Starting phenix.real_space_refine on Sun Mar 17 13:26:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdg_33147/03_2024/7xdg_33147_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdg_33147/03_2024/7xdg_33147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdg_33147/03_2024/7xdg_33147.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdg_33147/03_2024/7xdg_33147.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdg_33147/03_2024/7xdg_33147_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdg_33147/03_2024/7xdg_33147_updated.pdb" } resolution = 2.84 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= 0.002 sd= 0.064 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 92 5.16 5 C 11364 2.51 5 N 3020 2.21 5 O 3344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 91": "NH1" <-> "NH2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A ARG 197": "NH1" <-> "NH2" Residue "A TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A ASP 278": "OD1" <-> "OD2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 484": "NH1" <-> "NH2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A GLU 555": "OE1" <-> "OE2" Residue "A ARG 556": "NH1" <-> "NH2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B ASP 278": "OD1" <-> "OD2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B ARG 397": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B ARG 484": "NH1" <-> "NH2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B ARG 556": "NH1" <-> "NH2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C ASP 278": "OD1" <-> "OD2" Residue "C GLU 378": "OE1" <-> "OE2" Residue "C ARG 397": "NH1" <-> "NH2" Residue "C ARG 405": "NH1" <-> "NH2" Residue "C ARG 484": "NH1" <-> "NH2" Residue "C GLU 506": "OE1" <-> "OE2" Residue "C GLU 555": "OE1" <-> "OE2" Residue "C ARG 556": "NH1" <-> "NH2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D GLU 152": "OE1" <-> "OE2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D ASP 278": "OD1" <-> "OD2" Residue "D GLU 378": "OE1" <-> "OE2" Residue "D ARG 397": "NH1" <-> "NH2" Residue "D ARG 405": "NH1" <-> "NH2" Residue "D ARG 484": "NH1" <-> "NH2" Residue "D GLU 506": "OE1" <-> "OE2" Residue "D GLU 555": "OE1" <-> "OE2" Residue "D ARG 556": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17836 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4350 Classifications: {'peptide': 551} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 519} Chain: "B" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4350 Classifications: {'peptide': 551} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 519} Chain: "C" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4350 Classifications: {'peptide': 551} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 519} Chain: "D" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4350 Classifications: {'peptide': 551} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 519} Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 109 Unusual residues: {'D5S': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 109 Unusual residues: {'D5S': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 109 Unusual residues: {'D5S': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 109 Unusual residues: {'D5S': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.15, per 1000 atoms: 0.51 Number of scatterers: 17836 At special positions: 0 Unit cell: (81.18, 135.3, 133.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 16 15.00 O 3344 8.00 N 3020 7.00 C 11364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 6.92 Conformation dependent library (CDL) restraints added in 3.2 seconds 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4088 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 8 sheets defined 47.0% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 42 through 48 Processing helix chain 'A' and resid 61 through 74 Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 93 through 102 Processing helix chain 'A' and resid 104 through 111 Proline residue: A 109 - end of helix Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 143 through 149 Processing helix chain 'A' and resid 173 through 189 removed outlier: 3.686A pdb=" N GLY A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY A 178 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Proline residue: A 180 - end of helix Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 229 through 246 Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 281 through 297 Processing helix chain 'A' and resid 314 through 330 removed outlier: 3.694A pdb=" N ASN A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.621A pdb=" N LYS A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 384 Processing helix chain 'A' and resid 401 through 410 Processing helix chain 'A' and resid 430 through 436 Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 471 through 481 Processing helix chain 'A' and resid 489 through 500 Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 516 through 536 removed outlier: 3.594A pdb=" N ILE A 519 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLN A 520 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 521 " --> pdb=" O ASN A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 556 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 42 through 48 Processing helix chain 'B' and resid 61 through 74 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 93 through 102 Processing helix chain 'B' and resid 104 through 111 Proline residue: B 109 - end of helix Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 137 through 139 No H-bonds generated for 'chain 'B' and resid 137 through 139' Processing helix chain 'B' and resid 143 through 149 Processing helix chain 'B' and resid 173 through 189 removed outlier: 3.685A pdb=" N GLY B 176 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY B 178 " --> pdb=" O TYR B 175 " (cutoff:3.500A) Proline residue: B 180 - end of helix Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 