Starting phenix.real_space_refine on Sat Jan 20 08:58:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pls_13499/01_2024/7pls_13499.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pls_13499/01_2024/7pls_13499.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/7pls_13499/01_2024/7pls_13499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pls_13499/01_2024/7pls_13499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pls_13499/01_2024/7pls_13499.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pls_13499/01_2024/7pls_13499.pdb" } 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= 0.005 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 9240 2.51 5 N 2332 2.21 5 O 2612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 312": "OE1" <-> "OE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 312": "OE1" <-> "OE2" Residue "D GLU 406": "OE1" <-> "OE2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 14224 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3529 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 400} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3529 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 400} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3529 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 400} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3529 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 400} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 7.69, per 1000 atoms: 0.54 Number of scatterers: 14224 At special positions: 0 Unit cell: (159.714, 114.882, 59.776, 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 2612 8.00 N 2332 7.00 C 9240 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=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.04 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 274 " distance=2.04 Simple disulfide: pdb=" SG CYS D 266 " - pdb=" SG CYS D 274 " distance=2.04 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: 5.73 Conformation dependent library (CDL) restraints added in 2.4 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 37.4% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 35 through 40 Processing helix chain 'A' and resid 45 through 52 removed outlier: 4.311A pdb=" N ASP A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) removed outlier: 3.745A 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 105 Proline residue: A 103 - end of helix Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 158 through 170 removed outlier: 3.605A pdb=" N ARG A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) 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 306 through 310 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 343 through 361 removed outlier: 3.712A 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: 4.311A pdb=" N ASP B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) removed outlier: 3.745A 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 105 Proline residue: B 103 - end of helix Processing helix chain 'B' and resid 111 through 122 Processing helix chain 'B' and resid 158 through 170 removed outlier: 3.605A pdb=" N ARG B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) 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 306 through 310 Processing helix chain 'B' and resid 312 through 326 Processing helix chain 'B' and resid 343 through 361 removed outlier: 3.712A 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: 4.311A pdb=" N ASP C 49 " --> pdb=" O PRO C 45 " (cutoff:3.500A) removed outlier: 3.745A 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 105 Proline residue: C 103 - end of helix Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 158 through 170 removed outlier: 3.605A pdb=" N ARG C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) 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 306 through 310 Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'C' and resid 343 through 361 removed outlier: 3.712A 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: 4.311A pdb=" N ASP D 49 " --> pdb=" O PRO D 45 " (cutoff:3.500A) removed outlier: 3.745A 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 105 Proline residue: D 103 - end of helix Processing helix chain 'D' and resid 111 through 122 Processing helix chain 'D' and resid 158 through 170 removed outlier: 3.605A pdb=" N ARG D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) 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 306 through 310 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'D' and resid 343 through 361 removed outlier: 3.712A 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: 6.801A pdb=" N TYR A 174 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N TRP A 223 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 176 " --> pdb=" O TRP A 223 