Starting phenix.real_space_refine on Tue Feb 20 00:18:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiz_28167/02_2024/8eiz_28167_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiz_28167/02_2024/8eiz_28167.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiz_28167/02_2024/8eiz_28167_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiz_28167/02_2024/8eiz_28167_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiz_28167/02_2024/8eiz_28167_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiz_28167/02_2024/8eiz_28167.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiz_28167/02_2024/8eiz_28167.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiz_28167/02_2024/8eiz_28167_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eiz_28167/02_2024/8eiz_28167_trim_updated.pdb" } resolution = 3.13 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= 0.006 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: 5 Type Number sf(0) Gaussians S 75 5.16 5 C 8770 2.51 5 N 1985 2.21 5 O 2445 1.98 5 H 12825 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 50": "OE1" <-> "OE2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "E GLU 187": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26100 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 5155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5155 Classifications: {'peptide': 315} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 304} Chain breaks: 1 Chain: "B" Number of atoms: 5155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5155 Classifications: {'peptide': 315} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 304} Chain breaks: 1 Chain: "C" Number of atoms: 5154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5154 Classifications: {'peptide': 315} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 304} Chain breaks: 1 Chain: "D" Number of atoms: 5156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5156 Classifications: {'peptide': 315} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 304} Chain breaks: 1 Chain: "E" Number of atoms: 5155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5155 Classifications: {'peptide': 315} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 304} Chain breaks: 1 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'WK3': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'WK3': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'WK3': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'WK3': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'WK3': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 10.82, per 1000 atoms: 0.41 Number of scatterers: 26100 At special positions: 0 Unit cell: (95.141, 94.072, 124.004, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 O 2445 8.00 N 1985 7.00 C 8770 6.00 H 12825 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 181 " distance=2.02 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 181 " distance=2.03 Simple disulfide: pdb=" SG CYS D 129 " - pdb=" SG CYS D 143 " distance=2.03 Simple disulfide: pdb=" SG CYS D 164 " - pdb=" SG CYS D 181 " distance=2.02 Simple disulfide: pdb=" SG CYS E 129 " - pdb=" SG CYS E 143 " distance=2.03 Simple disulfide: pdb=" SG CYS E 164 " - pdb=" SG CYS E 181 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 114 " " NAG G 1 " - " ASN B 114 " " NAG H 1 " - " ASN C 114 " " NAG I 1 " - " ASN D 114 " " NAG J 1 " - " ASN E 114 " Time building additional restraints: 19.62 Conformation dependent library (CDL) restraints added in 2.4 seconds 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 22 sheets defined 31.6% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.67 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 Processing helix chain 'A' and resid 204 through 222 removed outlier: 4.566A pdb=" N VAL A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU A 210 " --> pdb=" O CYS A 206 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Proline residue: A 212 - end of helix Processing helix chain 'A' and resid 231 through 254 Processing helix chain 'A' and resid 264 through 288 Processing helix chain 'A' and resid 368 through 389 Processing helix chain 'B' and resid 4 through 12 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 204 through 221 removed outlier: 3.687A pdb=" N SER B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU B 210 " --> pdb=" O CYS B 206 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Proline residue: B 212 - end of helix Processing helix chain 'B' and resid 231 through 254 removed outlier: 3.842A pdb=" N ILE B 248 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP B 249 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 288 Processing helix chain 'B' and resid 368 through 389 Processing helix chain 'C' and resid 4 through 13 Processing helix chain 'C' and resid 204 through 224 removed outlier: 4.056A pdb=" N SER C 208 " --> pdb=" O GLN C 205 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU