Starting phenix.real_space_refine on Sun Jul 21 12:06:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/07_2024/7pm4_13520.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/07_2024/7pm4_13520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/07_2024/7pm4_13520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/07_2024/7pm4_13520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/07_2024/7pm4_13520.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/07_2024/7pm4_13520.cif" } resolution = 2.49 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= 0.002 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 40 5.16 5 C 9276 2.51 5 N 2340 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A GLU 362": "OE1" <-> "OE2" Residue "B PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "C PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C GLU 362": "OE1" <-> "OE2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D GLU 362": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14288 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3533 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 30, 'TRANS': 400} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3533 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 30, 'TRANS': 400} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3533 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 30, 'TRANS': 400} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3533 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 30, 'TRANS': 400} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'DFU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'DFU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'DFU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'DFU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Time building chain proxies: 9.24, per 1000 atoms: 0.65 Number of scatterers: 14288 At special positions: 0 Unit cell: (159.408, 113.488, 59.696, 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 40 16.00 O 2632 8.00 N 2340 7.00 C 9276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS D 266 " - pdb=" SG CYS D 274 " 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 236 " " NAG B 501 " - " ASN B 236 " " NAG C 501 " - " ASN C 236 " " NAG D 501 " - " ASN D 236 " Time building additional restraints: 5.99 Conformation dependent library (CDL) restraints added in 2.8 seconds 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 12 sheets defined 36.0% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 35 through 40 Processing helix chain 'A' and resid 45 through 52 removed outlier: 4.197A pdb=" N ASP A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 71 through 77 Processing helix chain 'A' and resid 81 through 92 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 100 through 105 removed outlier: 4.476A pdb=" N GLN A 104 " --> pdb=" O ASP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 158 through 169 Processing helix chain 'A' and resid 185 through 194 Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 343 through 361 removed outlier: 3.668A pdb=" N ILE A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'B' and resid 35 through 40 Processing helix chain 'B' and resid 45 through 52 removed outlier: 4.197A pdb=" N ASP B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 71 through 77 Processing helix chain 'B' and resid 81 through 92 Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 100 through 105 removed outlier: 4.476A pdb=" N GLN B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 122 Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 312 through 326 Processing helix chain 'B' and resid 343 through 361 removed outlier: 3.668A pdb=" N ILE B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'C' and resid 35 through 40 Processing helix chain 'C' and resid 45 through 52 removed outlier: 4.197A pdb=" N ASP C 49 " --> pdb=" O PRO C 45 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS C 52 " --> pdb=" O PHE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 64 Processing helix chain 'C' and resid 71 through 77 Processing helix chain 'C' and resid 81 through 92 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 100 through 105 removed outlier: 4.476A pdb=" N GLN C 104 " --> pdb=" O ASP C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 158 through 169 Processing helix chain 'C' and resid 185 through 194 Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 205 through 216 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 236 through 247 Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'C' and resid 343 through 361 removed outlier: 3.668A pdb=" N ILE C 359 " --> pdb=" O LYS C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'D' and resid 35 through 40 Processing helix chain 'D' and resid 45 through 52 removed outlier: 4.197A pdb=" N ASP D 49 " --> pdb=" O PRO D 45 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS D 52 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 