Starting phenix.real_space_refine on Fri Feb 16 22:11:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frx_29410/02_2024/8frx_29410_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frx_29410/02_2024/8frx_29410.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frx_29410/02_2024/8frx_29410_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frx_29410/02_2024/8frx_29410_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frx_29410/02_2024/8frx_29410_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frx_29410/02_2024/8frx_29410.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frx_29410/02_2024/8frx_29410.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frx_29410/02_2024/8frx_29410_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frx_29410/02_2024/8frx_29410_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 10985 2.51 5 N 2705 2.21 5 O 2930 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16670 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3270 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "B" Number of atoms: 3270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3270 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "C" Number of atoms: 3270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3270 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "D" Number of atoms: 3270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3270 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "E" Number of atoms: 3270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3270 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {'NAG': 3, 'Y82': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {'NAG': 3, 'Y82': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {'NAG': 3, 'Y82': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {'NAG': 3, 'Y82': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {'NAG': 3, 'Y82': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.30, per 1000 atoms: 0.56 Number of scatterers: 16670 At special positions: 0 Unit cell: (94.6, 95.7, 172.7, 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 50 16.00 O 2930 8.00 N 2705 7.00 C 10985 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 502 " - " ASN A 82 " " NAG A 503 " - " ASN A 148 " " NAG A 504 " - " ASN A 164 " " NAG B 502 " - " ASN B 82 " " NAG B 503 " - " ASN B 148 " " NAG B 504 " - " ASN B 164 " " NAG C 502 " - " ASN C 82 " " NAG C 503 " - " ASN C 148 " " NAG C 504 " - " ASN C 164 " " NAG D 502 " - " ASN D 82 " " NAG D 503 " - " ASN D 148 " " NAG D 504 " - " ASN D 164 " " NAG E 502 " - " ASN E 82 " " NAG E 503 " - " ASN E 148 " " NAG E 504 " - " ASN E 164 " Time building additional restraints: 6.83 Conformation dependent library (CDL) restraints added in 3.1 seconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 20 sheets defined 39.7% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 220 through 223 Processing helix chain 'A' and resid 229 through 243 removed outlier: 3.690A pdb=" N PHE A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N CYS A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 270 Processing helix chain 'A' and resid 282 through 307 Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.933A pdb=" N ALA A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 460 removed outlier: 4.060A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU A 455 " --> pdb=" O THR A 451 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 220 through 223 Processing helix chain 'B' and resid 229 through 243 removed outlier: 3.690A pdb=" N PHE B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 270 Processing helix chain 'B' and resid 282 through 307 Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.932A pdb=" N ALA B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 460 removed outlier: 4.061A pdb=" N SER B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU B 455 " --> pdb=" O THR B 451 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 20 Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 220 through 223 Processing helix chain 'C' and resid 229 through 243 removed outlier: 3.690A pdb=" N PHE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N CYS C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 270 Processing helix chain 'C' and resid 282 through 307 Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 326 through 331 removed outlier: 3.933A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 460 removed outlier: 4.059A pdb=" N SER C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU C 455 " --> pdb=" O THR C 451 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TRP C 456 " --> pdb=" O LEU C 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 20 Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 220 through 223 Processing helix chain 'D' and