C 211 " --> pdb=" O SER C 208 " (cutoff:3.500A) Proline residue: C 212 - end of helix Processing helix chain 'C' and resid 231 through 253 removed outlier: 3.552A pdb=" N SER C 252 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 288 Processing helix chain 'C' and resid 368 through 388 removed outlier: 3.586A pdb=" N LEU C 377 " --> pdb=" O PHE C 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 12 Processing helix chain 'D' and resid 204 through 223 removed outlier: 4.201A pdb=" N VAL D 209 " --> pdb=" O GLN D 205 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU D 210 " --> pdb=" O CYS D 206 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU D 211 " --> pdb=" O LEU D 207 " (cutoff:3.500A) Proline residue: D 212 - end of helix removed outlier: 3.654A pdb=" N PHE D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 252 Processing helix chain 'D' and resid 264 through 288 Processing helix chain 'D' and resid 368 through 389 Processing helix chain 'E' and resid 4 through 12 Processing helix chain 'E' and resid 48 through 50 No H-bonds generated for 'chain 'E' and resid 48 through 50' Processing helix chain 'E' and resid 205 through 221 removed outlier: 3.753A pdb=" N SER E 208 " --> pdb=" O GLN E 205 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL E 209 " --> pdb=" O CYS E 206 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU E 210 " --> pdb=" O LEU E 207 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Proline residue: E 212 - end of helix removed outlier: 4.090A pdb=" N ILE E 215 " --> pdb=" O PRO E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 253 Processing helix chain 'E' and resid 264 through 288 Processing helix chain 'E' and resid 368 through 389 removed outlier: 3.859A pdb=" N SER E 389 " --> pdb=" O LEU E 385 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 116 through 128 removed outlier: 3.561A pdb=" N LYS A 42 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TYR A 58 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE A 40 " --> pdb=" O TYR A 58 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE A 60 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU A 38 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLN A 62 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE A 36 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N TYR A 64 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N VAL A 34 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE A 36 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE A 162 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU A 38 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N CYS A 164 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE A 40 " --> pdb=" O CYS A 164 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 79 through 82 Processing sheet with id= C, first strand: chain 'A' and resid 92 through 94 removed outlier: 4.774A pdb=" N PHE A 149 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N SER A 190 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 189 " --> pdb=" O GLY A 186 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 129 through 132 Processing sheet with id= E, first strand: chain 'B' and resid 116 through 128 removed outlier: 3.526A pdb=" N LYS B 42 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TYR B 58 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ILE B 40 " --> pdb=" O TYR B 58 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE B 60 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU B 38 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLN B 62 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ILE B 36 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N TYR B 64 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N VAL B 34 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE B 36 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE B 162 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU B 38 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N CYS B 164 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE B 40 " --> pdb=" O CYS B 164 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N SER B 166 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N LYS B 42 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 79 through 82 Processing sheet with id= G, first strand: chain 'B' and resid 92 through 94 removed outlier: 4.554A pdb=" N PHE B 149 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N SER B 190 " --> pdb=" O PHE B 149 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 129 through 132 Processing sheet with id= I, first strand: chain 'C' and resid 116 through 128 removed outlier: 3.600A pdb=" N LYS C 42 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR C 58 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE C 40 " --> pdb=" O TYR C 58 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE C 60 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU C 38 " --> pdb=" O ILE C 60 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLN C 62 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ILE C 36 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N TYR C 64 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N VAL C 34 " --> pdb=" O TYR C 64 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE C 36 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE C 162 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU C 38 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N CYS C 164 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE C 40 " --> pdb=" O CYS C 164 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N SER C 166 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N LYS C 42 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 79 through 82 Processing sheet with id= K, first strand: chain 'C' and resid 92 through 94 removed outlier: 4.557A pdb=" N PHE C 149 " --> pdb=" O SER C 190 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N SER C 190 " --> pdb=" O PHE C 149 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 129 through 132 Processing sheet with id= M, first strand: chain 'D' and resid 116 through 128 removed outlier: 3.542A pdb=" N LYS D 42 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR D 58 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE D 40 " --> pdb=" O TYR D 58 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE D 60 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU D 38 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLN D 62 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE D 36 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N TYR D 64 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL D 34 " --> pdb=" O TYR D 64 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE D 36 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE D 162 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU D 38 " --> pdb=" O PHE D 162 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N CYS D 164 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE D 40 " --> pdb=" O CYS D 164 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N SER D 166 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N LYS D 42 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 79 through 82 Processing sheet with id= O, first strand: chain 'D' and resid 92 through 94 Processing sheet with id= P, first strand: chain 'D' and resid 129 through 132 Processing sheet with id= Q, first strand: chain 'D' and resid 183 through 185 Processing sheet with id= R, first strand: chain 'E' and resid 32 through 34 Processing sheet with id= S, first strand: chain 'E' and resid 162 through 166 removed outlier: 6.750A pdb=" N ILE E 36 " --> pdb=" O ARG E 163 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ILE E 165 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU E 38 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS E 37 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN E 56 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N MET E 43 " --> pdb=" O LYS E 54 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS E 54 " --> pdb=" O MET E 43 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 79 through 82 Processing sheet with id= U, first strand: chain 'E' and resid 92 through 94 removed outlier: 4.696A pdb=" N PHE E 149 " --> pdb=" O SER E 190 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N SER E 190 " --> pdb=" O PHE E 149 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 129 through 132 580 hydrogen bonds defined for protein. 1347 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: 9.77 Time building geometry restraints manager: 20.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 12805 1.02 - 1.21: 22 1.21 - 1.41: 5737 1.41 - 1.61: 7761 1.61 - 1.81: 110 Bond restraints: 26435 Sorted by residual: bond pdb=" C5 WK3 D 401 " pdb=" N6 WK3 D 401 " ideal model delta sigma weight residual 1.487 1.349 0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C5 WK3 B 401 " pdb=" N6 WK3 B 401 " ideal model delta sigma weight residual 1.487 1.349 0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C5 WK3 E 401 " pdb=" N6 WK3 E 401 " ideal model delta sigma weight residual 1.487 1.349 0.138 2.00e-02 2.50e+03 4.73e+01 bond pdb=" C5 WK3 C 401 " pdb=" N6 WK3 C 401 " ideal model delta sigma weight residual 1.487 1.350 0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" C5 WK3 A 401 " pdb=" N6 WK3 A 401 " ideal model delta sigma weight residual 1.487 1.350 0.137 2.00e-02 2.50e+03 4.69e+01 ... (remaining 26430 not shown) Histogram of bond angle deviations from ideal: 98.57 - 106.15: 238 106.15 - 113.73: 31069 113.73 - 121.31: 11342 121.31 - 128.89: 4831 128.89 - 136.47: 86 Bond angle restraints: 47566 Sorted by residual: angle pdb=" N SER A 384 " pdb=" CA SER A 384 " pdb=" C SER A 384 " ideal model delta sigma weight residual 111.07 104.78 6.29 