TYR D 229 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL D 99 " --> pdb=" O TYR D 229 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LYS D 129 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR D 121 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEU D 108 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR D 119 " --> pdb=" O LEU D 108 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 103 through 105 Processing sheet with id= U, first strand: chain 'D' and resid 110 through 112 removed outlier: 3.836A pdb=" N SER D 110 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.734A pdb=" N GLU D 215 " --> pdb=" O VAL D 161 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 254 through 262 Processing sheet with id= X, first strand: chain 'D' and resid 163 through 168 removed outlier: 6.873A pdb=" N THR D 195 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER D 166 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR D 193 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 226 through 230 removed outlier: 6.311A pdb=" N ILE E 97 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N TYR E 229 " --> pdb=" O ILE E 97 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL E 99 " --> pdb=" O TYR E 229 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LYS E 129 " --> pdb=" O PRO E 98 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR E 121 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LEU E 108 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR E 119 " --> pdb=" O LEU E 108 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 103 through 105 Processing sheet with id= AA, first strand: chain 'E' and resid 110 through 112 removed outlier: 3.963A pdb=" N SER E 110 " --> pdb=" O THR E 119 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.679A pdb=" N GLU E 215 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 254 through 262 Processing sheet with id= AD, first strand: chain 'E' and resid 163 through 168 removed outlier: 6.840A pdb=" N THR E 195 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER E 166 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR E 193 " --> pdb=" O SER E 166 " (cutoff:3.500A) 660 hydrogen bonds defined for protein. 1875 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.19 Time building geometry restraints manager: 5.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2350 1.32 - 1.44: 4148 1.44 - 1.57: 8005 1.57 - 1.69: 1 1.69 - 1.81: 140 Bond restraints: 14644 Sorted by residual: bond pdb=" CG1 ILE E 111 " pdb=" CD1 ILE E 111 " ideal model delta sigma weight residual 1.513 1.422 0.091 3.90e-02 6.57e+02 5.45e+00 bond pdb=" CB ASP D 102 " pdb=" CG ASP D 102 " ideal model delta sigma weight residual 1.516 1.458 0.058 2.50e-02 1.60e+03 5.36e+00 bond pdb=" C15 RI5 A 510 " pdb=" O16 RI5 A 510 " ideal model delta sigma weight residual 1.396 1.442 -0.046 2.00e-02 2.50e+03 5.30e+00 bond pdb=" CG1 ILE D 111 " pdb=" CD1 ILE D 111 " ideal model delta sigma weight residual 1.513 1.424 0.089 3.90e-02 6.57e+02 5.22e+00 bond pdb=" CB PRO D 206 " pdb=" CG PRO D 206 " ideal model delta sigma weight residual 1.506 1.422 0.084 3.90e-02 6.57e+02 4.69e+00 ... (remaining 14639 not shown) Histogram of bond angle deviations from ideal: 59.64 - 74.56: 3 74.56 - 89.48: 0 89.48 - 104.39: 205 104.39 - 119.31: 12184 119.31 - 134.23: 7391 Bond angle restraints: 19783 Sorted by residual: angle pdb=" N GLU C 252 " pdb=" CA GLU C 252 " pdb=" C GLU C 252 " ideal model delta sigma weight residual 110.91 114.52 -3.61 1.17e+00 7.31e-01 9.53e+00 angle pdb=" CA LEU B 190 " pdb=" CB LEU B 190 " pdb=" CG LEU B 190 " ideal model delta sigma weight residual 116.30 125.56 -9.26 3.50e+00 8.16e-02 7.01e+00 angle pdb=" CA LEU C 190 " pdb=" CB LEU C 190 " pdb=" CG LEU C 190 " ideal model delta sigma weight residual 116.30 125.50 -9.20 3.50e+00 8.16e-02 6.92e+00 angle pdb=" CA TYR A 340 " pdb=" CB TYR A 340 " pdb=" CG TYR A 340 " ideal model delta sigma weight residual 113.90 118.48 -4.58 1.80e+00 3.09e-01 6.48e+00 angle pdb=" N THR B 265 " pdb=" CA THR B 265 " pdb=" C THR B 265 " ideal model delta sigma weight residual 110.80 116.15 -5.35 2.13e+00 2.20e-01 6.31e+00 ... (remaining 19778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 8336 17.79 - 35.57: 376 35.57 - 53.36: 73 53.36 - 71.14: 22 71.14 - 88.93: 2 Dihedral angle restraints: 8809 sinusoidal: 3794 harmonic: 5015 Sorted by residual: dihedral pdb=" CA SER C 339 " pdb=" C SER C 339 " pdb=" N TYR C 340 " pdb=" CA TYR C 340 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA SER B 339 " pdb=" C SER