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP A 225 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS A 178 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL A 127 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR A 177 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 129 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N SER A 179 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N THR A 131 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE A 53 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL A 128 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL A 55 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR A 130 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE A 57 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS A 132 " --> pdb=" O ILE A 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 368 through 374 removed outlier: 4.182A pdb=" N TRP A 370 " --> pdb=" O TYR A 383 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N TYR A 383 " --> pdb=" O TRP A 370 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N VAL A 372 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N VAL A 381 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N ILE A 455 " --> pdb=" O LYS A 415 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N LYS A 415 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N LEU A 457 " --> pdb=" O THR A 413 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N THR A 413 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLY A 459 " --> pdb=" O THR A 411 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 411 " --> pdb=" O GLY A 459 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 405 Processing sheet with id=AA4, first strand: chain 'B' and resid 255 through 256 removed outlier: 6.801A pdb=" N TYR B 174 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N TRP B 223 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU B 176 " --> pdb=" O TRP B 223 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP B 225 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS B 178 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL B 127 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR B 177 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 129 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N SER B 179 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N THR B 131 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE B 53 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL B 128 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 55 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR B 130 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE B 57 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS B 132 " --> pdb=" O ILE B 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 368 through 374 removed outlier: 4.182A pdb=" N TRP B 370 " --> pdb=" O TYR B 383 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N TYR B 383 " --> pdb=" O TRP B 370 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N VAL B 372 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N VAL B 381 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N ILE B 455 " --> pdb=" O LYS B 415 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N LYS B 415 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N LEU B 457 " --> pdb=" O THR B 413 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N THR B 413 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLY B 459 " --> pdb=" O THR B 411 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR B 411 " --> pdb=" O GLY B 459 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 402 through 405 Processing sheet with id=AA7, first strand: chain 'C' and resid 255 through 256 removed outlier: 6.801A pdb=" N TYR C 174 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N TRP C 223 " --> pdb=" O TYR C 174 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU C 176 " --> pdb=" O TRP C 223 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP C 225 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS C 178 " --> pdb=" O ASP C 225 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL C 127 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR C 177 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU C 129 " --> pdb=" O TYR C 177 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N SER C 179 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N THR C 131 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE C 53 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL C 128 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL C 55 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR C 130 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE C 57 " --> pdb=" O THR C 130 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS C 132 