1.07e+00 8.73e-01 3.45e+01 angle pdb=" N LYS C 173 " pdb=" CA LYS C 173 " pdb=" C LYS C 173 " ideal model delta sigma weight residual 109.39 118.52 -9.13 1.59e+00 3.96e-01 3.29e+01 angle pdb=" C PHE D 136 " pdb=" N PRO D 137 " pdb=" CD PRO D 137 " ideal model delta sigma weight residual 120.60 110.64 9.96 2.20e+00 2.07e-01 2.05e+01 angle pdb=" C PHE D 136 " pdb=" N PRO D 137 " pdb=" CA PRO D 137 " ideal model delta sigma weight residual 127.00 136.47 -9.47 2.40e+00 1.74e-01 1.56e+01 angle pdb=" N ARG C 172 " pdb=" CA ARG C 172 " pdb=" C ARG C 172 " ideal model delta sigma weight residual 111.28 115.29 -4.01 1.09e+00 8.42e-01 1.35e+01 ... (remaining 47561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 11734 21.92 - 43.84: 757 43.84 - 65.76: 191 65.76 - 87.68: 44 87.68 - 109.60: 20 Dihedral angle restraints: 12746 sinusoidal: 6781 harmonic: 5965 Sorted by residual: dihedral pdb=" CB CYS B 164 " pdb=" SG CYS B 164 " pdb=" SG CYS B 181 " pdb=" CB CYS B 181 " ideal model delta sinusoidal sigma weight residual 93.00 136.70 -43.70 1 1.00e+01 1.00e-02 2.66e+01 dihedral pdb=" CB CYS D 164 " pdb=" SG CYS D 164 " pdb=" SG CYS D 181 " pdb=" CB CYS D 181 " ideal model delta sinusoidal sigma weight residual 93.00 135.91 -42.91 1 1.00e+01 1.00e-02 2.57e+01 dihedral pdb=" CB CYS E 164 " pdb=" SG CYS E 164 " pdb=" SG CYS E 181 " pdb=" CB CYS E 181 " ideal model delta sinusoidal sigma weight residual 93.00 135.02 -42.02 1 1.00e+01 1.00e-02 2.47e+01 ... (remaining 12743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1659 0.055 - 0.109: 358 0.109 - 0.164: 63 0.164 - 0.218: 5 0.218 - 0.273: 5 Chirality restraints: 2090 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2087 not shown) Planarity restraints: 3746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 220 " -0.188 2.00e-02 2.50e+03 1.88e-01 5.33e+02 pdb=" CG ASN A 220 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 220 " 0.177 2.00e-02 2.50e+03 pdb=" ND2 ASN A 220 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 220 " 0.263 2.00e-02 2.50e+03 pdb="HD22 ASN A 220 " -0.277 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 WK3 A 401 " 0.159 2.00e-02 2.50e+03 2.05e-01 5.24e+02 pdb=" C5 WK3 A 401 " -0.064 2.00e-02 2.50e+03 pdb=" C7 WK3 A 401 " 0.243 2.00e-02 2.50e+03 pdb=" N6 WK3 A 401 " -0.348 2.00e-02 2.50e+03 pdb=" O15 WK3 A 401 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 WK3 B 401 " 0.158 2.00e-02 2.50e+03 1.96e-01 4.79e+02 pdb=" C5 WK3 B 401 " -0.069 2.00e-02 2.50e+03 pdb=" C7 WK3 B 401 " 0.233 2.00e-02 2.50e+03 pdb=" N6 WK3 B 401 " -0.328 2.00e-02 2.50e+03 pdb=" O15 WK3 B 401 " 0.005 2.00e-02 2.50e+03 ... (remaining 3743 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 903 2.14 - 2.75: 48365 2.75 - 3.37: 71192 3.37 - 3.98: 94512 3.98 - 4.60: 147091 Nonbonded interactions: 362063 Sorted by model distance: nonbonded pdb=" O SER A 167 " pdb=" HG1 THR A 168 " model vdw 1.523 1.850 nonbonded pdb=" OD2 ASP C 45 " pdb=" HE1 TRP C 175 " model vdw 1.556 1.850 nonbonded pdb=" HG SER E 167 " pdb=" OD1 ASP E 169 " model vdw 1.581 1.850 nonbonded pdb="HD22 ASN D 47 " pdb=" OE1 GLU D 50 " model vdw 1.625 1.850 nonbonded pdb=" HD2 PHE C 217 " pdb="HD13 ILE C 218 " model vdw 1.642 2.270 ... (remaining 362058 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 1 through 200 or (resid 201 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name H \ E2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 202 through 390 or \ (resid 391 and (name N or name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG or name HD11 \ or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) or resid 392 \ or resid 401)) selection = (chain 'B' and (resid 1 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or \ name HB2 or name HB3)) or resid 72 through 390 or (resid 391 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name H \ A or name HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or n \ ame HD21 or name HD22 or name HD23)) or resid 392 or resid 401)) selection = (chain 'C' and (resid 1 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or \ name HB2 or name HB3)) or resid 72 through 392 or resid 401)) selection = (chain 'D' and (resid 1 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or \ name HB2 or name HB3)) or resid 72 through 200 or (resid 201 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name CE or name NZ \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 202 th \ rough 390 or (resid 391 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG o \ r name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) o \ r resid 392 or resid 401)) selection = (chain 'E' and (resid 1 through 70 or (resid 71 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or \ name HB2 or name HB3)) or resid 72 through 390 or (resid 391 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name H \ A or name HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or n \ ame HD21 or name HD22 or name