Starting phenix.real_space_refine on Fri Feb 16 22:16:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frw_29409/02_2024/8frw_29409_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frw_29409/02_2024/8frw_29409.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frw_29409/02_2024/8frw_29409_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frw_29409/02_2024/8frw_29409_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frw_29409/02_2024/8frw_29409_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frw_29409/02_2024/8frw_29409.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frw_29409/02_2024/8frw_29409.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frw_29409/02_2024/8frw_29409_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frw_29409/02_2024/8frw_29409_updated.pdb" } resolution = 2.92 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 10990 2.51 5 N 2705 2.21 5 O 2935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 315": "NH1" <-> "NH2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "C ARG 315": "NH1" <-> "NH2" Residue "D ARG 315": "NH1" <-> "NH2" Residue "E ARG 315": "NH1" <-> "NH2" 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: 16680 Number of models: 1 Model: "" Number of chains: 15 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: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'NAG': 3, 'Y7H': 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: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'NAG': 3, 'Y7H': 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: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'NAG': 3, 'Y7H': 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: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'NAG': 3, 'Y7H': 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: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'NAG': 3, 'Y7H': 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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 9.08, per 1000 atoms: 0.54 Number of scatterers: 16680 At special positions: 0 Unit cell: (95.7, 96.8, 171.6, 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 2935 8.00 N 2705 7.00 C 10990 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 501 " - " ASN A 82 " " NAG A 502 " - " ASN A 148 " " NAG A 503 " - " 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: 6.39 Conformation dependent library (CDL) restraints added in 2.9 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: 40 helices and 20 sheets defined 40.3% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 11 through 20 removed outlier: 3.682A pdb=" N SER A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) 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 171 through 174 No H-bonds generated for 'chain 'A' and resid 171 through 174' Processing helix chain 'A' and resid 221 through 242 removed outlier: 4.001A pdb=" N VAL A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 251 through 269 Processing helix chain 'A' and resid 282 through 308 Processing helix chain 'A' and resid 318 through 327 removed outlier: 4.498A pdb=" N HIS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 461 removed outlier: 3.695A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 20 removed outlier: 3.681A pdb=" N SER B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) 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 171 through 174 No H-bonds generated for 'chain 'B' and resid 171 through 174' Processing helix chain 'B' and resid 221 through 242 removed outlier: 4.002A pdb=" N VAL B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 251 through 269 Processing helix chain 'B' and resid 282 through 308 Processing helix chain 'B' and resid 318 through 327 removed outlier: 4.498A pdb=" N HIS B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 461 removed outlier: 3.694A pdb=" N ILE B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 20 removed outlier: 3.681A pdb=" N SER C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) 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 171 through 174 No H-bonds generated for 'chain 'C' and resid 171 through 174' Processing helix chain 'C' and resid 221 through 242 removed outlier: 4.001A pdb=" N VAL C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 251 through 269 Processing helix chain 'C' and resid 282 through 308 Processing helix chain 'C' and resid 318 through 327 removed outlier: 4.498A pdb=" N HIS C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 461 removed outlier: 3.695A pdb=" N ILE C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 20 removed outlier: 3.682A pdb=" N SER D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) 