resid 229 through 243 removed outlier: 3.690A pdb=" N PHE D 242 " --> pdb=" O ASP D 238 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N CYS D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 270 Processing helix chain 'D' and resid 282 through 307 Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.933A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 460 removed outlier: 4.059A pdb=" N SER D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU D 455 " --> pdb=" O THR D 451 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TRP D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 20 Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 142 through 144 No H-bonds generated for 'chain 'E' and resid 142 through 144' Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 220 through 223 Processing helix chain 'E' and resid 229 through 243 removed outlier: 3.690A pdb=" N PHE E 242 " --> pdb=" O ASP E 238 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N CYS E 243 " --> pdb=" O ILE E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 270 Processing helix chain 'E' and resid 282 through 307 Processing helix chain 'E' and resid 318 through 320 No H-bonds generated for 'chain 'E' and resid 318 through 320' Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.933A pdb=" N ALA E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 460 removed outlier: 4.060A pdb=" N SER E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU E 455 " --> pdb=" O THR E 451 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TRP E 456 " --> pdb=" O LEU E 452 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.307A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 50 through 52 Processing sheet with id= C, first strand: chain 'A' and resid 85 through 89 Processing sheet with id= D, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.424A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 163 through 167 removed outlier: 6.308A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 50 through 52 Processing sheet with id= G, first strand: chain 'B' and resid 85 through 89 Processing sheet with id= H, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.424A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 163 through 167 removed outlier: 6.307A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 50 through 52 Processing sheet with id= K, first strand: chain 'C' and resid 85 through 89 Processing sheet with id= L, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.424A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 163 through 167 removed outlier: 6.308A pdb=" N THR D 37 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N THR D 166 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR D 38 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR D 69 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 50 through 52 Processing sheet with id= O, first strand: chain 'D' and resid 85 through 89 Processing sheet with id= P, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.424A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 163 through 167 removed outlier: 6.308A pdb=" N THR E 37 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THR E 166 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR E 38 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR E 69 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR E 59 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 50 through 52 Processing sheet with id= S, first strand: chain 'E' and resid 85 through 89 Processing sheet with id= T, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.424A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 790 hydrogen bonds defined for protein. 2220 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: 4.93 Time building geometry restraints manager: 7.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5065 1.34 - 1.46: 3908 1.46 - 1.58: 8092 1.58 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 17140 Sorted by residual: bond pdb=" C10 Y82 D 501 " pdb=" N3 Y82 D 501 " ideal model delta sigma weight residual 1.028 1.480 -0.452 2.00e-02 2.50e+03 5.10e+02 bond pdb=" C10 Y82 E 501 " pdb=" N3 Y82 E 501 " ideal model delta sigma weight residual 1.028 1.479 -0.451 2.00e-02 2.50e+03 5.09e+02 bond pdb=" C10 Y82 B 501 " pdb=" N3 Y82 B 501 " ideal model delta sigma weight residual 1.028 1.479 -0.451 2.00e-02 2.50e+03 5.09e+02 bond pdb=" C10 Y82 A 501 " pdb=" N3 Y82 A 501 " ideal model delta sigma weight residual 1.028 1.479 -0.451 2.00e-02 2.50e+03 5.09e+02 bond pdb=" C10 Y82 C 501 " pdb=" N3 Y82 C 501 " ideal model delta sigma weight residual 1.028 1.479 -0.451 2.00e-02 2.50e+03 5.08e+02 ... (remaining 17135 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.54: 824 107.54 - 114.42: 10033 114.42 - 121.29: 8196 