HD23)) or resid 392 or resid 401)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.070 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: 0.370 Extract box with map and model: 4.930 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 79.860 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 : 0.007 0.138 13610 Z= 0.461 Angle : 0.769 9.964 18435 Z= 0.396 Chirality : 0.048 0.273 2090 Planarity : 0.010 0.205 2230 Dihedral : 18.059 109.596 5110 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 14.08 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.21), residues: 1555 helix: 1.11 (0.24), residues: 493 sheet: -0.48 (0.24), residues: 469 loop : -1.40 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 2 HIS 0.003 0.001 HIS C 118 PHE 0.030 0.002 PHE E 241 TYR 0.012 0.002 TYR C 247 ARG 0.009 0.001 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.7645 (t80) cc_final: 0.7136 (t80) REVERT: A 213 LEU cc_start: 0.9112 (tp) cc_final: 0.8911 (tt) REVERT: E 134 ARG cc_start: 0.8359 (ttt90) cc_final: 0.8084 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.5574 time to fit residues: 172.4499 Evaluate side-chains 200 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.5980 chunk 117 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 0.2980 chunk 140 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8161 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13610 Z= 0.167 Angle : 0.578 8.926 18435 Z= 0.293 Chirality : 0.043 0.148 2090 Planarity : 0.005 0.058 2230 Dihedral : 10.241 63.035 2025 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.54 % Allowed : 15.78 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.21), residues: 1555 helix: 0.82 (0.23), residues: 504 sheet: -0.21 (0.24), residues: 448 loop : -1.40 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 2 HIS 0.003 0.001 HIS B 118 PHE 0.013 0.001 PHE C 271 TYR 0.012 0.001 TYR A 247 ARG 0.004 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 211 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.7714 (t80) cc_final: 0.7370 (t80) REVERT: A 134 ARG cc_start: 0.7740 (ttt180) cc_final: 0.7498 (tpt-90) REVERT: B 247 TYR cc_start: 0.8962 (t80) cc_final: 0.8721 (t80) REVERT: D 146 MET cc_start: 0.9121 (mtt) cc_final: 0.8759 (mtt) REVERT: E 134 ARG cc_start: 0.8366 (ttt90) cc_final: 0.8083 (ttm-80) outliers start: 8 outliers final: 5 residues processed: 216 average time/residue: 0.5572 time to fit residues: 174.8869 Evaluate side-chains 208 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 203 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 272 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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: 0.8198 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13610 Z= 0.307 Angle : 0.552 5.696 18435 Z= 0.289 Chirality : 0.044 0.143 2090 Planarity : 0.004 0.050 2230 Dihedral : 7.387 57.911 2025 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.09 % Allowed : 15.85 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.63 (0.21), residues: 1555 helix: 0.69 (0.24), residues: 505 sheet: -0.33 (0.24), residues: 466 loop : -1.39 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 2 HIS 0.002 0.001 HIS C 118 PHE 0.019 0.001 PHE C 271 TYR 0.009 0.001 TYR D 8 ARG 0.006 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 210 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.7803 (t80) cc_final: 0.7193 (t80) REVERT: A 134 ARG cc_start: 0.7827 (ttt180) cc_final: 0.7564 (tpt-90) REVERT: C 50 GLU cc_start: 0.7347 (tt0) cc_final: 0.7135 (tt0) REVERT: E 134 ARG cc_start: 0.8402 (ttt90) cc_final: 0.8188 (ttt90) outliers start: 16 outliers final: 13 residues processed: 216 average time/residue: 0.5592 time to fit residues: 176.2681 Evaluate side-chains 212 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 199 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 272 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN B 220 ASN E 254 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13610 Z= 0.232 Angle : 0.511 5.365 18435 Z= 0.271 Chirality : 0.042 0.140 2090 Planarity : 0.004 0.050 2230 Dihedral : 6.354 59.249 2025 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.50 % Allowed : 15.92 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.21), residues: 1555 helix: 0.72 (0.24), residues: 504 sheet: -0.19 (0.24), residues: 456 loop : -1.40 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 2 HIS 0.002 0.001 HIS C 118 PHE 0.012 0.001 PHE C 271 TYR 0.009 0.001 TYR D 8 ARG 0.006 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 204 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.7820 (t80) cc_final: 0.7192 (t80) REVERT: A 134 ARG cc_start: 0.7842 (ttt180) cc_final: 0.7579 (tpt-90) REVERT: C 50 GLU cc_start: 0.7364 (tt0) cc_final: 0.7129 (tt0) REVERT: E 134 ARG cc_start: 0.8420 (ttt90) cc_final: 0.8136 (ttt90) outliers start: 22 outliers final: 17 residues processed: 214 average time/residue: 0.5349 time to