B 339 " pdb=" N TYR B 340 " pdb=" CA TYR B 340 " ideal model delta harmonic sigma weight residual 180.00 161.94 18.06 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA SER D 339 " pdb=" C SER D 339 " pdb=" N TYR D 340 " pdb=" CA TYR D 340 " ideal model delta harmonic sigma weight residual 180.00 163.04 16.96 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 8806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.287: 2233 0.287 - 0.574: 3 0.574 - 0.860: 0 0.860 - 1.147: 1 1.147 - 1.434: 2 Chirality restraints: 2239 Sorted by residual: chirality pdb=" C1 NAG B 503 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B 503 " pdb=" O5 NAG B 503 " both_signs ideal model delta sigma weight residual False -2.40 -0.97 -1.43 2.00e-01 2.50e+01 5.14e+01 chirality pdb=" C1 NAG C 503 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C 503 " pdb=" O5 NAG C 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.07 -1.33 2.00e-01 2.50e+01 4.40e+01 chirality pdb=" C1 NAG E 503 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E 503 " pdb=" O5 NAG E 503 " both_signs ideal model delta sigma weight residual False -2.40 -3.36 0.96 2.00e-01 2.50e+01 2.29e+01 ... (remaining 2236 not shown) Planarity restraints: 2404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 234 " 0.361 2.00e-02 2.50e+03 3.77e-01 1.78e+03 pdb=" CG ASN E 234 " -0.129 2.00e-02 2.50e+03 pdb=" OD1 ASN E 234 " -0.123 2.00e-02 2.50e+03 pdb=" ND2 ASN E 234 " -0.576 2.00e-02 2.50e+03 pdb=" C1 NAG E 503 " 0.466 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 234 " 0.296 2.00e-02 2.50e+03 3.73e-01 1.74e+03 pdb=" CG ASN D 234 " -0.133 2.00e-02 2.50e+03 pdb=" OD1 ASN D 234 " -0.079 2.00e-02 2.50e+03 pdb=" ND2 ASN D 234 " -0.580 2.00e-02 2.50e+03 pdb=" C1 NAG D 503 " 0.496 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.171 2.00e-02 2.50e+03 3.32e-01 1.38e+03 pdb=" CG ASN A 234 " 0.108 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " -0.087 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.571 2.00e-02 2.50e+03 pdb=" C1 NAG A 502 " -0.421 2.00e-02 2.50e+03 ... (remaining 2401 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 824 2.72 - 3.26: 12582 3.26 - 3.81: 21086 3.81 - 4.35: 27931 4.35 - 4.90: 49234 Nonbonded interactions: 111657 Sorted by model distance: nonbonded pdb=" OD1 ASN C 269 " pdb=" O HOH C 601 " model vdw 2.175 2.440 nonbonded pdb=" OD1 ASN D 269 " pdb=" O HOH D 601 " model vdw 2.194 2.440 nonbonded pdb=" O HOH A 605 " pdb=" O HOH A 620 " model vdw 2.241 2.440 nonbonded pdb=" OD1 ASP E 115 " pdb=" O HOH E 601 " model vdw 2.250 2.440 nonbonded pdb=" O ASP C 174 " pdb=" O HOH C 602 " model vdw 2.286 2.440 ... (remaining 111652 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 74 through 372 or (resid 373 through 374 and (name N or na \ me CA or name C or name O or name CB )) or resid 375 or (resid 376 through 380 a \ nd (name N or name CA or name C or name O or name CB )) or resid 451 through 479 \ or resid 502 or resid 504 through 505)) selection = (chain 'B' and (resid 74 through 372 or (resid 373 through 374 and (name N or na \ me CA or name C or name O or name CB )) or resid 375 through 479 or resid 502 or \ resid 504 through 505)) selection = (chain 'C' and (resid 74 through 372 or (resid 373 through 374 and (name N or na \ me CA or name C or name O or name CB )) or resid 375 or (resid 376 through 380 a \ nd (name N or name CA or name C or name O or name CB )) or resid 451 through 479 \ or resid 502 or resid 504 through 505)) selection = (chain 'D' and (resid 74 through 373 or (resid 374 and (name N or name CA or nam \ e C or name O or name CB )) or resid 375 or (resid 376 through 380 and (name N o \ r name CA or name C or name O or name CB )) or resid 451 through 479 or resid 50 \ 2 or resid 504 through 505)) selection = (chain 'E' and (resid 74 through 372 or (resid 373 through 374 and (name N or na \ me CA or name C or name O or name CB )) or resid 375 or (resid 376 through 380 a \ nd (name N or name CA or name C or name O or name CB )) or resid 451 through 479 \ or resid 502 or resid 504 through 505)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 15.450 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 39.110 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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 0.096 14644 Z= 0.885 Angle : 0.967 9.265 19783 Z= 0.495 Chirality : 0.081 1.434 2239 Planarity : 0.008 0.052 2394 Dihedral : 11.030 88.930 5549 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.84 % Allowed : 2.98 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.82 (0.20), residues: 1660 helix: 1.88 (0.22), residues: 530 sheet: 1.30 (0.23), residues: 440 loop : 0.77 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 300 HIS 0.009 0.003 HIS A 254 PHE 0.024 0.004 PHE B 253 TYR 0.021 0.004 TYR D 219 ARG 0.020 0.003 ARG C 337 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 290 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.7602 (mt) cc_final: 0.7334 (mp) REVERT: A 179 ARG cc_start: 0.8106 (ttp-170) cc_final: 0.7549 (ttm-80) REVERT: A 238 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8054 (mmtp) REVERT: A 269 ASN cc_start: 0.8418 (m-40) cc_final: 0.7562 (t0) REVERT: A 335 MET cc_start: 0.7636 (mtm) cc_final: 0.6924 (mmp) REVERT: A 345 ASP cc_start: 0.8059 (m-30) cc_final: 0.7578 (m-30) REVERT: B 143 MET cc_start: 0.8680 (mtm) cc_final: 0.8432 (mtp) REVERT: B 151 LYS cc_start: 0.8368 (mmtt) cc_final: 0.7865 (mptt) REVERT: B 235 ASP cc_start: 0.7904 (m-30) cc_final: 0.7676 (m-30) REVERT: B 269 ASN cc_start: 0.8360 (m-40) cc_final: 0.7990 (m-40) REVERT: B 308 ARG cc_start: 0.7422 (mtm180) cc_final: 0.7141 (mtm110) REVERT: C 82 ASP cc_start: 0.7457 (m-30) cc_final: 0.6129 (p0) REVERT: C 92 PHE cc_start: 0.8223 (t80) cc_final: 0.7874 (t80) REVERT: C 116 MET cc_start: 0.8704 (mtm) cc_final: 0.8372 (mtp) REVERT: C 151 LYS cc_start: 0.8390 (mmtt) cc_final: 0.8064 (mmtp) REVERT: C 179 ARG cc_start: 0.7947 (ttp-170) cc_final: 0.7677 (ttp-170) REVERT: C 269 ASN cc_start: 0.8263 (m-40) cc_final: 0.8015 (t0) REVERT: D 114 VAL cc_start: 0.7958 (t) cc_final: 0.7581 (p) REVERT: D 179 ARG cc_start: 0.7796 (ttp-170) cc_final: 0.7592 (ttp-170) REVERT: E 106 GLU cc_start: 0.7373 (tt0) cc_final: 0.6809 (tt0) REVERT: E 116 MET cc_start: 0.8779 (mtm) cc_final: 0.8515 (mtp) REVERT: E 232 LYS cc_start: 0.8023 (mtmm) cc_final: 0.7553 (mmtt) REVERT: E 269 ASN cc_start: 0.8679 (m-40) cc_final: 0.8173 (m-40) REVERT: E 372 GLN cc_start: 0.7789 (tp40) cc_final: 0.7474 (mm-40) outliers start: 13 outliers final: 8 residues processed: 301 average time/residue: 1.4957 time to fit residues: 486.0387 Evaluate side-chains 242 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 234 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 461 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 269 ASN A 287 GLN C 251 GLN C 287 GLN C 372 GLN D 162 HIS ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN E 251 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14644 Z= 0.188 Angle : 0.562 7.694 19783 Z= 0.301 Chirality : 0.046 0.646 2239 Planarity : 0.004 0.032 2394 Dihedral : 8.528 59.997 2346 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.85 % Allowed : 9.06 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.91 (0.21), residues: 1660 helix: 2.16 (0.23), residues: 555 sheet: 1.20 (0.24), residues: 440 loop : 0.67 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 349 HIS 0.004 0.001 HIS B 126 PHE 0.015 0.001 PHE B 92 TYR 0.021 0.002 TYR E 272 ARG 0.006 0.000 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 260 time to evaluate : 1.602 Fit side-chains REVERT: A 179 ARG cc_start: 0.7760 (ttp-170) cc_final: 0.7194 (ttm-80) REVERT: A 269 ASN cc_start: 0.8194 (m110) cc_final: 0.7455 (t0) REVERT: A 335 MET cc_start: 0.7494 (mtm) cc_final: 0.6806 (mmp) REVERT: A 345 ASP cc_start: 0.7779 (m-30) cc_final: 0.7309 (m-30) REVERT: B 151 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7780 (mptt) REVERT: B 269 ASN cc_start: 0.8185 (m-40) cc_final: 0.7870 (m-40) REVERT: B 308 ARG cc_start: 0.7354 (mtm180) cc_final: 0.7075 (mtm110) REVERT: C 82 ASP cc_start: 0.7464 (m-30) cc_final: 0.6180 (p0) REVERT: C 116 MET cc_start: 0.8544 (mtm) cc_final: 0.7973 (mtp) REVERT: C 151 LYS cc_start: 0.8322 (mmtt) cc_final: 0.8025 (mmtp) REVERT: C 179 ARG cc_start: 0.7748 (ttp-170) cc_final: 0.7370 (ttm-80) REVERT: C 240 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.6719 (t70) REVERT: C 242 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.6323 (mtt90) REVERT: D 114 VAL cc_start: 0.7746 (t) cc_final: 0.7464 (p) REVERT: D 179 ARG cc_start: 0.7596 (ttp-170) cc_final: 0.7396 (ttp-170) REVERT: D 457 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7138 (mtmp) REVERT: E 106 GLU cc_start: 0.7333 (tt0) cc_final: 0.6712 (tt0) REVERT: E 116 MET cc_start: 0.8608 (mtm) cc_final: 0.8301 (mtp) REVERT: E 143 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7762 (mmm) REVERT: E 232 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7350 (mmtt) REVERT: E 269 ASN cc_start: 0.8448 (m-40) cc_final: 0.7908 (t0) outliers start: 44 outliers final: 20 residues processed: 280 average time/residue: 