121.29 - 128.17: 4175 128.17 - 135.05: 207 Bond angle restraints: 23435 Sorted by residual: angle pdb=" C9 Y82 D 501 " pdb=" C7 Y82 D 501 " pdb=" N2 Y82 D 501 " ideal model delta sigma weight residual 67.36 125.54 -58.18 3.00e+00 1.11e-01 3.76e+02 angle pdb=" C9 Y82 C 501 " pdb=" C7 Y82 C 501 " pdb=" N2 Y82 C 501 " ideal model delta sigma weight residual 67.36 125.52 -58.16 3.00e+00 1.11e-01 3.76e+02 angle pdb=" C9 Y82 A 501 " pdb=" C7 Y82 A 501 " pdb=" N2 Y82 A 501 " ideal model delta sigma weight residual 67.36 125.51 -58.15 3.00e+00 1.11e-01 3.76e+02 angle pdb=" C9 Y82 B 501 " pdb=" C7 Y82 B 501 " pdb=" N2 Y82 B 501 " ideal model delta sigma weight residual 67.36 125.50 -58.14 3.00e+00 1.11e-01 3.76e+02 angle pdb=" C9 Y82 E 501 " pdb=" C7 Y82 E 501 " pdb=" N2 Y82 E 501 " ideal model delta sigma weight residual 67.36 125.50 -58.14 3.00e+00 1.11e-01 3.76e+02 ... (remaining 23430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.91: 9510 18.91 - 37.83: 640 37.83 - 56.74: 115 56.74 - 75.66: 15 75.66 - 94.57: 15 Dihedral angle restraints: 10295 sinusoidal: 4400 harmonic: 5895 Sorted by residual: dihedral pdb=" C1 Y82 E 501 " pdb=" C11 Y82 E 501 " pdb=" N3 Y82 E 501 " pdb=" C12 Y82 E 501 " ideal model delta sinusoidal sigma weight residual 166.69 72.12 94.57 1 3.00e+01 1.11e-03 1.15e+01 dihedral pdb=" C1 Y82 B 501 " pdb=" C11 Y82 B 501 " pdb=" N3 Y82 B 501 " pdb=" C12 Y82 B 501 " ideal model delta sinusoidal sigma weight residual 166.69 72.15 94.54 1 3.00e+01 1.11e-03 1.15e+01 dihedral pdb=" C1 Y82 A 501 " pdb=" C11 Y82 A 501 " pdb=" N3 Y82 A 501 " pdb=" C12 Y82 A 501 " ideal model delta sinusoidal sigma weight residual 166.69 72.16 94.53 1 3.00e+01 1.11e-03 1.15e+01 ... (remaining 10292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2468 0.087 - 0.175: 275 0.175 - 0.262: 2 0.262 - 0.350: 4 0.350 - 0.437: 6 Chirality restraints: 2755 Sorted by residual: chirality pdb=" C15 Y82 C 501 " pdb=" C11 Y82 C 501 " pdb=" C14 Y82 C 501 " pdb=" C16 Y82 C 501 " both_signs ideal model delta sigma weight residual False 2.74 3.18 -0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" C15 Y82 B 501 " pdb=" C11 Y82 B 501 " pdb=" C14 Y82 B 501 " pdb=" C16 Y82 B 501 " both_signs ideal model delta sigma weight residual False 2.74 3.18 -0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" C15 Y82 D 501 " pdb=" C11 Y82 D 501 " pdb=" C14 Y82 D 501 " pdb=" C16 Y82 D 501 " both_signs ideal model delta sigma weight residual False 2.74 3.18 -0.44 2.00e-01 2.50e+01 4.74e+00 ... (remaining 2752 not shown) Planarity restraints: 2855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 280 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO B 281 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 281 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 281 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 280 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO A 281 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 281 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 281 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 280 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO C 281 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 281 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 281 " -0.024 5.00e-02 4.00e+02 ... (remaining 2852 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3270 2.78 - 3.31: 15082 3.31 - 3.84: 27172 3.84 - 4.37: 30236 4.37 - 4.90: 53640 Nonbonded interactions: 129400 Sorted by model distance: nonbonded pdb=" OH TYR A 64 " pdb=" OE1 GLN A 66 " model vdw 2.253 2.440 nonbonded pdb=" OH TYR C 64 " pdb=" OE1 GLN C 66 " model vdw 2.253 2.440 nonbonded pdb=" OH TYR B 64 " pdb=" OE1 GLN B 66 " model vdw 2.253 2.440 nonbonded pdb=" OH TYR E 64 " pdb=" OE1 GLN E 66 " model vdw 2.253 2.440 nonbonded pdb=" OH TYR D 64 " pdb=" OE1 GLN D 66 " model vdw 2.253 2.440 ... (remaining 129395 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.970 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 45.880 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.110 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:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 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 0.452 17140 Z= 1.041 Angle : 1.366 58.176 23435 Z= 0.579 Chirality : 0.053 0.437 2755 Planarity : 0.004 0.042 2840 Dihedral : 13.287 94.575 6440 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.20), residues: 1955 helix: 1.92 (0.20), residues: 775 sheet: -0.62 (0.25), residues: 425 loop : -1.31 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 456 HIS 0.001 0.000 HIS E 158 PHE 0.018 0.001 PHE C 199 TYR 0.018 0.001 TYR B 67 ARG 0.003 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 1.0966 time to fit residues: 171.0764 Evaluate side-chains 84 