fit residues: 166.8525 Evaluate side-chains 206 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 189 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 172 ARG Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 272 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 127 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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: 0.8198 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13610 Z= 0.268 Angle : 0.516 5.154 18435 Z= 0.274 Chirality : 0.042 0.142 2090 Planarity : 0.004 0.049 2230 Dihedral : 6.060 59.113 2025 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.36 % Allowed : 15.99 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.21), residues: 1555 helix: 0.69 (0.24), residues: 504 sheet: -0.23 (0.24), residues: 458 loop : -1.38 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 2 HIS 0.002 0.001 HIS B 269 PHE 0.015 0.001 PHE B 274 TYR 0.009 0.001 TYR A 176 ARG 0.005 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 197 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.7860 (t80) cc_final: 0.7226 (t80) REVERT: A 134 ARG cc_start: 0.7864 (ttt180) cc_final: 0.7600 (tpt-90) REVERT: A 172 ARG cc_start: 0.7881 (ttp-110) cc_final: 0.7635 (ptm-80) REVERT: C 50 GLU cc_start: 0.7399 (tt0) cc_final: 0.7148 (tt0) REVERT: E 134 ARG cc_start: 0.8423 (ttt90) cc_final: 0.8162 (ttt90) outliers start: 20 outliers final: 19 residues processed: 207 average time/residue: 0.5514 time to fit residues: 166.4134 Evaluate side-chains 211 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 192 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 172 ARG Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 268 CYS Chi-restraints excluded: chain E residue 272 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 69 optimal weight: 0.0970 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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: 0.8206 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13610 Z= 0.279 Angle : 0.509 4.790 18435 Z= 0.273 Chirality : 0.042 0.143 2090 Planarity : 0.004 0.049 2230 Dihedral : 5.930 59.296 2025 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.63 % Allowed : 16.39 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.21), residues: 1555 helix: 0.72 (0.24), residues: 504 sheet: -0.21 (0.24), residues: 458 loop : -1.39 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 2 HIS 0.002 0.001 HIS C 118 PHE 0.014 0.001 PHE C 271 TYR 0.010 0.001 TYR A 176 ARG 0.008 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 201 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.7907 (t80) cc_final: 0.7283 (t80) REVERT: A 134 ARG cc_start: 0.7894 (ttt180) cc_final: 0.7635 (tpt-90) REVERT: B 52 ARG cc_start: 0.8411 (mtm180) cc_final: 0.8016 (ptp90) REVERT: C 50 GLU cc_start: 0.7458 (tt0) cc_final: 0.7195 (tt0) REVERT: E 134 ARG cc_start: 0.8429 (ttt90) cc_final: 0.8194 (ttt90) outliers start: 24 outliers final: 20 residues processed: 216 average time/residue: 0.5776 time to fit residues: 181.5772 Evaluate side-chains 213 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 193 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 172 ARG Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 268 CYS Chi-restraints excluded: chain E residue 272 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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: 0.8214 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 13610 Z= 0.299 Angle : 0.518 6.078 18435 Z= 0.277 Chirality : 0.042 0.144 2090 Planarity : 0.004 0.049 2230 Dihedral : 5.945 58.480 2025 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.84 % Allowed : 16.46 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.64 (0.21), residues: 1555 helix: 0.71 (0.24), residues: 504 sheet: -0.36 (0.23), residues: 474 loop : -1.39 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 2 HIS 0.002 0.001 HIS C 118 PHE 0.017 0.001 PHE B 274 TYR 0.009 0.001 TYR C 75 ARG 0.007 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 196 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.7932 (t80) cc_final: 0.7334 (t80) REVERT: B 52 ARG cc_start: 0.8388 (mtm180) cc_final: 0.8005 (ptp90) REVERT: C 50 GLU cc_start: 0.7487 (tt0) cc_final: 0.7210 (tt0) REVERT: C 261 GLU cc_start: 0.8216 (pm20) cc_final: 0.7695 (mp0) outliers start: 27 outliers final: 22 residues processed: 211 average time/residue: 0.5647 time to fit residues: 174.9562 Evaluate side-chains 211 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 189 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 172 ARG Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 268 CYS Chi-restraints excluded: chain E residue 272 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 29 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8193 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13610 Z= 0.171 Angle : 0.484 5.361 18435 Z= 0.260 Chirality : 0.041 0.142 2090 Planarity : 