1.4260 time to fit residues: 433.6425 Evaluate side-chains 262 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 238 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 251 GLN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 457 LYS Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 240 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 124 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN C 251 GLN C 287 GLN C 372 GLN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14644 Z= 0.233 Angle : 0.586 8.027 19783 Z= 0.317 Chirality : 0.045 0.506 2239 Planarity : 0.004 0.034 2394 Dihedral : 8.645 59.762 2341 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.95 % Allowed : 9.90 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.80 (0.21), residues: 1660 helix: 2.08 (0.23), residues: 560 sheet: 1.15 (0.24), residues: 445 loop : 0.57 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 349 HIS 0.005 0.001 HIS C 254 PHE 0.015 0.002 PHE B 92 TYR 0.017 0.002 TYR E 272 ARG 0.004 0.000 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 230 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.7860 (ttp-170) cc_final: 0.7231 (ttm-80) REVERT: A 227 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.5878 (tmt) REVERT: A 269 ASN cc_start: 0.8201 (m110) cc_final: 0.7789 (m-40) REVERT: A 335 MET cc_start: 0.7519 (mtm) cc_final: 0.6830 (mmp) REVERT: A 337 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6600 (mtm-85) REVERT: A 345 ASP cc_start: 0.7773 (m-30) cc_final: 0.7306 (m-30) REVERT: B 158 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8501 (mpm) REVERT: B 269 ASN cc_start: 0.8224 (m-40) cc_final: 0.7829 (m-40) REVERT: B 308 ARG cc_start: 0.7352 (mtm180) cc_final: 0.7083 (mtm110) REVERT: B 337 ARG cc_start: 0.7603 (ttm-80) cc_final: 0.7371 (tpp-160) REVERT: C 75 SER cc_start: 0.8416 (p) cc_final: 0.8148 (m) REVERT: C 82 ASP cc_start: 0.7531 (m-30) cc_final: 0.6319 (p0) REVERT: C 116 MET cc_start: 0.8584 (mtm) cc_final: 0.8019 (mtp) REVERT: C 151 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8041 (mmtp) REVERT: C 179 ARG cc_start: 0.7750 (ttp-170) cc_final: 0.7386 (ttm-80) REVERT: C 242 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.5858 (mtt90) REVERT: D 114 VAL cc_start: 0.7827 (t) cc_final: 0.7499 (p) REVERT: D 457 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7185 (mtmp) REVERT: E 106 GLU cc_start: 0.7324 (tt0) cc_final: 0.6724 (tt0) REVERT: E 111 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8020 (mt) REVERT: E 116 MET cc_start: 0.8664 (mtm) cc_final: 0.8279 (mtp) REVERT: E 143 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7759 (mmm) REVERT: E 232 LYS cc_start: 0.7885 (mtmm) cc_final: 0.7377 (mmtt) REVERT: E 269 ASN cc_start: 0.8471 (m-40) cc_final: 0.7977 (m-40) outliers start: 61 outliers final: 31 residues processed: 266 average time/residue: 1.3884 time to fit residues: 401.0308 Evaluate side-chains 263 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 225 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 457 LYS Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 159 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN B 247 GLN C 251 GLN C 287 GLN C 372 GLN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN E 247 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14644 Z= 0.158 Angle : 0.512 6.832 19783 Z= 0.276 Chirality : 0.043 0.472 2239 Planarity : 0.004 0.034 2394 Dihedral : 8.190 59.399 2341 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.69 % Allowed : 10.87 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.86 (0.21), residues: 1660 helix: 2.17 (0.23), residues: 560 sheet: 1.30 (0.24), residues: 440 loop : 0.45 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 349 HIS 0.004 0.001 HIS C 254 PHE 0.016 0.001 PHE B 92 TYR 0.016 0.002 TYR E 272 ARG 0.004 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 225 time to evaluate : 1.651 Fit side-chains revert: symmetry clash REVERT: A 179 ARG cc_start: 0.7714 (ttp-170) cc_final: 0.7097 (ttm-80) REVERT: A 227 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.5786 (tmt) REVERT: A 269 ASN cc_start: 0.8129 (m110) cc_final: 0.7740 (m-40) REVERT: A 335 MET cc_start: 0.7441 (mtm) cc_final: 0.6765 (mmp) REVERT: A 345 ASP cc_start: 0.7681 (m-30) cc_final: 0.7236 (m-30) REVERT: B 269 ASN cc_start: 0.8133 (m-40) cc_final: 0.7818 (m-40) REVERT: B 308 ARG cc_start: 0.7316 (mtm180) cc_final: 0.7049 (mtm110) REVERT: C 75 SER cc_start: 0.8351 (p) cc_final: 0.8095 (m) REVERT: C 82 ASP cc_start: 0.7499 (m-30) cc_final: 0.6319 (p0) REVERT: C 116 MET cc_start: 