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.6980 chunk 147 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN E 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 17140 Z= 0.395 Angle : 1.249 49.189 23435 Z= 0.476 Chirality : 0.047 0.238 2755 Planarity : 0.004 0.038 2840 Dihedral : 8.672 84.861 2560 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.08 % Allowed : 7.21 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.20), residues: 1955 helix: 1.93 (0.19), residues: 780 sheet: -0.62 (0.23), residues: 445 loop : -1.10 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 320 HIS 0.003 0.001 HIS B 18 PHE 0.010 0.001 PHE C 254 TYR 0.028 0.002 TYR E 67 ARG 0.010 0.001 ARG D 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 322 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8007 (mmp80) REVERT: B 419 MET cc_start: 0.7771 (mmm) cc_final: 0.7494 (mmm) outliers start: 20 outliers final: 5 residues processed: 120 average time/residue: 1.1387 time to fit residues: 155.6763 Evaluate side-chains 97 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain E residue 141 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 147 optimal weight: 0.1980 chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 177 optimal weight: 8.9990 chunk 191 optimal weight: 9.9990 chunk 157 optimal weight: 0.6980 chunk 175 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 17140 Z= 0.254 Angle : 1.223 49.382 23435 Z= 0.451 Chirality : 0.045 0.297 2755 Planarity : 0.003 0.031 2840 Dihedral : 8.298 82.349 2560 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.19 % Allowed : 8.13 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.20), residues: 1955 helix: 2.08 (0.19), residues: 780 sheet: -0.55 (0.24), residues: 445 loop : -1.11 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 320 HIS 0.001 0.000 HIS A 119 PHE 0.007 0.001 PHE A 199 TYR 0.015 0.001 TYR D 67 ARG 0.009 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 322 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7975 (mmp80) REVERT: B 419 MET cc_start: 0.7628 (mmm) cc_final: 0.7376 (mmm) REVERT: C 324 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8416 (tt) REVERT: D 324 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8431 (tt) REVERT: E 324 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8298 (tt) outliers start: 22 outliers final: 6 residues processed: 115 average time/residue: 0.9067 time to fit residues: 122.4710 Evaluate side-chains 102 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 324 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 119 optimal weight: 0.0370 chunk 178 optimal weight: 4.9990 chunk 188 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 168 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 overall best weight: 1.5264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 17140 Z= 0.273 Angle : 1.220 49.396 23435 Z= 0.451 Chirality : 0.045 0.298 2755 Planarity : 0.003 0.029 2840 Dihedral : 8.283 82.007 2560 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.79 % Allowed : 9.43 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.20), residues: 1955 helix: 2.09 (0.19), residues: 780 sheet: -0.50 (0.24), residues: 445 loop : -1.11 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 320 HIS 0.001 0.000 HIS D 119 PHE 0.009 0.001 PHE D 233 TYR 0.017 0.001 TYR D 67 ARG 0.007 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 100 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9134 (OUTLIER) cc_final: 0.7651 (m-80) REVERT: B 322 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7987 (mmp80) REVERT: B 419 MET cc_start: 0.7646 (mmm) cc_final: 0.7389 (mmm) REVERT: C 324 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8410 (tt) REVERT: D 324 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8392 (tt) REVERT: E 324 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8373 (tt) outliers start: 33 outliers final: 17 residues processed: 129 average time/residue: 0.8526 time to fit residues: 130.1997 Evaluate side-chains 117 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 324 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 140 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 169 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 17140 Z= 0.230 Angle : 1.207 49.358 23435 Z= 0.441 Chirality : 0.044 0.313 2755 Planarity : 0.003 0.029 2840 Dihedral : 8.109 82.361 2560 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.90 % Allowed : 10.24 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.20), residues: 1955 helix: 2.18 (0.20), residues: 780 sheet: -0.44 (0.24), residues: 445 loop : -1.08 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 320 HIS 0.001 0.000 HIS B 460 PHE 0.010 0.001 PHE D 233 TYR 0.012 0.001 TYR C 67 ARG 0.006 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 