0.004 0.052 2230 Dihedral : 5.808 59.351 2025 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.02 % Allowed : 17.55 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.21), residues: 1555 helix: 0.86 (0.24), residues: 503 sheet: -0.32 (0.23), residues: 474 loop : -1.28 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 2 HIS 0.002 0.001 HIS B 118 PHE 0.016 0.001 PHE C 271 TYR 0.009 0.001 TYR A 176 ARG 0.009 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 199 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.7901 (t80) cc_final: 0.7295 (t80) REVERT: A 134 ARG cc_start: 0.7971 (ttt180) cc_final: 0.7683 (tpt-90) REVERT: B 52 ARG cc_start: 0.8369 (mtm180) cc_final: 0.7991 (ptp90) REVERT: C 50 GLU cc_start: 0.7473 (tt0) cc_final: 0.7215 (tt0) outliers start: 15 outliers final: 12 residues processed: 206 average time/residue: 0.5835 time to fit residues: 175.2043 Evaluate side-chains 203 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 191 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 272 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 60 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 131 optimal weight: 0.0570 chunk 138 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 overall best weight: 1.3304 ------------------------------------------------------------------------------- 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: 0.8205 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13610 Z= 0.243 Angle : 0.499 5.070 18435 Z= 0.266 Chirality : 0.042 0.140 2090 Planarity : 0.004 0.056 2230 Dihedral : 5.710 58.336 2025 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.43 % Allowed : 16.80 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.46 (0.21), residues: 1555 helix: 0.89 (0.24), residues: 503 sheet: -0.32 (0.23), residues: 476 loop : -1.25 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 2 HIS 0.001 0.000 HIS C 118 PHE 0.018 0.001 PHE B 274 TYR 0.009 0.001 TYR A 8 ARG 0.009 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 196 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.7961 (t80) cc_final: 0.7348 (t80) REVERT: A 134 ARG cc_start: 0.7943 (ttt180) cc_final: 0.7672 (tpt-90) REVERT: B 52 ARG cc_start: 0.8386 (mtm180) cc_final: 0.7989 (ptp90) REVERT: C 50 GLU cc_start: 0.7510 (tt0) cc_final: 0.7237 (tt0) REVERT: C 261 GLU cc_start: 0.8212 (pm20) cc_final: 0.7725 (mp0) outliers start: 21 outliers final: 15 residues processed: 208 average time/residue: 0.5595 time to fit residues: 168.0801 Evaluate side-chains 209 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 194 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 268 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8196 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13610 Z= 0.195 Angle : 0.483 4.896 18435 Z= 0.259 Chirality : 0.042 0.141 2090 Planarity : 0.004 0.059 2230 Dihedral : 5.594 59.078 2025 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.02 % Allowed : 17.28 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.40 (0.22), residues: 1555 helix: 0.95 (0.24), residues: 503 sheet: -0.40 (0.23), residues: 482 loop : -1.14 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 2 HIS 0.002 0.001 HIS C 118 PHE 0.018 0.001 PHE B 214 TYR 0.008 0.001 TYR A 176 ARG 0.009 0.000 ARG C 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 198 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.7943 (t80) cc_final: 0.7351 (t80) REVERT: A 134 ARG cc_start: 0.7962 (ttt180) cc_final: 0.7691 (tpt-90) REVERT: B 52 ARG cc_start: 0.8367 (mtm180) cc_final: 0.7971 (ptp90) REVERT: C 50 GLU cc_start: 0.7491 (tt0) cc_final: 0.7225 (tt0) REVERT: C 261 GLU cc_start: 0.8215 (pm20) cc_final: 0.7695 (mp0) outliers start: 15 outliers final: 15 residues processed: 208 average time/residue: 0.5685 time to fit residues: 172.8660 Evaluate side-chains 209 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 194 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 268 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 123 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.135043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.096291 restraints weight = 51752.337| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.26 r_work: 0.2964 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13610 Z= 0.170 Angle : 0.474 4.932 18435 Z= 0.254 Chirality : 0.041 0.140 2090 Planarity : 0.004 0.060 2230 Dihedral : 5.456 59.121 2025 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.16 % Allowed : 17.21 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.33 (0.22), residues: 1555 helix: 1.01 (0.24), residues: 503 sheet: -0.36 (0.23), residues: 484 loop : -1.09 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 2 HIS 0.002 0.001 HIS B 118 PHE 0.019 0.001 PHE B 274 TYR 0.008 0.001 TYR A 176 ARG 0.009 0.001 ARG C 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5651.73 seconds wall clock time: 104 minutes 49.39 seconds (6289.39 seconds total)