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 171 through 174 No H-bonds generated for 'chain 'D' and resid 171 through 174' Processing helix chain 'D' and resid 221 through 242 removed outlier: 4.002A pdb=" N VAL D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 251 through 269 Processing helix chain 'D' and resid 282 through 308 Processing helix chain 'D' and resid 318 through 327 removed outlier: 4.498A pdb=" N HIS D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D 325 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 461 removed outlier: 3.695A pdb=" N ILE D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 20 removed outlier: 3.681A pdb=" N SER E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) 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 171 through 174 No H-bonds generated for 'chain 'E' and resid 171 through 174' Processing helix chain 'E' and resid 221 through 242 removed outlier: 4.003A pdb=" N VAL E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) Proline residue: E 230 - end of helix Processing helix chain 'E' and resid 251 through 269 Processing helix chain 'E' and resid 282 through 308 Processing helix chain 'E' and resid 318 through 327 removed outlier: 4.499A pdb=" N HIS E 323 " --> pdb=" O ASP E 319 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL E 325 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU E 326 " --> pdb=" O ARG E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 461 removed outlier: 3.694A pdb=" N ILE E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.648A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.178A 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: 4.495A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.054A 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: 6.648A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.177A 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: 4.496A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.054A 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: 6.648A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.178A 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: 4.496A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.054A 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: 6.647A pdb=" N THR D 37 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR D 166 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR D 38 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR D 69 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 7.178A 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: 4.496A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.054A 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: 6.648A pdb=" N THR E 37 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N THR E 166 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR E 38 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR E 69 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.177A 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: 4.495A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 830 hydrogen bonds defined for protein. 2445 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: 4.68 Time building geometry restraints manager: 6.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2550 1.32 - 1.44: 4900 1.44 - 1.57: 9620 1.57 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 17145 Sorted by residual: bond pdb=" C7 Y7H A 504 " pdb=" C9 Y7H A 504 " ideal model delta sigma weight residual 1.894 1.469 0.425 2.00e-02 2.50e+03 4.51e+02 bond pdb=" C7 Y7H E 501 " pdb=" C9 Y7H E 501 " ideal model delta sigma weight residual 1.894 1.469 0.425 2.00e-02 2.50e+03 4.51e+02 bond pdb=" C7 Y7H D 501 " pdb=" C9 Y7H D 501 " ideal model delta sigma weight residual 1.894 1.469 0.425 2.00e-02 2.50e+03 4.51e+02 bond pdb=" C7 Y7H C 501 " pdb=" C9 Y7H C 501 " ideal model delta sigma weight residual 1.894 1.469 0.425 2.00e-02 2.50e+03 4.51e+02 bond pdb=" C7 Y7H B 501 " pdb=" C9 Y7H B 501 " ideal model delta sigma weight residual 1.894 1.470 0.424 2.00e-02 2.50e+03 4.50e+02 ... (remaining 17140 not shown) Histogram of bond angle deviations from ideal: 100.70 - 107.38: 717 107.38 - 114.05: 9860 114.05 - 120.73: 7088 120.73 - 127.40: 5537 127.40 - 134.08: 238 Bond angle restraints: 23440 Sorted by residual: angle pdb=" C2 Y7H C 501 " pdb=" C8 Y7H C 501 " pdb=" C7 Y7H C 501 " ideal model delta sigma weight residual 110.98 133.98 -23.00 3.00e+00 1.11e-01 5.88e+01 angle pdb=" C2 Y7H A 504 " pdb=" C8 Y7H A 504 " pdb=" C7 Y7H A 504 " ideal model delta sigma weight residual 110.98 133.95 -22.97 3.00e+00 1.11e-01 5.86e+01 angle pdb=" C2 Y7H B 501 " pdb=" C8 Y7H B 501 " pdb=" C7 Y7H B 501 " ideal model delta sigma weight residual 110.98 133.94 -22.96 3.00e+00 1.11e-01 5.86e+01 angle pdb=" C2 Y7H D 501 " pdb=" C8 Y7H D 501 " pdb=" C7 Y7H D 501 " ideal model delta sigma weight residual 110.98 133.94 -22.96 3.00e+00 1.11e-01 5.86e+01 angle pdb=" C2 Y7H E 501 " pdb=" C8 Y7H E 501 " pdb=" C7 Y7H E 501 " ideal model delta sigma weight residual 110.98 133.93 -22.95 3.00e+00 1.11e-01 5.85e+01 ... (remaining 23435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.42: 10012 33.42 - 66.84: 253 66.84 - 100.26: 10 100.26 - 133.68: 5 133.68 - 167.10: 20 Dihedral angle restraints: 10300 sinusoidal: 4405 harmonic: 5895 Sorted by residual: dihedral pdb=" C14 Y7H A 504 " pdb=" C15 Y7H A 504 " pdb=" N4 Y7H A 504 " pdb=" C18 Y7H A 504 " ideal model delta sinusoidal sigma weight residual 80.04 -87.06 167.10 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C14 Y7H B 501 " pdb=" C15 Y7H B 501 " pdb=" N4 Y7H B 501 " pdb=" C18 Y7H B 501 " ideal model delta sinusoidal sigma weight residual 80.04 -87.06 167.10 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C14 Y7H C 501 " pdb=" C15 Y7H C 501 " pdb=" N4 Y7H C 501 " pdb=" C18 Y7H C 501 " ideal model delta sinusoidal sigma weight residual 80.04 -87.06 167.10 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 10297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.048: 2750 1.048 - 2.095: 0 2.095 - 3.142: 0 3.142 - 4.190: 0 4.190 - 5.237: 5 Chirality restraints: 2755 Sorted by residual: chirality pdb=" C13 Y7H E 501 " pdb=" C12 Y7H E 501 " pdb=" C14 Y7H E 501 " pdb=" C17 Y7H E 501 " both_signs ideal model delta sigma weight residual False 2.74 -2.49 5.24 2.00e-01 2.50e+01 6.86e+02 chirality pdb=" C13 Y7H C 501 " pdb=" C12 Y7H C 501 " pdb=" C14 Y7H C 501 " pdb=" C17 Y7H C 501 " both_signs ideal model delta sigma weight residual False 2.74 -2.49 5.24 2.00e-01 2.50e+01 6.86e+02 chirality pdb=" C13 Y7H B 501 " pdb=" C12 Y7H B 501 " pdb=" C14 Y7H B 501 " pdb=" C17 Y7H B 501 " both_signs ideal model delta sigma weight residual False 2.74 -2.49 5.24 2.00e-01 2.50e+01 6.85e+02 ... (remaining 2752 not shown) Planarity restraints: 2855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 44 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" C ILE A 44 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE A 44 " -0.020 2.00e-02 2.50e+03 pdb=" N MET A 45 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 44 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.04e+00 pdb=" C ILE C 44 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE C 44 " -0.019 2.00e-02 2.50e+03 pdb=" N MET C 45 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 44 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.04e+00 pdb=" C ILE B 44 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE B 44 " -0.019 2.00e-02 2.50e+03 pdb=" N MET B 45 " -0.017 2.00e-02 2.50e+03 ... (remaining 2852 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4693 2.83 - 3.35: 15340 3.35 - 3.86: 27588 3.86 - 4.38: 29718 4.38 - 4.90: 52163 Nonbonded interactions: 129502 Sorted by model distance: nonbonded pdb=" OH TYR C 64 " pdb=" OE1 GLN C 66 " model vdw 2.312 2.440 nonbonded pdb=" OH TYR A 64 " pdb=" OE1 GLN A 66 " model vdw 2.312 2.440 nonbonded pdb=" OH TYR E 64 " pdb=" OE1 GLN E 66 " model vdw 2.312 2.440 nonbonded pdb=" OH TYR B 64 " pdb=" OE1 GLN B 66 " model vdw 2.312 2.440 nonbonded pdb=" OH TYR D 64 " pdb=" OE1 GLN D 66 " model vdw 2.312 2.440 ... (remaining 129497 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 7 through 462 or resid 502 through 503)) selection = (chain 'B' and (resid 7 through 462 or resid 502 through 503)) selection = (chain 'C' and (resid 7 through 462 or resid 502 through 503)) selection = (chain 'D' and (resid 7 through 462 or resid 502 through 503)) selection = (chain 'E' and (resid 7 through 462 or resid 502 through 503)) } 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: 1.280 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: 6.510 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 45.120 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.120 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:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.013 0.425 17145 Z= 0.856 Angle : 1.016 22.998 23440 Z= 0.465 Chirality : 0.229 5.237 2755 Planarity : 0.005 0.038 2840 Dihedral : 16.373 167.103 6445 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.11 % Allowed : 0.98 % Favored : 98.92 % 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: 0.72 (0.19), residues: 1955 helix: 2.24 (0.19), residues: 735 sheet: -0.03 (0.26), residues: 355 loop : -0.86 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 320 HIS 0.003 0.001 HIS E 323 PHE 0.017 0.002 PHE