71 through 77 Processing helix chain 'D' and resid 81 through 92 Processing helix chain 'D' and resid 97 through 99 No H-bonds generated for 'chain 'D' and resid 97 through 99' Processing helix chain 'D' and resid 100 through 105 removed outlier: 4.476A pdb=" N GLN D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 122 Processing helix chain 'D' and resid 158 through 169 Processing helix chain 'D' and resid 185 through 194 Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 236 through 247 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'D' and resid 343 through 361 removed outlier: 3.668A pdb=" N ILE D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing sheet with id=AA1, first strand: chain 'A' and resid 255 through 256 removed outlier: 6.314A pdb=" N VAL A 127 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR A 177 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU A 129 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N SER A 179 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N THR A 131 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A 126 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 368 through 374 removed outlier: 4.258A pdb=" N TRP A 370 " --> pdb=" O TYR A 383 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N TYR A 383 " --> pdb=" O TRP A 370 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N VAL A 372 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N VAL A 381 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL A 460 " --> pdb=" O THR A 413 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N THR A 413 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 405 removed outlier: 4.371A pdb=" N LYS A 426 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 255 through 256 removed outlier: 6.314A pdb=" N VAL B 127 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR B 177 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU B 129 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N SER B 179 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N THR B 131 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B 126 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 368 through 374 removed outlier: 4.258A pdb=" N TRP B 370 " --> pdb=" O TYR B 383 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N TYR B 383 " --> pdb=" O TRP B 370 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N VAL B 372 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N VAL B 381 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B 460 " --> pdb=" O THR B 413 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N THR B 413 " --> pdb=" O VAL B 460 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 402 through 405 removed outlier: 4.371A pdb=" N LYS B 426 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 255 through 256 removed outlier: 6.314A pdb=" N VAL C 127 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR C 177 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU C 129 " --> pdb=" O TYR C 177 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N SER C 179 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N THR C 131 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR C 126 " --> pdb=" O PHE C 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 368 through 374 removed outlier: 4.258A pdb=" N TRP C 370 " --> pdb=" O TYR C 383 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N TYR C 383 " --> pdb=" O TRP C 370 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N VAL C 372 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N VAL C 381 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL C 460 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N THR C 413 " --> pdb=" O VAL C 460 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 402 through 405 removed outlier: 4.371A pdb=" N LYS C 426 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 255 through 256 removed outlier: 6.314A pdb=" N VAL D 127 " --> pdb=" O GLY D 175 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR D 177 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU D 129 " --> pdb=" O TYR D 177 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N SER D 179 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N THR D 131 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR D 126 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 368 through 374 removed outlier: 4.258A pdb=" N TRP D 370 " --> pdb=" O TYR D 383 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N TYR D 383 " --> pdb=" O TRP D 370 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N VAL D 372 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N VAL D 381 " --> pdb=" O VAL D 372 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL D 460 " --> pdb=" O THR D 413 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N THR D 413 " --> pdb=" O VAL D 460 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 402 through 405 removed outlier: 4.371A pdb=" N LYS D 426 " --> pdb=" O SER D 438 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1440 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: 4.43 Time building geometry restraints manager: 6.