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 368 through 374 removed outlier: 4.182A pdb=" N TRP C 370 " --> pdb=" O TYR C 383 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N TYR C 383 " --> pdb=" O TRP C 370 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N VAL C 372 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N VAL C 381 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N ILE C 455 " --> pdb=" O LYS C 415 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N LYS C 415 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N LEU C 457 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N THR C 413 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLY C 459 " --> pdb=" O THR C 411 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR C 411 " --> pdb=" O GLY C 459 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 402 through 405 Processing sheet with id=AB1, first strand: chain 'D' and resid 255 through 256 removed outlier: 6.801A pdb=" N TYR D 174 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N TRP D 223 " --> pdb=" O TYR D 174 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU D 176 " --> pdb=" O TRP D 223 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP D 225 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS D 178 " --> pdb=" O ASP D 225 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL D 127 " --> pdb=" O GLY D 175 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR D 177 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU D 129 " --> pdb=" O TYR D 177 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N SER D 179 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N THR D 131 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE D 53 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL D 128 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL D 55 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR D 130 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE D 57 " --> pdb=" O THR D 130 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS D 132 " --> pdb=" O ILE D 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 368 through 374 removed outlier: 4.182A pdb=" N TRP D 370 " --> pdb=" O TYR D 383 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N TYR D 383 " --> pdb=" O TRP D 370 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N VAL D 372 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N VAL D 381 " --> pdb=" O VAL D 372 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N ILE D 455 " --> pdb=" O LYS D 415 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N LYS D 415 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N LEU D 457 " --> pdb=" O THR D 413 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N THR D 413 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLY D 459 " --> pdb=" O THR D 411 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR D 411 " --> pdb=" O GLY D 459 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 402 through 405 488 hydrogen bonds defined for protein. 1320 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: 4.03 Time building geometry restraints manager: 6.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4104 1.34 - 1.46: 3588 1.46 - 1.58: 6972 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 14724 Sorted by residual: bond pdb=" N ILE D 317 " pdb=" CA ILE D 317 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.67e+00 bond pdb=" N ILE B 317 " pdb=" CA ILE B 317 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.67e+00 bond pdb=" N ILE C 317 " pdb=" CA ILE C 317 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.67e+00 bond pdb=" N ILE A 317 " pdb=" CA ILE A 317 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.67e+00 bond pdb=" N ILE C 316 " pdb=" CA ILE C 316 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.19e-02 7.06e+03 7.67e+00 ... (remaining 14719 not shown) Histogram of bond angle deviations from ideal: 100.75 - 107.47: 920 107.47 - 114.19: 7844 114.19 - 120.91: 6456 120.91 - 127.63: 4572 127.63 - 134.35: 356 Bond angle restraints: 20148 Sorted by residual: angle pdb=" CA VAL B 321 " pdb=" C VAL B 321 " pdb=" O VAL B 321 " ideal model delta sigma weight residual 121.17 118.11 3.06 1.06e+00 8.90e-01 8.31e+00 angle pdb=" CA VAL A 321 " pdb=" C VAL A 321 " pdb=" O VAL A 321 " ideal model delta sigma weight residual 121.17 118.11 3.06 1.06e+00 8.90e-01 8.31e+00 angle pdb=" CA VAL C 321 " pdb=" C VAL C 321 " pdb=" O VAL C 321 " ideal model delta sigma weight residual 121.17 118.11 3.06 1.06e+00 8.90e-01 8.31e+00 angle pdb=" CA VAL D 321 " pdb=" C VAL D 321 " pdb=" O VAL D 321 " ideal model delta sigma weight residual 121.17 118.11 3.06 1.06e+00 8.90e-01 8.31e+00 angle pdb=" O ILE D 317 " pdb=" C ILE D 317 " pdb=" N SER D 318 " ideal model delta sigma weight residual 121.87 124.66 -2.79 9.70e-01 