B 233 TYR 0.016 0.001 TYR B 67 ARG 0.007 0.000 ARG D 424 *********************** 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 161 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 159 time to evaluate : 2.079 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 159 average time/residue: 0.9788 time to fit residues: 179.4035 Evaluate side-chains 65 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.795 ------------------------------------------------------------------------------- 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: 0.0040 chunk 147 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- 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: 0.8379 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17145 Z= 0.244 Angle : 1.000 21.285 23440 Z= 0.393 Chirality : 0.091 1.859 2755 Planarity : 0.004 0.029 2840 Dihedral : 17.237 171.358 2565 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.46 % Allowed : 8.62 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.20), residues: 1955 helix: 2.71 (0.20), residues: 730 sheet: -0.05 (0.27), residues: 355 loop : -0.57 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 320 HIS 0.003 0.001 HIS A 323 PHE 0.008 0.001 PHE A 242 TYR 0.022 0.002 TYR E 116 ARG 0.004 0.000 ARG E 424 *********************** 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 108 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 81 time to evaluate : 1.910 Fit side-chains REVERT: A 267 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8489 (tp) REVERT: C 233 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7729 (t80) REVERT: C 242 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8340 (t80) REVERT: D 242 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8340 (t80) REVERT: D 267 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8606 (tp) REVERT: E 235 MET cc_start: 0.8690 (mmm) cc_final: 0.8463 (mmm) REVERT: E 267 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8543 (tp) outliers start: 27 outliers final: 6 residues processed: 104 average time/residue: 0.8613 time to fit residues: 106.1497 Evaluate side-chains 69 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 295 VAL 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: 3.9990 chunk 147 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 177 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 157 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17145 Z= 0.199 Angle : 0.964 21.648 23440 Z= 0.374 Chirality : 0.093 1.944 2755 Planarity : 0.003 0.027 2840 Dihedral : 17.080 172.145 2565 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.73 % Allowed : 10.73 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.20), residues: 1955 helix: 2.94 (0.20), residues: 725 sheet: -0.00 (0.26), residues: 375 loop : -0.39 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 320 HIS 0.003 0.001 HIS A 323 PHE 0.007 0.001 PHE E 254 TYR 0.016 0.001 TYR C 67 ARG 0.004 0.000 ARG A 315 *********************** 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 102 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 70 time to evaluate : 2.084 Fit side-chains REVERT: A 267 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8453 (tp) REVERT: B 235 MET cc_start: 0.8537 (mmm) cc_final: 0.8076 (mpp) REVERT: B 267 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8622 (tp) REVERT: B 419 MET cc_start: 0.8360 (mmp) cc_final: 0.8126 (mmp) REVERT: C 235 MET cc_start: 0.8854 (mmt) cc_final: 0.8380 (mpp) REVERT: C 267 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8528 (tp) REVERT: D 242 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8456 (t80) REVERT: D 267 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8587 (tp) REVERT: E 235 MET cc_start: 0.8662 (mmm) cc_final: 0.8343 (mmm) REVERT: E 267 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8511 (tp) outliers start: 32 outliers final: 13 residues processed: 101 average time/residue: 0.9073 time to fit residues: 107.9622 Evaluate side-chains 78 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 59 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 0.5980 chunk 133 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 119 optimal weight: 0.4980 chunk 178 optimal weight: 0.9990 chunk 188 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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: 0.8397 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17145 Z= 0.177 Angle : 0.954 21.026 23440 Z= 0.368 Chirality : 0.094 1.962 2755 Planarity : 0.003 0.026 2840 Dihedral : 16.972 171.464 2565 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.90 % Allowed : 11.38 % 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: 1.38 (0.20), residues: 1955 helix: 2.96 (0.20), residues: 725 sheet: -0.08 (0.26), residues: 375 loop : -0.42 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 320 HIS 0.001 0.000 HIS D 323 PHE 0.007 0.001 PHE C 233 TYR 0.015 0.001 TYR C 67 ARG 0.001 0.000 ARG C 424 *********************** 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 101 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 66 time to evaluate : 2.092 Fit side-chains revert: symmetry clash REVERT: A 141 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.8021 (OUTLIER) REVERT: A 267 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8394 (tp) REVERT: B 235 MET cc_start: 0.8624 (mmm) cc_final: 0.8106 (mpp) REVERT: B 267 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8671 (tp) REVERT: C 141 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7969 (OUTLIER) REVERT: C 235 MET cc_start: 0.8790 (mmt) cc_final: 0.8383 (mpp) REVERT: C 267 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8486 (tp) REVERT: D 267 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8568 (tp) REVERT: E 141 ASN cc_start: 0.8047 (OUTLIER) cc_final: 0.7801 (OUTLIER) REVERT: E 235 MET cc_start: 0.8720 (mmm) cc_final: 0.8444 (mmm) REVERT: E 267 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8513 (tp) outliers start: 35 outliers final: 12 residues processed: 96 average time/residue: 0.8735 time to fit residues: 100.0052 Evaluate side-chains 76 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.8453 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17145 Z= 0.226 Angle : 0.975 21.374 23440 Z= 0.382 Chirality : 0.094 1.947 2755 Planarity : 0.003 0.025 2840 Dihedral : 17.031 171.649 2565 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.73 % Allowed : 12.52 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.20), residues: 1955 helix: 2.97 (0.20), residues: 725 sheet: -0.12 (0.25), residues: 375 loop : -0.47 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 320 HIS 0.002 0.001 HIS C 119 PHE 0.007 0.001 PHE C 233 TYR 0.020 0.001 TYR C 67 ARG 0.003 0.000 ARG C 65 *********************** 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 109 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 77 time to evaluate : 1.789 Fit side-chains REVERT: A 267 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8445 (tp) REVERT: B 182 ILE cc_start: 0.6545 (mm) cc_final: 0.6239 (mt) REVERT: B 267 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8694 (tp) REVERT: B 291 MET cc_start: 0.8755 (mmm) cc_final: 0.8534 (mmm) REVERT: C 267 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8580 (tp) REVERT: D 182 ILE cc_start: 0.6905 (mm) cc_final: 0.6667 (mt) REVERT: D 267 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8661 (tp) REVERT: E 182 ILE cc_start: 0.6834 (mm) cc_final: 0.6509 (mt) REVERT: E 267 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8511 (tp) outliers start: 32 outliers final: 14 residues processed: 108 average time/residue: 0.7907 time to fit residues: 102.5819 Evaluate side-chains 81 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 62 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 156 optimal weight: 0.0060 chunk 87 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- 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: 0.8441 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17145 Z= 0.191 Angle : 0.967 21.166 23440 Z= 0.373 Chirality : 0.094 1.957 2755 Planarity : 0.003 0.027 2840 Dihedral : 16.989 171.364 2565 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.36 % Allowed : 13.77 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.20), residues: 1955 helix: 3.02 (0.20), residues: 725 sheet: -0.16 (0.25), residues: 375 loop : -0.50 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 320 HIS 0.002 0.000 HIS A 18 PHE 0.008 0.001 PHE C 233 TYR 0.015 0.001 TYR C 67 ARG 0.008 0.000 ARG D 315 *********************** 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 97 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 72 time to evaluate : 2.169 Fit side-chains REVERT: A 267 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8405 (tp) REVERT: A 291 MET cc_start: 0.8800 (mmm) cc_final: 0.8595 (mmm) REVERT: B 182 ILE cc_start: 0.6791 (mm) cc_final: 0.6411 (mt) REVERT: B 267 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8644 (tp) REVERT: C 267 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8593 (tp) REVERT: D 182 ILE cc_start: 0.6923 (mm) cc_final: 0.6687 (mt) REVERT: D 267 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8605 (tp) REVERT: E 182 ILE cc_start: 0.6854 (mm) cc_final: 0.6535 (mt) REVERT: E 267 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8500 (tp) outliers start: 