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4368 1.34 - 1.46: 4052 1.46 - 1.58: 6300 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 14780 Sorted by residual: bond pdb=" C1 DFU A 502 " pdb=" N5 DFU A 502 " ideal model delta sigma weight residual 1.459 1.503 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" C1 DFU D 502 " pdb=" N5 DFU D 502 " ideal model delta sigma weight residual 1.459 1.503 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" C1 DFU B 502 " pdb=" N5 DFU B 502 " ideal model delta sigma weight residual 1.459 1.503 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" C1 DFU C 502 " pdb=" N5 DFU C 502 " ideal model delta sigma weight residual 1.459 1.503 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" C5 DFU D 502 " pdb=" N5 DFU D 502 " ideal model delta sigma weight residual 1.465 1.500 -0.035 2.00e-02 2.50e+03 3.10e+00 ... (remaining 14775 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.34: 828 107.34 - 114.02: 7880 114.02 - 120.70: 5972 120.70 - 127.39: 5168 127.39 - 134.07: 372 Bond angle restraints: 20220 Sorted by residual: angle pdb=" C THR D 410 " pdb=" N THR D 411 " pdb=" CA THR D 411 " ideal model delta sigma weight residual 122.44 117.91 4.53 1.19e+00 7.06e-01 1.45e+01 angle pdb=" C THR B 410 " pdb=" N THR B 411 " pdb=" CA THR B 411 " ideal model delta sigma weight residual 122.44 117.91 4.53 1.19e+00 7.06e-01 1.45e+01 angle pdb=" C THR C 410 " pdb=" N THR C 411 " pdb=" CA THR C 411 " ideal model delta sigma weight residual 122.44 117.91 4.53 1.19e+00 7.06e-01 1.45e+01 angle pdb=" C THR A 410 " pdb=" N THR A 411 " pdb=" CA THR A 411 " ideal model delta sigma weight residual 122.44 117.91 4.53 1.19e+00 7.06e-01 1.45e+01 angle pdb=" CG LYS D 426 " pdb=" CD LYS D 426 " pdb=" CE LYS D 426 " ideal model delta sigma weight residual 111.30 117.30 -6.00 2.30e+00 1.89e-01 6.80e+00 ... (remaining 20215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 7388 17.61 - 35.21: 748 35.21 - 52.82: 228 52.82 - 70.42: 76 70.42 - 88.03: 24 Dihedral angle restraints: 8464 sinusoidal: 3468 harmonic: 4996 Sorted by residual: dihedral pdb=" CB CYS D 266 " pdb=" SG CYS D 266 " pdb=" SG CYS D 274 " pdb=" CB CYS D 274 " ideal model delta sinusoidal sigma weight residual 93.00 161.31 -68.31 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CB CYS C 266 " pdb=" SG CYS C 266 " pdb=" SG CYS C 274 " pdb=" CB CYS C 274 " ideal model delta sinusoidal sigma weight residual 93.00 161.31 -68.31 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CB CYS B 266 " pdb=" SG CYS B 266 " pdb=" SG CYS B 274 " pdb=" CB CYS B 274 " ideal model delta sinusoidal sigma weight residual 93.00 161.31 -68.31 1 1.00e+01 1.00e-02 6.05e+01 ... (remaining 8461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1172 0.029 - 0.058: 540 0.058 - 0.087: 196 0.087 - 0.115: 124 0.115 - 0.144: 20 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CA ILE C 455 " pdb=" N ILE C 455 " pdb=" C ILE C 455 " pdb=" CB ILE C 455 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ILE B 455 " pdb=" N ILE B 455 " pdb=" C ILE B 455 " pdb=" CB ILE B 455 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ILE A 455 " pdb=" N ILE A 455 " pdb=" C ILE A 455 " pdb=" CB ILE A 455 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 2049 not shown) Planarity restraints: 2552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 418 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C MET A 418 " 0.031 2.00e-02 2.50e+03 pdb=" O MET A 418 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 419 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 418 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C MET C 418 " -0.031 2.00e-02 2.50e+03 pdb=" O MET C 418 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU C 419 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 418 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C MET B 418 " 0.031 2.00e-02 2.50e+03 pdb=" O MET B 418 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU B 419 " -0.010 2.00e-02 2.50e+03 ... (remaining 2549 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2536 2.77 - 3.30: 13354 3.30 - 3.83: 26460 3.83 - 4.37: 32936 4.37 - 4.90: 52980 Nonbonded interactions: 128266 Sorted by model distance: nonbonded pdb=" OG1 THR C 378 " pdb=" N THR C 379 " model vdw 2.237 2.520 nonbonded pdb=" OG1 THR D 378 " pdb=" N THR D 379 " model vdw 2.237 2.520 nonbonded pdb=" OG1 THR A 378 " pdb=" N THR A 379 " model vdw 2.237 2.520 nonbonded pdb=" OG1 THR B 378 " pdb=" N THR B 379 " model vdw 2.237 2.520 nonbonded pdb=" O SER B 445 " pdb=" OG SER B 445 " model vdw 2.253 2.440 ... (remaining 128261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 3.960 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 41.330 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 