0.8518 (mtm) cc_final: 0.7968 (mtp) REVERT: C 151 LYS cc_start: 0.8337 (mmtt) cc_final: 0.8010 (mmtp) REVERT: C 179 ARG cc_start: 0.7697 (ttp-170) cc_final: 0.7317 (ttm-80) REVERT: D 114 VAL cc_start: 0.7733 (t) cc_final: 0.7429 (p) REVERT: D 178 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8371 (tp) REVERT: D 247 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7402 (pt0) REVERT: E 106 GLU cc_start: 0.7331 (tt0) cc_final: 0.6732 (tt0) REVERT: E 116 MET cc_start: 0.8590 (mtm) cc_final: 0.8217 (mtp) REVERT: E 269 ASN cc_start: 0.8382 (m-40) cc_final: 0.7971 (m-40) REVERT: E 372 GLN cc_start: 0.7453 (tm-30) cc_final: 0.7245 (tm-30) REVERT: E 375 LYS cc_start: 0.6589 (OUTLIER) cc_final: 0.6371 (tmtt) outliers start: 57 outliers final: 28 residues processed: 257 average time/residue: 1.4518 time to fit residues: 404.1773 Evaluate side-chains 250 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 218 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 375 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 40 optimal weight: 0.0030 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN B 247 GLN C 251 GLN C 372 GLN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14644 Z= 0.197 Angle : 0.548 7.306 19783 Z= 0.295 Chirality : 0.044 0.484 2239 Planarity : 0.004 0.041 2394 Dihedral : 8.257 59.797 2340 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.75 % Allowed : 11.38 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.79 (0.21), residues: 1660 helix: 2.09 (0.23), residues: 565 sheet: 1.26 (0.24), residues: 440 loop : 0.43 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 128 HIS 0.005 0.001 HIS C 254 PHE 0.017 0.001 PHE B 92 TYR 0.015 0.002 TYR A 340 ARG 0.002 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 220 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.7819 (ttp-170) cc_final: 0.7178 (ttm-80) REVERT: A 227 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.5879 (tmt) REVERT: A 308 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.6763 (mtp85) REVERT: A 335 MET cc_start: 0.7477 (mtm) cc_final: 0.6803 (mmp) REVERT: A 345 ASP cc_start: 0.7746 (m-30) cc_final: 0.7292 (m-30) REVERT: B 269 ASN cc_start: 0.8156 (m-40) cc_final: 0.7814 (m-40) REVERT: B 308 ARG cc_start: 0.7316 (mtm180) cc_final: 0.7049 (mtm110) REVERT: C 82 ASP cc_start: 0.7508 (m-30) cc_final: 0.6355 (p0) REVERT: C 92 PHE cc_start: 0.8212 (t80) cc_final: 0.7953 (t80) REVERT: C 111 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.7754 (mt) REVERT: C 116 MET cc_start: 0.8551 (mtm) cc_final: 0.8033 (mtp) REVERT: C 151 LYS cc_start: 0.8359 (mmtt) cc_final: 0.8041 (mmtp) REVERT: C 179 ARG cc_start: 0.7682 (ttp-170) cc_final: 0.7336 (ttm-80) REVERT: C 181 GLN cc_start: 0.8203 (mm110) cc_final: 0.7903 (mt0) REVERT: D 114 VAL cc_start: 0.7767 (t) cc_final: 0.7442 (p) REVERT: D 165 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8042 (ptt90) REVERT: D 247 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7459 (pt0) REVERT: D 457 LYS cc_start: 0.7713 (ttmp) cc_final: 0.7058 (ttpt) REVERT: E 106 GLU cc_start: 0.7325 (tt0) cc_final: 0.6769 (tt0) REVERT: E 111 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.7985 (mt) REVERT: E 116 MET cc_start: 0.8631 (mtm) cc_final: 0.8260 (mtp) REVERT: E 232 LYS cc_start: 0.7940 (mtmm) cc_final: 0.7377 (mmtt) REVERT: E 269 ASN cc_start: 0.8435 (m-40) cc_final: 0.7952 (m-40) REVERT: E 375 LYS cc_start: 0.6609 (OUTLIER) cc_final: 0.6382 (tmtt) outliers start: 58 outliers final: 33 residues processed: 257 average time/residue: 1.4330 time to fit residues: 399.3855 Evaluate side-chains 260 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 220 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 251 GLN Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 375 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN B 247 GLN C 251 GLN C 287 GLN C 372 GLN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14644 Z= 0.173 Angle : 0.517 6.753 19783 Z= 0.279 Chirality : 0.043 0.451 2239 Planarity : 0.004 0.041 2394 Dihedral : 8.035 59.587 2339 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.82 % Allowed : 11.77 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.81 (0.21), residues: 1660 helix: 2.18 (0.23), residues: 560 sheet: 1.24 (0.24), residues: 445 loop : 0.39 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 128 HIS 0.004 0.001 HIS C 254 PHE 0.017 0.001 PHE B 92 TYR 0.015 0.002 TYR A 340 ARG 0.002 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 218 time to evaluate : 1.702 Fit side-chains revert: symmetry clash REVERT: A 179 ARG