99 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9128 (OUTLIER) cc_final: 0.7668 (m-80) REVERT: B 322 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7973 (mmp80) REVERT: B 419 MET cc_start: 0.7613 (mmm) cc_final: 0.7374 (mmm) REVERT: D 116 TYR cc_start: 0.9155 (OUTLIER) cc_final: 0.8055 (m-80) REVERT: D 324 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8382 (tt) REVERT: E 324 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8315 (tt) outliers start: 35 outliers final: 22 residues processed: 129 average time/residue: 0.9141 time to fit residues: 138.7476 Evaluate side-chains 120 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 324 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 0.0970 chunk 169 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 chunk 188 optimal weight: 20.0000 chunk 156 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 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 0.100 17140 Z= 0.272 Angle : 1.220 49.382 23435 Z= 0.451 Chirality : 0.045 0.304 2755 Planarity : 0.003 0.028 2840 Dihedral : 8.188 82.087 2560 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.01 % Allowed : 10.84 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.20), residues: 1955 helix: 2.11 (0.19), residues: 780 sheet: -0.43 (0.24), residues: 445 loop : -1.10 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 320 HIS 0.001 0.000 HIS C 158 PHE 0.011 0.001 PHE D 233 TYR 0.017 0.001 TYR B 67 ARG 0.008 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 97 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9150 (OUTLIER) cc_final: 0.7619 (m-80) REVERT: B 116 TYR cc_start: 0.9157 (OUTLIER) cc_final: 0.8632 (m-10) REVERT: B 322 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7983 (mmp80) REVERT: B 419 MET cc_start: 0.7628 (mmm) cc_final: 0.7403 (mmm) REVERT: C 315 ARG cc_start: 0.7167 (tpt170) cc_final: 0.6874 (tpt170) REVERT: D 116 TYR cc_start: 0.9181 (OUTLIER) cc_final: 0.8063 (m-80) REVERT: D 324 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8419 (tt) REVERT: E 324 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8365 (tt) outliers start: 37 outliers final: 24 residues processed: 133 average time/residue: 0.8644 time to fit residues: 137.9589 Evaluate side-chains 122 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 92 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 17140 Z= 0.308 Angle : 1.234 49.382 23435 Z= 0.459 Chirality : 0.046 0.297 2755 Planarity : 0.003 0.028 2840 Dihedral : 8.279 82.001 2560 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.90 % Allowed : 11.17 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.20), residues: 1955 helix: 2.05 (0.19), residues: 780 sheet: -0.47 (0.24), residues: 445 loop : -1.13 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 456 HIS 0.002 0.000 HIS D 119 PHE 0.014 0.001 PHE D 233 TYR 0.019 0.001 TYR D 67 ARG 0.006 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 95 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9150 (OUTLIER) cc_final: 0.7541 (m-80) REVERT: B 116 TYR cc_start: 0.9154 (OUTLIER) cc_final: 0.8635 (m-10) REVERT: B 322 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7991 (mmp80) REVERT: B 419 MET cc_start: 0.7656 (mmm) cc_final: 0.7441 (mmm) REVERT: C 324 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8392 (tt) REVERT: D 116 TYR cc_start: 0.9139 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: D 324 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8417 (tt) REVERT: E 324 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8397 (tt) outliers start: 35 outliers final: 26 residues processed: 129 average time/residue: 0.8520 time to fit residues: 130.1365 Evaluate side-chains 126 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 93 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 119 optimal weight: 0.2980 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 17140 Z= 0.246 Angle : 1.225 49.367 23435 Z= 0.450 Chirality : 0.045 0.311 2755 Planarity : 0.003 0.028 2840 Dihedral : 8.152 82.239 2560 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.84 % Allowed : 11.44 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.20), residues: 1955 helix: 2.15 (0.20), residues: 780 sheet: -0.45 (0.24), residues: 445 loop : -1.08 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 456 HIS 0.001 0.000 HIS B 119 PHE 0.013 0.001 PHE D 233 TYR 0.014 0.001 TYR C 67 ARG 0.006 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 97 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9134 (OUTLIER) cc_final: 0.7517 (m-80) REVERT: B 116 TYR cc_start: 0.9135 (OUTLIER) cc_final: 0.8608 (m-10) REVERT: B 322 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7956 (mmp80) REVERT: B 419 MET cc_start: 0.7635 (mmm) cc_final: 0.7415 (mmm) REVERT: C 324 