25 outliers final: 15 residues processed: 96 average time/residue: 0.7341 time to fit residues: 86.1438 Evaluate side-chains 84 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 64 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 158 optimal weight: 0.0870 chunk 105 optimal weight: 0.0870 chunk 187 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- 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: 0.8436 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17145 Z= 0.183 Angle : 0.968 21.127 23440 Z= 0.372 Chirality : 0.094 1.958 2755 Planarity : 0.003 0.031 2840 Dihedral : 16.960 171.348 2565 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.46 % Allowed : 14.31 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.20), residues: 1955 helix: 3.04 (0.20), residues: 725 sheet: -0.19 (0.25), residues: 375 loop : -0.48 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 320 HIS 0.001 0.000 HIS A 18 PHE 0.007 0.001 PHE C 233 TYR 0.014 0.001 TYR C 67 ARG 0.006 0.000 ARG D 315 *********************** 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 94 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 67 time to evaluate : 1.745 Fit side-chains REVERT: A 267 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8395 (tp) REVERT: B 182 ILE cc_start: 0.6805 (mm) cc_final: 0.6421 (mt) REVERT: B 264 VAL cc_start: 0.8352 (p) cc_final: 0.8129 (t) REVERT: B 267 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8624 (tp) REVERT: B 291 MET cc_start: 0.8741 (mmm) cc_final: 0.8506 (mmm) REVERT: C 141 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.8099 (OUTLIER) REVERT: C 267 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8561 (tp) REVERT: D 182 ILE cc_start: 0.6890 (mm) cc_final: 0.6652 (mt) REVERT: D 267 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8591 (tp) REVERT: E 182 ILE cc_start: 0.6869 (mm) cc_final: 0.6544 (mt) REVERT: E 267 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8446 (tp) outliers start: 27 outliers final: 17 residues processed: 94 average time/residue: 0.8518 time to fit residues: 95.2419 Evaluate side-chains 86 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 64 time to evaluate : 2.129 ------------------------------------------------------------------------------- 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 267 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 119 optimal weight: 0.0970 chunk 128 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 147 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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: 0.8493 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17145 Z= 0.291 Angle : 1.006 21.574 23440 Z= 0.397 Chirality : 0.094 1.940 2755 Planarity : 0.003 0.034 2840 Dihedral : 17.101 171.645 2565 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.52 % Allowed : 14.74 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.20), residues: 1955 helix: 2.99 (0.20), residues: 725 sheet: -0.18 (0.25), residues: 375 loop : -0.54 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 320 HIS 0.003 0.001 HIS E 18 PHE 0.011 0.001 PHE D 233 TYR 0.023 0.001 TYR B 67 ARG 0.005 0.000 ARG D 315 *********************** 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 92 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 64 time to evaluate : 1.874 Fit side-chains REVERT: A 267 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8495 (tp) REVERT: B 267 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8727 (tp) REVERT: C 141 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8222 (OUTLIER) REVERT: C 267 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8604 (tp) REVERT: D 267 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8675 (tp) REVERT: E 267 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8534 (tp) outliers start: 28 outliers final: 16 residues processed: 91 average time/residue: 0.8484 time to fit residues: 92.1978 Evaluate side-chains 81 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 60 time to evaluate : 1.854 ------------------------------------------------------------------------------- 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 267 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 105 optimal weight: 0.0470 chunk 76 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 158 optimal weight: 0.0060 chunk 165 optimal weight: 0.4980 chunk 174 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 overall best weight: 0.4694 ------------------------------------------------------------------------------- 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: 0.8441 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17145 Z= 0.175 Angle : 