1.06e+00 8.29e+00 ... (remaining 20143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 7372 17.16 - 34.32: 668 34.32 - 51.48: 264 51.48 - 68.64: 48 68.64 - 85.80: 28 Dihedral angle restraints: 8380 sinusoidal: 3384 harmonic: 4996 Sorted by residual: 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 58.32 34.68 1 1.00e+01 1.00e-02 1.71e+01 dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 274 " pdb=" CB CYS A 274 " ideal model delta sinusoidal sigma weight residual 93.00 58.32 34.68 1 1.00e+01 1.00e-02 1.71e+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 58.32 34.68 1 1.00e+01 1.00e-02 1.71e+01 ... (remaining 8377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1232 0.033 - 0.066: 492 0.066 - 0.099: 184 0.099 - 0.132: 100 0.132 - 0.165: 28 Chirality restraints: 2036 Sorted by residual: chirality pdb=" CA ILE B 316 " pdb=" N ILE B 316 " pdb=" C ILE B 316 " pdb=" CB ILE B 316 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA ILE A 316 " pdb=" N ILE A 316 " pdb=" C ILE A 316 " pdb=" CB ILE A 316 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA ILE C 316 " pdb=" N ILE C 316 " pdb=" C ILE C 316 " pdb=" CB ILE C 316 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 2033 not shown) Planarity restraints: 2552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 501 " -0.059 2.00e-02 2.50e+03 4.82e-02 2.91e+01 pdb=" C7 NAG B 501 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG B 501 " -0.045 2.00e-02 2.50e+03 pdb=" N2 NAG B 501 " 0.076 2.00e-02 2.50e+03 pdb=" O7 NAG B 501 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 501 " -0.059 2.00e-02 2.50e+03 4.82e-02 2.91e+01 pdb=" C7 NAG D 501 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG D 501 " -0.045 2.00e-02 2.50e+03 pdb=" N2 NAG D 501 " 0.076 2.00e-02 2.50e+03 pdb=" O7 NAG D 501 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 501 " 0.059 2.00e-02 2.50e+03 4.82e-02 2.91e+01 pdb=" C7 NAG A 501 " -0.016 2.00e-02 2.50e+03 pdb=" C8 NAG A 501 " 0.045 2.00e-02 2.50e+03 pdb=" N2 NAG A 501 " -0.076 2.00e-02 2.50e+03 pdb=" O7 NAG A 501 " -0.012 2.00e-02 2.50e+03 ... (remaining 2549 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3614 2.80 - 3.33: 12958 3.33 - 3.85: 26466 3.85 - 4.38: 32558 4.38 - 4.90: 52340 Nonbonded interactions: 127936 Sorted by model distance: nonbonded pdb=" OE2 GLU B 362 " pdb=" OH TYR B 391 " model vdw 2.275 2.440 nonbonded pdb=" OE2 GLU C 362 " pdb=" OH TYR C 391 " model vdw 2.275 2.440 nonbonded pdb=" OE2 GLU D 362 " pdb=" OH TYR D 391 " model vdw 2.275 2.440 nonbonded pdb=" OE2 GLU A 362 " pdb=" OH TYR A 391 " model vdw 2.275 2.440 nonbonded pdb=" O PHE A 137 " pdb=" O HOH A 601 " model vdw 2.294 2.440 ... (remaining 127931 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: 5.910 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: 0.000 Extract box with map and model: 8.410 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 39.240 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.090 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 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 0.033 14724 Z= 0.211 Angle : 0.578 5.397 20148 Z= 0.341 Chirality : 0.047 0.165 2036 Planarity : 0.005 0.048 2548 Dihedral : 16.349 85.803 5168 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.33 % Allowed : 12.00 % Favored : 86.67 % 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: 0.35 (0.21), residues: 1716 helix: 0.95 (0.22), residues: 544 sheet: 0.21 (0.28), residues: 284 loop : -0.11 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 183 HIS 0.002 0.001 HIS C 134 PHE 0.012 0.001 PHE C 137 TYR 0.008 0.001 TYR A 126 ARG 0.001 0.000 ARG D 89 *********************** 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 140 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 1.642 Fit side-chains REVERT: A 312 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6973 (mt-10) REVERT: A 315 GLU cc_start: 0.7375 (tp30) cc_final: 0.7040 (tp30) REVERT: B 312 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6976 (mt-10) REVERT: B 315 GLU cc_start: 0.7374 (tp30) cc_final: 0.7041 (tp30) REVERT: C 312 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6976 (mt-10) REVERT: C 315 GLU cc_start: 0.7379 (tp30) cc_final: 0.7046 (tp30) REVERT: D 312 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6974 (mt-10) REVERT: D 315 GLU cc_start: 0.7373 (tp30) cc_final: 0.7038 (tp30) outliers start: 20 outliers final: 16 residues processed: 132 average time/residue: 1.2373 time to fit residues: 180.9231 Evaluate side-chains 132 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 429 THR 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: 1.