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8363 (tt) REVERT: D 116 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8053 (m-80) REVERT: D 324 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8435 (tt) REVERT: E 324 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8382 (tt) outliers start: 34 outliers final: 26 residues processed: 128 average time/residue: 0.8278 time to fit residues: 125.8930 Evaluate side-chains 126 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 93 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 20.0000 chunk 164 optimal weight: 0.0970 chunk 175 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 158 optimal weight: 0.6980 chunk 165 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 17140 Z= 0.235 Angle : 1.222 49.369 23435 Z= 0.448 Chirality : 0.045 0.317 2755 Planarity : 0.003 0.028 2840 Dihedral : 8.062 82.335 2560 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.84 % Allowed : 11.38 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.20), residues: 1955 helix: 2.18 (0.20), residues: 780 sheet: -0.43 (0.24), residues: 445 loop : -1.02 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 456 HIS 0.001 0.000 HIS B 323 PHE 0.012 0.001 PHE D 233 TYR 0.014 0.001 TYR C 67 ARG 0.006 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 96 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.7587 (m-80) REVERT: B 116 TYR cc_start: 0.9126 (OUTLIER) cc_final: 0.8579 (m-10) REVERT: B 322 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7933 (mmp80) REVERT: B 419 MET cc_start: 0.7614 (mmm) cc_final: 0.7383 (mmm) REVERT: C 324 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8280 (tt) REVERT: D 116 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: D 324 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8423 (tt) REVERT: E 324 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8364 (tt) outliers start: 34 outliers final: 25 residues processed: 127 average time/residue: 0.9070 time to fit residues: 138.4160 Evaluate side-chains 124 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 92 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 0.4980 chunk 113 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 16 optimal weight: 0.0980 chunk 119 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 17140 Z= 0.235 Angle : 1.227 49.371 23435 Z= 0.449 Chirality : 0.045 0.319 2755 Planarity : 0.003 0.029 2840 Dihedral : 8.020 82.311 2560 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.84 % Allowed : 11.60 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.20), residues: 1955 helix: 2.18 (0.20), residues: 780 sheet: -0.42 (0.24), residues: 445 loop : -0.99 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 456 HIS 0.002 0.000 HIS A 323 PHE 0.011 0.001 PHE D 233 TYR 0.013 0.001 TYR B 67 ARG 0.006 0.000 ARG B 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 96 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.9123 (OUTLIER) cc_final: 0.7578 (m-80) REVERT: A 324 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8276 (tt) REVERT: B 116 TYR cc_start: 0.9127 (OUTLIER) cc_final: 0.8563 (m-10) REVERT: B 322 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7914 (mmp80) REVERT: B 419 MET cc_start: 0.7606 (mmm) cc_final: 0.7401 (mmm) REVERT: C 324 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8250 (tt) REVERT: D 116 TYR cc_start: 0.9098 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: D 324 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8409 (tt) REVERT: E 324 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8330 (tt) outliers start: 34 outliers final: 25 residues processed: 126 average time/residue: 0.8318 time to fit residues: 124.0986 Evaluate side-chains 123 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 90 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 433 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 154 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.098016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.064203 restraints weight = 34081.471| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.51 r_work: 0.2784 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 17140 Z= 0.288 Angle : 1.248 49.398 23435 Z= 0.461 Chirality : 0.046 0.303 2755 Planarity : 0.003 0.028 2840 Dihedral : 8.156 82.131 2560 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.84 % Allowed : 11.82 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1955 helix: 2.10 (0.19), residues: 780 sheet: -0.44 (0.24), residues: 445 loop : -1.07 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 456 HIS 0.002 0.000 HIS D 119 PHE 0.016 0.001 PHE D 233 TYR 0.019 0.001 TYR E 67 ARG 0.005 0.000 ARG B 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4075.32 seconds wall clock time: 74 minutes 9.04 seconds (4449.04 seconds total)