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:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 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 : 0.003 0.044 14780 Z= 0.198 Angle : 0.560 6.924 20220 Z= 0.287 Chirality : 0.043 0.144 2052 Planarity : 0.004 0.034 2548 Dihedral : 16.861 88.029 5252 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.06 % Allowed : 16.22 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1716 helix: 1.44 (0.23), residues: 512 sheet: 0.06 (0.29), residues: 284 loop : 0.23 (0.23), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 223 HIS 0.002 0.000 HIS A 286 PHE 0.010 0.001 PHE A 394 TYR 0.010 0.001 TYR D 177 ARG 0.001 0.000 ARG C 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 1.673 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 116 average time/residue: 1.2374 time to fit residues: 159.4230 Evaluate side-chains 108 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.9980 chunk 130 optimal weight: 0.0770 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 0.0270 chunk 69 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 156 optimal weight: 0.5980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.0479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14780 Z= 0.135 Angle : 0.494 5.779 20220 Z= 0.254 Chirality : 0.042 0.140 2052 Planarity : 0.004 0.032 2548 Dihedral : 4.660 36.960 2024 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.39 % Allowed : 13.83 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.22), residues: 1716 helix: 1.44 (0.23), residues: 560 sheet: 0.22 (0.29), residues: 284 loop : 0.11 (0.24), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 183 HIS 0.001 0.000 HIS D 156 PHE 0.009 0.001 PHE D 394 TYR 0.008 0.001 TYR A 92 ARG 0.002 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 108 time to evaluate : 1.621 Fit side-chains REVERT: A 315 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7469 (tp30) REVERT: B 315 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7468 (tp30) REVERT: C 315 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7467 (tp30) REVERT: D 315 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7468 (tp30) outliers start: 36 outliers final: 8 residues processed: 132 average time/residue: 1.1504 time to fit residues: 169.2353 Evaluate side-chains 112 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.060 14780 Z= 0.574 Angle : 0.744 6.698 20220 Z= 0.395 Chirality : 0.056 0.154 2052 Planarity : 0.006 0.052 2548 Dihedral : 5.630 38.019 2012 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.46 % Allowed : 12.50 % Favored : 84.04 % 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: 0.26 (0.21), residues: 1716 helix: 1.25 (0.23), residues: 508 sheet: -0.06 (0.30), residues: 284 loop : -0.30 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 260 HIS 0.003 0.001 HIS D 111 PHE 0.019 0.003 PHE C 109 TYR 0.019 0.003 TYR D 92 ARG 0.007 0.001 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 92 time to evaluate : 1.616 Fit side-chains REVERT: A 400 ASN cc_start: 0.7360 (OUTLIER) cc_final: 0.6996 (p0) REVERT: B 400 ASN cc_start: 0.7355 (OUTLIER) cc_final: 0.6990 (p0) REVERT: C 400 ASN cc_start: 0.7357 (OUTLIER) cc_final: 0.6991 (p0) REVERT: D 400 ASN cc_start: 0.7360 (OUTLIER) cc_final: 0.6995 (p0) outliers start: 52 outliers final: 28 residues processed: 132 average time/residue: 1.2102 time to fit residues: 177.0112 Evaluate side-chains 124 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 92 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 400 ASN Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 400 ASN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 400 ASN Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 216 SER Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 457 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.0020 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 157 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 148 optimal weight: 0.5980 chunk 44 optimal weight: 0.0970 overall best weight: 0.3786 ------------------------------------------------------------------------------- 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: 0.8574 moved from start: 0.0631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14780 Z= 0.129 Angle : 0.498 5.755 20220 Z= 0.258 Chirality : 0.043 0.136 2052 Planarity : 0.004 0.034 2548 Dihedral : 4.464 34.907 2012 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.39 % Allowed : 13.56 % Favored : 84.04 % 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: 0.64 (0.21), residues: 1716 helix: 1.45 (0.23), residues: 560 sheet: 0.21 (0.30), residues: 284 loop : -0.10 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 183 HIS 0.001 0.000 HIS A 286 PHE 0.008 0.001 PHE A 96 TYR 0.007 0.001 TYR D 92 ARG 0.001 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 104 time to evaluate : 1.573 Fit side-chains REVERT: A 315 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7459 (tp30) REVERT: B 315 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7460 (tp30) REVERT: C 315 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7457 (tp30) REVERT: D 315 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7459 (tp30) outliers start: 36 outliers final: 16 residues processed: 128 average time/residue: 1.1506 time to fit residues: 164.3426 Evaluate side-chains 116 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 68 optimal weight: 0.1980 chunk 141 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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: 0.8634 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14780 Z= 0.313 Angle : 0.606 6.219 20220 Z= 0.318 Chirality : 0.047 0.147 2052 Planarity : 0.005 0.035 2548 Dihedral : 5.096 38.116 2012 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.93 % Allowed : 13.83 % Favored : 83.24 % 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: 0.40 (0.21), residues: 1716 helix: 1.24 (0.23), residues: 560 sheet: 0.09 (0.30), residues: 284 loop : -0.23 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 260 HIS 0.002 0.001 HIS D 111 PHE 0.013 0.002 PHE C 96 TYR 0.013 0.002 TYR D 92 ARG 0.003 0.001 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 96 time to evaluate : 1.585 Fit side-chains REVERT: A 315 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7506 (tp30) REVERT: B 315 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7507 (tp30) REVERT: C 315 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7505 (tp30) REVERT: D 315 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7503 (tp30) outliers start: 44 outliers final: 28 residues processed: 128 average time/residue: 1.1253 time to fit residues: 160.6860 Evaluate side-chains 124 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 92 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 216 SER Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 166 optimal weight: 1.9990 chunk 138 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 87 optimal weight: 0.0970 chunk 160 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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: 0.8583 moved from start: 0.0649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14780 Z= 0.146 Angle : 0.507 5.823 20220 Z= 0.262 Chirality : 0.043 0.137 2052 Planarity : 0.004 0.035 2548 Dihedral : 4.459 34.952 2012 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.33 % Allowed : 15.43 % Favored : 83.24 % 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 (0.22), residues: 1716 helix: 1.51 (0.23), residues: 560 sheet: 0.19 (0.30), residues: 284 loop : -0.02 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 183 HIS 0.001 0.000 HIS B 111 PHE 0.010 0.001 PHE A 96 TYR 0.008 0.001 TYR A 92 ARG 0.002 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.541 Fit side-chains REVERT: A 315 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7466 (tp30) REVERT: B 315 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7467 (tp30) REVERT: C 315 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7467 (tp30) REVERT: D 315 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7467 (tp30) outliers start: 20 outliers final: 16 residues processed: 104 average time/residue: 1.2549 time to fit residues: 144.8170 Evaluate side-chains 112 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 92 optimal weight: 0.0970 chunk 165 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8596 moved from start: 0.0613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14780 Z= 0.173 Angle : 0.522 5.896 20220 Z= 0.270 Chirality : 0.043 0.141 2052 Planarity : 0.004 0.034 2548 Dihedral : 4.519 35.009 2012 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.60 % Allowed : 14.89 % Favored : 83.51 % 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: 0.74 (0.22), residues: 1716 helix: 1.49 (0.23), residues: 560 sheet: 0.26 (0.31), residues: 284 loop : -0.00 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 223 HIS 0.002 0.000 HIS D 111 PHE 0.010 0.002 PHE D 96 TYR 0.009 0.001 TYR A 92 ARG 0.002 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 1.612 Fit side-chains REVERT: A 315 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7472 (tp30) REVERT: B 315 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7472 (tp30) REVERT: C 315 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7473 (tp30) REVERT: D 315 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7472 (tp30) outliers start: 24 outliers final: 20 residues processed: 104 average time/residue: 1.2542 time to fit residues: 145.3487 Evaluate side-chains 116 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 81 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 158 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8589 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14780 Z= 0.165 Angle : 0.516 5.878 20220 Z= 0.266 Chirality : 0.043 0.141 2052 Planarity : 0.004 0.034 2548 Dihedral : 4.451 34.088 2012 