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 81 optimal weight: 0.2980 chunk 100 optimal weight: 0.3980 chunk 156 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.8339 moved from start: 0.0503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14724 Z= 0.179 Angle : 0.514 5.670 20148 Z= 0.266 Chirality : 0.044 0.138 2036 Planarity : 0.004 0.035 2548 Dihedral : 5.555 49.082 1976 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.33 % Allowed : 11.20 % Favored : 87.47 % 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: 0.59 (0.21), residues: 1716 helix: 1.55 (0.23), residues: 540 sheet: 0.19 (0.28), residues: 292 loop : -0.20 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 243 HIS 0.002 0.001 HIS D 286 PHE 0.011 0.002 PHE C 240 TYR 0.009 0.001 TYR C 126 ARG 0.001 0.000 ARG C 259 *********************** 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 132 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.665 Fit side-chains REVERT: A 402 VAL cc_start: 0.7985 (t) cc_final: 0.7710 (t) REVERT: B 402 VAL cc_start: 0.7982 (t) cc_final: 0.7708 (t) REVERT: C 402 VAL cc_start: 0.7987 (t) cc_final: 0.7714 (t) REVERT: D 402 VAL cc_start: 0.7983 (t) cc_final: 0.7709 (t) outliers start: 20 outliers final: 12 residues processed: 128 average time/residue: 1.2363 time to fit residues: 174.5501 Evaluate side-chains 124 residues out of total 1520 non------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.9980 chunk 117 optimal weight: 0.0970 chunk 81 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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: 0.8336 moved from start: 0.0684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14724 Z= 0.154 Angle : 0.506 5.596 20148 Z= 0.262 Chirality : 0.043 0.138 2036 Planarity : 0.005 0.041 2548 Dihedral : 4.211 16.534 1940 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.60 % Allowed : 10.93 % Favored : 87.47 % 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: 0.55 (0.21), residues: 1716 helix: 1.63 (0.23), residues: 540 sheet: -0.01 (0.28), residues: 288 loop : -0.24 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 243 HIS 0.001 0.001 HIS A 156 PHE 0.010 0.001 PHE B 394 TYR 0.007 0.001 TYR C 177 ARG 0.001 0.000 ARG C 349 *********************** 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 144 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 1.205 Fit side-chains REVERT: A 312 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7129 (mt-10) REVERT: A 402 VAL cc_start: 0.7943 (t) cc_final: 0.7678 (t) REVERT: B 312 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7131 (mt-10) REVERT: B 402 VAL cc_start: 0.7943 (t) cc_final: 0.7678 (t) REVERT: C 312 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7151 (mt-10) REVERT: C 402 VAL cc_start: 0.7942 (t) cc_final: 0.7674 (t) REVERT: D 312 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7152 (mt-10) REVERT: D 402 VAL cc_start: 0.7943 (t) cc_final: 0.7676 (t) outliers start: 24 outliers final: 12 residues processed: 136 average time/residue: 1.0163 time to fit residues: 152.9728 Evaluate side-chains 133 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.8382 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14724 Z= 0.342 Angle : 0.608 5.976 20148 Z= 0.320 Chirality : 0.048 0.147 2036 Planarity : 0.005 0.046 2548 Dihedral : 4.649 18.181 1940 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.33 % Allowed : 12.27 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), residues: 1716 helix: 1.20 (0.22), residues: 556 sheet: -0.21 (0.28), residues: 288 loop : -0.40 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 223 HIS 0.004 0.001 HIS A 133 PHE 0.020 0.003 PHE B 137 TYR 0.017 0.002 TYR A 126 ARG 0.003 0.001 ARG A 259 *********************** 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: 20 poor density : 120 time to evaluate : 1.786 Fit side-chains REVERT: A 312 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7167 (mt-10) REVERT: A 402 VAL cc_start: 0.7849 (t) cc_final: 0.7568 (t) REVERT: B 312 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7168 (mt-10) REVERT: C 312 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7168 (mt-10) REVERT: C 402 VAL cc_start: 0.7845 (t) cc_final: 0.7567 (t) REVERT: D 312 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7169 (mt-10) outliers start: 20 outliers final: 12 residues processed: 132 average time/residue: 1.2246 time to fit residues: 179.1240 Evaluate side-chains 136 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 166 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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: 0.8362 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14724 Z= 0.227 Angle : 0.560 6.339 20148 Z= 0.291 Chirality : 0.045 0.141 2036 Planarity : 0.005 0.046 2548 Dihedral : 4.513 17.619 1940 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.07 % Allowed : 11.73 % Favored : 87.20 % 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: 0.31 (0.21), residues: 1716 helix: 1.43 (0.23), residues: 