cc_start: 0.7739 (ttp-170) cc_final: 0.7129 (ttm-80) REVERT: A 227 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.5856 (tmt) REVERT: A 269 ASN cc_start: 0.8147 (m-40) cc_final: 0.7914 (m-40) REVERT: A 308 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.6763 (mtp85) REVERT: A 335 MET cc_start: 0.7439 (mtm) cc_final: 0.6741 (mmp) REVERT: A 345 ASP cc_start: 0.7705 (m-30) cc_final: 0.7260 (m-30) REVERT: B 269 ASN cc_start: 0.8118 (m-40) cc_final: 0.7827 (m-40) REVERT: B 308 ARG cc_start: 0.7308 (mtm180) cc_final: 0.7045 (mtm110) REVERT: C 75 SER cc_start: 0.8423 (p) cc_final: 0.8133 (m) REVERT: C 82 ASP cc_start: 0.7514 (m-30) cc_final: 0.6388 (p0) REVERT: C 92 PHE cc_start: 0.8190 (t80) cc_final: 0.7950 (t80) REVERT: C 111 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.7757 (mt) REVERT: C 116 MET cc_start: 0.8503 (mtm) cc_final: 0.7955 (mtp) REVERT: C 151 LYS cc_start: 0.8318 (mmtt) cc_final: 0.7995 (mmtp) REVERT: C 179 ARG cc_start: 0.7649 (ttp-170) cc_final: 0.7264 (ttm-80) REVERT: C 181 GLN cc_start: 0.8190 (mm110) cc_final: 0.7893 (mt0) REVERT: D 114 VAL cc_start: 0.7756 (t) cc_final: 0.7430 (p) REVERT: D 165 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8035 (ptt90) REVERT: D 183 ASP cc_start: 0.7103 (p0) cc_final: 0.6897 (p0) REVERT: D 247 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: E 106 GLU cc_start: 0.7367 (tt0) cc_final: 0.6811 (tt0) REVERT: E 111 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.7982 (mt) REVERT: E 116 MET cc_start: 0.8605 (mtm) cc_final: 0.8219 (mtp) REVERT: E 232 LYS cc_start: 0.7910 (mtmm) cc_final: 0.7370 (mmtt) REVERT: E 269 ASN cc_start: 0.8401 (m-40) cc_final: 0.7972 (m-40) REVERT: E 375 LYS cc_start: 0.6616 (OUTLIER) cc_final: 0.6406 (tmtt) outliers start: 59 outliers final: 36 residues processed: 256 average time/residue: 1.4425 time to fit residues: 399.9821 Evaluate side-chains 259 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 216 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 375 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 99 optimal weight: 0.3980 chunk 96 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 287 GLN B 247 GLN C 251 GLN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN E 372 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14644 Z= 0.200 Angle : 0.545 7.305 19783 Z= 0.294 Chirality : 0.044 0.481 2239 Planarity : 0.004 0.042 2394 Dihedral : 8.166 59.743 2339 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.88 % Allowed : 11.90 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.75 (0.21), residues: 1660 helix: 2.08 (0.23), residues: 565 sheet: 1.24 (0.25), residues: 440 loop : 0.38 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 128 HIS 0.005 0.001 HIS C 254 PHE 0.018 0.001 PHE B 92 TYR 0.015 0.002 TYR B 123 ARG 0.003 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 220 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.7804 (ttp-170) cc_final: 0.7139 (ttm-80) REVERT: A 227 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.5871 (tmt) REVERT: A 269 ASN cc_start: 0.8237 (m110) cc_final: 0.7959 (m-40) REVERT: A 308 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.6776 (mtp85) REVERT: A 335 MET cc_start: 0.7475 (mtm) cc_final: 0.6783 (mmp) REVERT: A 345 ASP cc_start: 0.7757 (m-30) cc_final: 0.7317 (m-30) REVERT: B 269 ASN cc_start: 0.8183 (m-40) cc_final: 0.7847 (m-40) REVERT: B 308 ARG cc_start: 0.7327 (mtm180) cc_final: 0.7064 (mtm110) REVERT: C 82 ASP cc_start: 0.7530 (m-30) cc_final: 0.6404 (p0) REVERT: C 111 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.7777 (mt) REVERT: C 116 MET cc_start: 0.8549 (mtm) cc_final: 0.8037 (mtp) REVERT: C 151 LYS cc_start: 0.8353 (mmtt) cc_final: 0.8010 (mmtp) REVERT: C 179 ARG cc_start: 0.7669 (ttp-170) cc_final: 0.7304 (ttm-80) REVERT: D 114 VAL cc_start: 0.7776 (t) cc_final: 0.7437 (p) REVERT: D 165 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8057 (ptt90) REVERT: D 247 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7470 (pt0) REVERT: D 457 LYS cc_start: 0.7731 (ttmp) cc_final: 0.7093 (ttpt) REVERT: E 106 GLU cc_start: 0.7415 (tt0) cc_final: 0.6854 (tt0) REVERT: E 111 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.7983 (mt) REVERT: E 116 MET cc_start: 0.8646 (mtm) cc_final: 0.8294 (mtp) REVERT: E 232 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7390 (mmtt) REVERT: E 269 ASN cc_start: 0.8454 (m-40) cc_final: 0.7980 (m-40) REVERT: E 375 LYS cc_start: 0.6623 (OUTLIER) cc_final: 0.6422 (tmtt) outliers start: 60 outliers final: 38 residues processed: 259 average time/residue: 1.4537 