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.13 % Allowed : 14.36 % Favored : 83.51 % 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: 0.78 (0.22), residues: 1716 helix: 1.51 (0.23), residues: 560 sheet: 0.29 (0.31), residues: 284 loop : 0.03 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 243 HIS 0.002 0.000 HIS A 111 PHE 0.010 0.001 PHE B 96 TYR 0.009 0.001 TYR D 92 ARG 0.002 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 92 time to evaluate : 1.621 Fit side-chains REVERT: A 315 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7457 (tp30) REVERT: B 315 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7456 (tp30) REVERT: C 315 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7458 (tp30) REVERT: D 315 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7454 (tp30) outliers start: 32 outliers final: 28 residues processed: 112 average time/residue: 1.1537 time to fit residues: 144.2230 Evaluate side-chains 124 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 92 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 216 SER Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.8608 moved from start: 0.0658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14780 Z= 0.219 Angle : 0.549 6.023 20220 Z= 0.285 Chirality : 0.045 0.144 2052 Planarity : 0.005 0.034 2548 Dihedral : 4.693 35.144 2012 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.13 % Allowed : 14.63 % Favored : 83.24 % 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: 0.63 (0.21), residues: 1716 helix: 1.38 (0.23), residues: 560 sheet: 0.21 (0.30), residues: 284 loop : -0.06 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 223 HIS 0.002 0.001 HIS D 111 PHE 0.011 0.002 PHE D 96 TYR 0.011 0.001 TYR A 177 ARG 0.002 0.000 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 1.671 Fit side-chains REVERT: A 315 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7471 (tp30) REVERT: B 315 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7472 (tp30) REVERT: C 315 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7472 (tp30) REVERT: D 315 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7470 (tp30) outliers start: 32 outliers final: 28 residues processed: 116 average time/residue: 1.2188 time to fit residues: 157.0032 Evaluate side-chains 128 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 216 SER Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 105 optimal weight: 0.0870 chunk 83 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 overall best weight: 1.7764 ------------------------------------------------------------------------------- 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: 0.8631 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14780 Z= 0.312 Angle : 0.611 6.246 20220 Z= 0.320 Chirality : 0.047 0.150 2052 Planarity : 0.005 0.034 2548 Dihedral : 5.094 37.559 2012 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.39 % Allowed : 14.30 % 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: 0.40 (0.21), residues: 1716 helix: 1.19 (0.23), residues: 560 sheet: 0.08 (0.31), residues: 284 loop : -0.19 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 260 HIS 0.003 0.001 HIS A 111 PHE 0.012 0.002 PHE D 109 TYR 0.013 0.002 TYR D 92 ARG 0.004 0.001 ARG A 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 104 time to evaluate : 1.420 Fit side-chains REVERT: A 315 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7489 (tp30) REVERT: B 315 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7488 (tp30) REVERT: C 315 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7490 (tp30) REVERT: D 315 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7488 (tp30) outliers start: 36 outliers final: 28 residues processed: 128 average time/residue: 1.3173 time to fit residues: 185.2915 Evaluate side-chains 132 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 100 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 216 SER Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 140 optimal weight: 0.0970 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.115709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.085487 restraints weight = 15878.240| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.49 r_work: 0.2776 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14780 Z= 0.197 Angle : 0.544 5.958 20220 Z= 0.282 Chirality : 0.044 0.146 2052 Planarity : 0.005 0.035 2548 Dihedral : 4.713 35.397 2012 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.13 % Allowed : 14.83 % Favored : 83.05 % 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: 0.57 (0.21), residues: 1716 helix: 1.35 (0.23), residues: 560 sheet: 0.11 (0.31), residues: 284 loop : -0.09 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 243 HIS 0.002 0.001 HIS A 111 PHE 0.011 0.002 PHE B 96 TYR 0.010 0.001 TYR D 92 ARG 0.002 0.000 ARG D 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4184.19 seconds wall clock time: 75 minutes 10.96 seconds (4510.96 seconds total)