540 sheet: -0.25 (0.28), residues: 288 loop : -0.34 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 243 HIS 0.002 0.001 HIS D 156 PHE 0.014 0.002 PHE A 137 TYR 0.012 0.001 TYR D 126 ARG 0.002 0.000 ARG B 259 *********************** 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 132 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.603 Fit side-chains REVERT: A 312 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7148 (mt-10) REVERT: A 402 VAL cc_start: 0.7846 (t) cc_final: 0.7576 (t) REVERT: B 312 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7152 (mt-10) REVERT: B 402 VAL cc_start: 0.7845 (t) cc_final: 0.7575 (t) REVERT: C 312 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7149 (mt-10) REVERT: C 402 VAL cc_start: 0.7843 (t) cc_final: 0.7576 (t) REVERT: D 312 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7152 (mt-10) REVERT: D 402 VAL cc_start: 0.7847 (t) cc_final: 0.7575 (t) outliers start: 16 outliers final: 12 residues processed: 124 average time/residue: 1.2682 time to fit residues: 174.1683 Evaluate side-chains 132 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8348 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14724 Z= 0.184 Angle : 0.525 5.640 20148 Z= 0.272 Chirality : 0.044 0.140 2036 Planarity : 0.005 0.044 2548 Dihedral : 4.329 17.134 1940 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.07 % Allowed : 12.27 % Favored : 86.67 % 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: 0.46 (0.21), residues: 1716 helix: 1.55 (0.23), residues: 540 sheet: -0.18 (0.28), residues: 288 loop : -0.23 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 243 HIS 0.002 0.001 HIS D 156 PHE 0.011 0.002 PHE A 137 TYR 0.010 0.001 TYR C 126 ARG 0.001 0.000 ARG B 259 *********************** 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 136 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.617 Fit side-chains REVERT: A 312 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7108 (mt-10) REVERT: A 402 VAL cc_start: 0.7848 (t) cc_final: 0.7573 (t) REVERT: B 312 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7109 (mt-10) REVERT: B 402 VAL cc_start: 0.7847 (t) cc_final: 0.7573 (t) REVERT: C 312 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7107 (mt-10) REVERT: C 402 VAL cc_start: 0.7845 (t) cc_final: 0.7571 (t) REVERT: D 312 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7110 (mt-10) REVERT: D 402 VAL cc_start: 0.7842 (t) cc_final: 0.7567 (t) outliers start: 16 outliers final: 12 residues processed: 128 average time/residue: 1.2611 time to fit residues: 178.6869 Evaluate side-chains 132 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 0.3980 chunk 81 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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: 0.8333 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14724 Z= 0.154 Angle : 0.501 5.573 20148 Z= 0.258 Chirality : 0.043 0.137 2036 Planarity : 0.005 0.043 2548 Dihedral : 4.140 16.421 1940 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.07 % Allowed : 12.27 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1716 helix: 1.69 (0.23), residues: 540 sheet: -0.08 (0.28), residues: 288 loop : -0.17 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 243 HIS 0.002 0.001 HIS C 156 PHE 0.009 0.001 PHE C 96 TYR 0.008 0.001 TYR D 126 ARG 0.001 0.000 ARG A 259 *********************** 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 136 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.623 Fit side-chains REVERT: A 312 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7096 (mt-10) REVERT: A 402 VAL cc_start: 0.7841 (t) cc_final: 0.7559 (t) REVERT: B 312 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7096 (mt-10) REVERT: B 402 VAL cc_start: 0.7864 (t) cc_final: 0.7586 (t) REVERT: C 312 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7095 (mt-10) REVERT: C 402 VAL cc_start: 0.7840 (t) cc_final: 0.7559 (t) REVERT: D 312 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: D 402 VAL cc_start: 0.7860 (t) cc_final: 0.7576 (t) outliers start: 16 outliers final: 12 residues processed: 128 average time/residue: 1.3047 time to fit residues: 184.1697 Evaluate side-chains 132 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.3980 chunk 158 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 101 optimal weight: 0.2980 chunk 163 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14724 Z= 0.161 Angle : 0.506 5.611 20148 Z= 0.261 Chirality : 0.043 0.138 2036 Planarity : 0.005 0.043 2548 Dihedral : 4.150 16.674 1940 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.07 % Allowed : 12.80 % Favored : 86.13 % 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: 1.69 (0.23), residues: 540 sheet: -0.04 (0.28), residues: 288 loop : -0.15 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 243 HIS 0.001 