0.972 20.983 23440 Z= 0.375 Chirality : 0.094 1.969 2755 Planarity : 0.003 0.035 2840 Dihedral : 16.993 171.546 2565 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.14 % Allowed : 15.28 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.20), residues: 1955 helix: 3.06 (0.20), residues: 725 sheet: -0.24 (0.25), residues: 375 loop : -0.51 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 320 HIS 0.001 0.000 HIS A 18 PHE 0.012 0.001 PHE D 233 TYR 0.012 0.001 TYR C 67 ARG 0.006 0.000 ARG A 315 *********************** 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 92 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 71 time to evaluate : 1.889 Fit side-chains REVERT: A 267 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8370 (tp) REVERT: B 182 ILE cc_start: 0.6822 (mm) cc_final: 0.6533 (mt) REVERT: B 267 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8579 (tp) REVERT: B 291 MET cc_start: 0.8738 (mmm) cc_final: 0.8459 (mmm) REVERT: C 267 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8468 (tp) REVERT: D 182 ILE cc_start: 0.7056 (mm) cc_final: 0.6834 (mt) REVERT: D 267 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8555 (tp) REVERT: E 182 ILE cc_start: 0.7078 (mm) cc_final: 0.6741 (mt) REVERT: E 267 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8417 (tp) outliers start: 21 outliers final: 14 residues processed: 92 average time/residue: 0.8489 time to fit residues: 92.9759 Evaluate side-chains 84 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 1.735 ------------------------------------------------------------------------------- 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 267 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 87 optimal weight: 0.0870 chunk 128 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 119 optimal weight: 0.0370 chunk 94 optimal weight: 0.0020 chunk 122 optimal weight: 5.9990 overall best weight: 0.9246 ------------------------------------------------------------------------------- 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: 0.8451 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17145 Z= 0.194 Angle : 0.983 21.197 23440 Z= 0.380 Chirality : 0.094 1.954 2755 Planarity : 0.003 0.038 2840 Dihedral : 16.983 171.360 2565 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.30 % Allowed : 15.39 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.20), residues: 1955 helix: 3.05 (0.20), residues: 725 sheet: -0.20 (0.25), residues: 375 loop : -0.50 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP E 320 HIS 0.002 0.000 HIS A 18 PHE 0.011 0.001 PHE D 233 TYR 0.015 0.001 TYR C 67 ARG 0.009 0.000 ARG B 315 ********************** 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 89 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 65 time to evaluate : 1.969 Fit side-chains REVERT: A 267 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8388 (tp) REVERT: B 182 ILE cc_start: 0.6806 (mm) cc_final: 0.6507 (mt) REVERT: B 267 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8581 (tp) REVERT: C 267 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8518 (tp) REVERT: D 182 ILE cc_start: 0.7086 (mm) cc_final: 0.6870 (mt) REVERT: D 267 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8560 (tp) REVERT: E 182 ILE cc_start: 0.6988 (mm) cc_final: 0.6626 (mt) REVERT: E 267 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8436 (tp) outliers start: 24 outliers final: 15 residues processed: 89 average time/residue: 0.7749 time to fit residues: 83.7871 Evaluate side-chains 84 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 64 time to evaluate : 2.101 ------------------------------------------------------------------------------- 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 267 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.083226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.056561 restraints weight = 41567.533| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.75 r_work: 0.2753 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17145 Z= 0.178 Angle : 0.981 21.098 23440 Z= 0.378 Chirality : 0.094 1.959 2755 Planarity : 0.003 0.039 2840 Dihedral : 16.958 171.310 2565 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.14 % Allowed : 15.50 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.20), residues: 1955 helix: 3.07 (0.20), residues: 725 sheet: -0.21 (0.25), residues: 375 loop : -0.48 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 320 HIS 0.001 0.000 HIS A 18 PHE 0.013 0.001 PHE D 233 TYR 0.013 0.001 TYR C 67 ARG 0.009 0.000 ARG C 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3346.14 seconds wall clock time: 61 minutes 49.87 seconds (3709.87 seconds total)