time to fit residues: 410.8257 Evaluate side-chains 262 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 217 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 375 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 31 optimal weight: 0.0270 chunk 30 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 0.0980 chunk 14 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN B 247 GLN C 251 GLN C 287 GLN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14644 Z= 0.157 Angle : 0.497 6.478 19783 Z= 0.269 Chirality : 0.043 0.444 2239 Planarity : 0.004 0.044 2394 Dihedral : 7.762 58.833 2339 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.36 % Allowed : 12.55 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.83 (0.21), residues: 1660 helix: 2.21 (0.23), residues: 560 sheet: 1.28 (0.25), residues: 445 loop : 0.38 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 349 HIS 0.004 0.001 HIS C 254 PHE 0.018 0.001 PHE B 92 TYR 0.015 0.002 TYR A 340 ARG 0.002 0.000 ARG D 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 223 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.7724 (ttp-170) cc_final: 0.7094 (ttm-80) REVERT: A 227 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.5781 (tmt) REVERT: A 269 ASN cc_start: 0.8171 (m110) cc_final: 0.7943 (m-40) REVERT: A 308 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.6759 (mtp85) REVERT: A 335 MET cc_start: 0.7379 (mtm) cc_final: 0.6680 (mmp) REVERT: A 345 ASP cc_start: 0.7690 (m-30) cc_final: 0.7250 (m-30) REVERT: B 269 ASN cc_start: 0.8114 (m-40) cc_final: 0.7835 (m-40) REVERT: B 308 ARG cc_start: 0.7297 (mtm180) cc_final: 0.7040 (mtm110) REVERT: C 75 SER cc_start: 0.8398 (p) cc_final: 0.8111 (m) REVERT: C 82 ASP cc_start: 0.7534 (m-30) cc_final: 0.6414 (p0) REVERT: C 111 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.7758 (mt) REVERT: C 116 MET cc_start: 0.8484 (mtm) cc_final: 0.7975 (mtp) REVERT: C 151 LYS cc_start: 0.8309 (mmtt) cc_final: 0.8008 (mmtp) REVERT: C 179 ARG cc_start: 0.7614 (ttp-170) cc_final: 0.7225 (ttm-80) REVERT: D 114 VAL cc_start: 0.7730 (t) cc_final: 0.7407 (p) REVERT: D 165 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8028 (ptt90) REVERT: D 183 ASP cc_start: 0.7070 (p0) cc_final: 0.6848 (p0) REVERT: D 247 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7474 (pt0) REVERT: D 457 LYS cc_start: 0.7612 (ttmp) cc_final: 0.6979 (ttpt) REVERT: E 106 GLU cc_start: 0.7403 (tt0) cc_final: 0.6854 (tt0) REVERT: E 111 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.7964 (mt) REVERT: E 116 MET cc_start: 0.8606 (mtm) cc_final: 0.8250 (mtp) REVERT: E 232 LYS cc_start: 0.7987 (mtmm) cc_final: 0.7470 (mmtt) REVERT: E 269 ASN cc_start: 0.8379 (m-40) cc_final: 0.7959 (m-40) REVERT: E 372 GLN cc_start: 0.7424 (tm-30) cc_final: 0.7161 (tm130) outliers start: 52 outliers final: 33 residues processed: 257 average time/residue: 1.4682 time to fit residues: 408.2190 Evaluate side-chains 258 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 219 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN B 247 GLN C 251 GLN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14644 Z= 0.268 Angle : 0.598 7.833 19783 Z= 0.323 Chirality : 0.045 0.463 2239 Planarity : 0.004 0.045 2394 Dihedral : 8.399 59.735 2337 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.36 % Allowed : 12.94 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.60 (0.21), residues: 1660 helix: 1.98 (0.23), residues: 565 sheet: 1.17 (0.25), residues: 440 loop : 0.26 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 128 HIS 0.006 0.002 HIS D 126 PHE 0.018 0.002 PHE B 92 TYR 0.017 0.002 TYR D 123 ARG 0.003 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 226 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.7885 (ttp-170) cc_final: 0.7218 (ttm-80) REVERT: A 227 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.5930 (tmt) REVERT: A 269 ASN cc_start: 0.8256 (m110) cc_final: 0.8025 (m-40) REVERT: A 308 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.6790 (mtp85) REVERT: A 335 MET cc_start: 0.7489 (mtm) cc_final: 0.6808 (mmp) REVERT: A 345 ASP cc_start: 0.7815 (m-30) cc_final: 0.7367 (m-30) REVERT: B 269 ASN cc_start: 0.8254 (m-40) cc_final: 0.7872 (m-40) REVERT: B 308 ARG cc_start: 0.7329 (mtm180) cc_final: 0.7068 (mtm110) REVERT: C 82 ASP cc_start: 0.7582 (m-30) cc_final: 0.6450 (p0) REVERT: C 111 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.7807 (mt) REVERT: C 116 MET cc_start: 0.8577 (mtm) cc_final: 0.8039 (mtp) REVERT: C 151 LYS cc_start: 0.8358 (mmtt) cc_final: 0.8000 (mmtp) REVERT: C 179 ARG cc_start: 