0.001 HIS A 156 PHE 0.010 0.001 PHE D 96 TYR 0.009 0.001 TYR D 126 ARG 0.001 0.000 ARG A 259 *********************** 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: 16 poor density : 112 time to evaluate : 2.104 Fit side-chains REVERT: A 312 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: A 402 VAL cc_start: 0.7846 (t) cc_final: 0.7565 (t) REVERT: B 312 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7103 (mt-10) REVERT: B 402 VAL cc_start: 0.7844 (t) cc_final: 0.7555 (t) REVERT: C 312 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7101 (mt-10) REVERT: C 402 VAL cc_start: 0.7847 (t) cc_final: 0.7565 (t) REVERT: D 312 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7105 (mt-10) REVERT: D 402 VAL cc_start: 0.7862 (t) cc_final: 0.7580 (t) outliers start: 16 outliers final: 8 residues processed: 120 average time/residue: 1.2733 time to fit residues: 169.0965 Evaluate side-chains 124 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 4.9990 chunk 77 optimal weight: 0.3980 chunk 113 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 157 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.8359 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14724 Z= 0.229 Angle : 0.549 5.759 20148 Z= 0.285 Chirality : 0.045 0.144 2036 Planarity : 0.005 0.043 2548 Dihedral : 4.395 17.755 1940 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.07 % Allowed : 12.80 % Favored : 86.13 % 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: 0.45 (0.21), residues: 1716 helix: 1.51 (0.23), residues: 540 sheet: -0.16 (0.28), residues: 288 loop : -0.24 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 243 HIS 0.002 0.001 HIS B 156 PHE 0.015 0.002 PHE B 240 TYR 0.013 0.001 TYR D 126 ARG 0.001 0.000 ARG D 259 ********************** 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 128 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.646 Fit side-chains REVERT: A 312 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7127 (mt-10) REVERT: A 402 VAL cc_start: 0.7852 (t) cc_final: 0.7570 (t) REVERT: B 312 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7128 (mt-10) REVERT: B 402 VAL cc_start: 0.7847 (t) cc_final: 0.7571 (t) REVERT: C 312 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7127 (mt-10) REVERT: C 402 VAL cc_start: 0.7850 (t) cc_final: 0.7569 (t) REVERT: D 312 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7129 (mt-10) REVERT: D 402 VAL cc_start: 0.7843 (t) cc_final: 0.7566 (t) outliers start: 16 outliers final: 8 residues processed: 120 average time/residue: 1.2806 time to fit residues: 169.9802 Evaluate side-chains 124 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.5015 > 50: distance: 43 - 73: 12.639 distance: 57 - 81: 28.347 distance: 68 - 73: 12.923 distance: 73 - 74: 10.836 distance: 74 - 75: 23.564 distance: 74 - 77: 31.348 distance: 75 - 76: 22.399 distance: 75 - 81: 34.172 distance: 77 - 78: 10.110 distance: 78 - 79: 11.583 distance: 78 - 80: 10.101 distance: 81 - 82: 43.072 distance: 82 - 83: 16.380 distance: 83 - 84: 31.274 distance: 83 - 85: 20.709 distance: 85 - 86: 5.491 distance: 86 - 87: 34.043 distance: 86 - 89: 26.205 distance: 87 - 88: 14.993 distance: 87 - 94: 19.059 distance: 89 - 90: 26.835 distance: 90 - 91: 7.119 distance: 91 - 92: 22.313 distance: 91 - 93: 15.771 distance: 94 - 95: 17.189 distance: 95 - 96: 31.079 distance: 95 - 98: 23.563 distance: 96 - 97: 16.976 distance: 96 - 99: 18.869 distance: 99 - 100: 22.533 distance: 100 - 101: 36.834 distance: 100 - 103: 34.203 distance: 101 - 102: 40.618 distance: 101 - 107: 40.474 distance: 103 - 104: 35.170 distance: 103 - 105: 9.386 distance: 104 - 106: 4.536 distance: 107 - 108: 42.801 distance: 108 - 109: 35.945 distance: 108 - 111: 38.098 distance: 109 - 110: 11.683 distance: 109 - 119: 36.144 distance: 111 - 112: 44.626 distance: 112 - 113: 38.754 distance: 112 - 114: 26.325 distance: 113 - 115: 23.956 distance: 114 - 116: 6.332 distance: 115 - 117: 25.627 distance: 116 - 117: 22.827 distance: 117 - 118: 7.133 distance: 119 - 120: 37.111 distance: 120 - 121: 22.528 distance: 120 - 123: 9.646 distance: 121 - 122: 13.147 distance: 121 - 124: 19.453 distance: 124 - 125: 18.479 distance: 125 - 126: 25.429 distance: 125 - 128: 19.686 distance: 126 - 127: 57.654 distance: 126 - 130: 18.639 distance: 128 - 129: 28.845 distance: 130 - 131: 27.611 distance: 130 - 166: 25.191 distance: 131 - 132: 33.304 distance: 131 - 134: 28.089 distance: 132 - 133: 43.627 distance: 132 - 139: 30.606 distance: 133 - 163: 24.845 distance: 134 - 135: 21.038 distance: 135 - 136: 20.481 distance: 136 - 137: 32.197 distance: 137 - 138: 24.592 distance: 139 - 140: 34.366 distance: 139 - 145: 16.442 distance: 140 - 141: 29.016 distance: 140 - 143: 35.890 distance: 141 - 142: 34.723 distance: 141 - 146: 22.596 distance: 143 - 144: 29.557 distance: 144 - 145: 22.177