0.7714 (ttp-170) cc_final: 0.7323 (ttm-80) REVERT: D 88 MET cc_start: 0.7265 (mtt) cc_final: 0.6512 (mmt) REVERT: D 114 VAL cc_start: 0.7794 (t) cc_final: 0.7452 (p) REVERT: D 165 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8110 (ptt90) REVERT: D 247 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7485 (pt0) REVERT: E 106 GLU cc_start: 0.7427 (tt0) cc_final: 0.6857 (tt0) REVERT: E 111 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8013 (mt) REVERT: E 116 MET cc_start: 0.8697 (mtm) cc_final: 0.8326 (mtp) REVERT: E 232 LYS cc_start: 0.7982 (mtmm) cc_final: 0.7463 (mmtt) REVERT: E 269 ASN cc_start: 0.8518 (m-40) cc_final: 0.7978 (m-40) outliers start: 52 outliers final: 37 residues processed: 259 average time/residue: 1.4908 time to fit residues: 417.2858 Evaluate side-chains 262 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 219 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 251 GLN Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN B 247 GLN C 251 GLN C 372 GLN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN E 372 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14644 Z= 0.179 Angle : 0.521 6.873 19783 Z= 0.282 Chirality : 0.043 0.458 2239 Planarity : 0.004 0.045 2394 Dihedral : 8.000 57.882 2337 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.04 % Allowed : 13.45 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.73 (0.21), residues: 1660 helix: 2.13 (0.23), residues: 560 sheet: 1.24 (0.25), residues: 440 loop : 0.31 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 349 HIS 0.005 0.001 HIS C 254 PHE 0.020 0.001 PHE B 92 TYR 0.016 0.002 TYR B 272 ARG 0.002 0.000 ARG D 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 214 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.7811 (ttp-170) cc_final: 0.7142 (ttm-80) REVERT: A 227 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.5856 (tmt) REVERT: A 308 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.6790 (mtp85) REVERT: A 335 MET cc_start: 0.7459 (mtm) cc_final: 0.6745 (mmp) REVERT: A 345 ASP cc_start: 0.7749 (m-30) cc_final: 0.7307 (m-30) REVERT: B 269 ASN cc_start: 0.8149 (m-40) cc_final: 0.7836 (m-40) REVERT: B 308 ARG cc_start: 0.7324 (mtm180) cc_final: 0.7066 (mtm110) REVERT: C 82 ASP cc_start: 0.7581 (m-30) cc_final: 0.6471 (p0) REVERT: C 111 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.7749 (mt) REVERT: C 116 MET cc_start: 0.8509 (mtm) cc_final: 0.7964 (mtp) REVERT: C 151 LYS cc_start: 0.8316 (mmtt) cc_final: 0.8004 (mmtp) REVERT: C 179 ARG cc_start: 0.7655 (ttp-170) cc_final: 0.7263 (ttm-80) REVERT: D 88 MET cc_start: 0.7235 (mtt) cc_final: 0.6458 (mmt) REVERT: D 114 VAL cc_start: 0.7731 (t) cc_final: 0.7401 (p) REVERT: D 165 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8042 (ptt90) REVERT: D 247 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7453 (pt0) REVERT: E 106 GLU cc_start: 0.7408 (tt0) cc_final: 0.6830 (tt0) REVERT: E 111 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.7987 (mt) REVERT: E 116 MET cc_start: 0.8619 (mtm) cc_final: 0.8251 (mtp) REVERT: E 232 LYS cc_start: 0.7968 (mtmm) cc_final: 0.7452 (mmpt) REVERT: E 269 ASN cc_start: 0.8451 (m-40) cc_final: 0.7976 (m-40) outliers start: 47 outliers final: 35 residues processed: 246 average time/residue: 1.4905 time to fit residues: 396.5552 Evaluate side-chains 258 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 217 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 471 ASN Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 212 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 358 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN B 247 GLN C 251 GLN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.116675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.089927 restraints weight = 16776.899| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 1.93 r_work: 0.2717 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14644 Z= 0.162 Angle : 0.504 6.541 19783 Z= 0.273 Chirality : 0.043 0.456 2239 Planarity : 0.004 0.044 2394 Dihedral : 7.698 58.720 2337 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.04 % Allowed : 13.39 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.78 (0.21), residues: 1660 helix: 2.21 (0.24), residues: 560 sheet: 1.16 (0.25), residues: 450 loop : 0.36 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 349 HIS 0.004 0.001 HIS C 254 PHE 0.020 0.001 PHE B 92 TYR 0.015 0.002 TYR A 340 ARG 0.002 0.000 ARG A 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6425.85 seconds wall clock time: 113 minutes 18.87 seconds (6798.87 seconds total)