229 through 246 Processing helix chain 'B' and resid 259 through 269 Processing helix chain 'B' and resid 281 through 297 Processing helix chain 'B' and resid 314 through 330 removed outlier: 3.694A pdb=" N ASN B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.622A pdb=" N LYS B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 384 Processing helix chain 'B' and resid 401 through 410 Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 471 through 481 Processing helix chain 'B' and resid 489 through 500 Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 516 through 536 removed outlier: 3.594A pdb=" N ILE B 519 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLN B 520 " --> pdb=" O ALA B 517 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B 521 " --> pdb=" O ASN B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 556 Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 42 through 48 Processing helix chain 'C' and resid 61 through 74 Processing helix chain 'C' and resid 78 through 91 Processing helix chain 'C' and resid 93 through 102 Processing helix chain 'C' and resid 104 through 111 Proline residue: C 109 - end of helix Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 137 through 139 No H-bonds generated for 'chain 'C' and resid 137 through 139' Processing helix chain 'C' and resid 143 through 149 Processing helix chain 'C' and resid 173 through 189 removed outlier: 3.685A pdb=" N GLY C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY C 178 " --> pdb=" O TYR C 175 " (cutoff:3.500A) Proline residue: C 180 - end of helix Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 229 through 246 Processing helix chain 'C' and resid 259 through 269 Processing helix chain 'C' and resid 281 through 297 Processing helix chain 'C' and resid 314 through 330 removed outlier: 3.695A pdb=" N ASN C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.621A pdb=" N LYS C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 384 Processing helix chain 'C' and resid 401 through 410 Processing helix chain 'C' and resid 430 through 436 Processing helix chain 'C' and resid 467 through 469 No H-bonds generated for 'chain 'C' and resid 467 through 469' Processing helix chain 'C' and resid 471 through 481 Processing helix chain 'C' and resid 489 through 500 Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 516 through 536 removed outlier: 3.594A pdb=" N ILE C 519 " --> pdb=" O LEU C 516 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLN C 520 " --> pdb=" O ALA C 517 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU C 521 " --> pdb=" O ASN C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 556 Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 42 through 48 Processing helix chain 'D' and resid 61 through 74 Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 93 through 102 Processing helix chain 'D' and resid 104 through 111 Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 115 through 123 Processing helix chain 'D' and resid 137 through 139 No H-bonds generated for 'chain 'D' and resid 137 through 139' Processing helix chain 'D' and resid 143 through 149 Processing helix chain 'D' and resid 173 through 189 removed outlier: 3.685A pdb=" N GLY D 176 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY D 178 " --> pdb=" O TYR D 175 " (cutoff:3.500A) Proline residue: D 180 - end of helix Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 210 through 214 Processing helix chain 'D' and resid 229 through 246 Processing helix chain 'D' and resid 259 through 269 Processing helix chain 'D' and resid 281 through 297 Processing helix chain 'D' and resid 314 through 330 removed outlier: 3.694A pdb=" N ASN D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 340 removed outlier: 3.622A pdb=" N LYS D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 384 Processing helix chain 'D' and resid 401 through 410 Processing helix chain 'D' and resid 430 through 436 Processing helix chain 'D' and resid 467 through 469 No H-bonds generated for 'chain 'D' and resid 467 through 469' Processing helix chain 'D' and resid 471 through 481 Processing helix chain 'D' and resid 489 through 500 Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'D' and resid 516 through 536 removed outlier: 3.595A pdb=" N ILE D 519 " --> pdb=" O LEU D 516 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLN D 520 " --> pdb=" O ALA D 517 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU D 521 " --> pdb=" O ASN D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 556 Processing sheet with id= A, first strand: chain 'A' and resid 133 through 136 removed outlier: 6.747A pdb=" N ALA A 157 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL A 201 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL A 159 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE A 203 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR A 161 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU A 251 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL A 160 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLN A 253 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 341 through 343 removed outlier: 6.540A pdb=" N ILE A 307 " --> pdb=" O TRP A 342 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N THR A 388 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A 415 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N GLY A 391 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N PHE A 417 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU A 442 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ALA A 418 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA A 444 " --> pdb=" O ALA A 418 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 133 through 136 removed outlier: 6.747A pdb=" N ALA B 157 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL B 201 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL B 159 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE B 203 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N THR B 161 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU B 251 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL B 160 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLN B 253 " --> pdb=" O VAL B 160 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 341 through 343 removed outlier: 6.541A pdb=" N ILE B 307 " --> pdb=" O TRP B 342 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR B 388 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL B 415 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N GLY B 391 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N PHE B 417 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU B 442 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ALA B 418 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 444 " --> pdb=" O ALA B 418 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 133 through 136 removed outlier: 6.747A pdb=" N ALA C 157 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL C 201 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL C 159 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE C 203 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR C 161 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU C 251 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL C 160 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLN C 253 " --> pdb=" O VAL C 160 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 341 through 343 removed outlier: 6.540A pdb=" N ILE C 307 " --> pdb=" O TRP C 342 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR C 388 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 415 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N GLY C 391 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N PHE C 417 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU C 442 " --> pdb=" O ILE C 416 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ALA C 418 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA C 444 " --> pdb=" O ALA C 418 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 133 through 136 removed outlier: 6.747A pdb=" N ALA D 157 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL D 201 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL D 159 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE D 203 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR D 161 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU D 251 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL D 160 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLN D 253 " --> pdb=" O VAL D 160 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 341 through 343 removed outlier: 6.541A pdb=" N ILE D 307 " --> pdb=" O TRP D 342 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR D 388 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL D 415 " --> pdb=" O ILE D 389 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N GLY D 391 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N PHE D 417 " --> pdb=" O GLY D 391 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU D 442 " --> pdb=" O ILE D 416 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ALA D 418 " --> pdb=" O LEU D 442 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA D 444 " --> pdb=" O ALA D 418 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 608 hydrogen bonds defined for protein. 1488 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: 5.01 Time building geometry restraints manager: 7.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2948 1.31 - 1.43: 4749 1.43 - 1.56: 10331 1.56 - 1.68: 72 1.68 - 1.81: 148 Bond restraints: 18248 Sorted by residual: bond pdb=" C2D NAD B 601 " pdb=" C3D NAD B 601 " ideal model delta sigma weight residual 1.531 1.233 0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" C2D NAD C 601 " pdb=" C3D NAD C 601 " ideal model delta sigma weight residual 1.531 1.233 0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" C2D NAD D 601 " pdb=" C3D NAD D 601 " ideal model delta sigma weight residual 1.531 1.233 0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" C2D NAD A 601 " pdb=" C3D NAD A 601 " ideal model delta sigma weight residual 1.531 1.233 0.298 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C2D NAD B 602 " pdb=" C3D NAD B 602 " ideal model delta sigma weight residual 1.531 1.242 0.289 2.00e-02 2.50e+03 2.08e+02 ... (remaining 18243 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.35: 456 105.35 - 112.51: 9471 112.51 - 119.67: 5652 119.67 - 126.83: 8977 126.83 - 133.99: 224 Bond angle restraints: 24780 Sorted by residual: angle pdb=" O1A NAD C 601 " pdb=" PA NAD C 601 " pdb=" O2A NAD C 601 " ideal model delta sigma weight residual 122.64 109.18 13.46 3.00e+00 1.11e-01 2.01e+01 angle pdb=" O1A NAD B 601 " pdb=" PA NAD B 601 " pdb=" O2A NAD B 601 " ideal model delta sigma weight residual 122.64 109.21 13.43 3.00e+00 1.11e-01 2.00e+01 angle pdb=" O1A NAD A 601 " pdb=" PA NAD A 601 " pdb=" O2A NAD A 601 " ideal model delta sigma weight residual 122.64 109.21 13.43 3.00e+00 1.11e-01 2.00e+01 angle pdb=" O1A NAD D 601 " pdb=" PA NAD D 601 " pdb=" O2A NAD D 601 " ideal model delta sigma weight residual 122.64 109.22 13.42 3.00e+00 1.11e-01 2.00e+01 angle pdb=" O1A NAD A 602 " pdb=" PA NAD A 602 " pdb=" O2A NAD A 602 " ideal model delta sigma weight residual 122.64 109.53 13.11 3.00e+00 1.11e-01 1.91e+01 ... (remaining 24775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 10017 15.07 - 30.14: 947 30.14 - 45.22: 220 45.22 - 60.29: 76 60.29 - 75.36: 20 Dihedral angle restraints: 11280 sinusoidal: 4896 harmonic: 6384 Sorted by residual: dihedral pdb=" CA ASP A 256 " pdb=" C ASP A 256 " pdb=" N PHE A 257 " pdb=" CA PHE A 257 " ideal model delta harmonic sigma weight residual 180.00 161.67 18.33 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA ASP D 256 " pdb=" C ASP D 256 " pdb=" N PHE D 257 " pdb=" CA PHE D 257 " ideal model delta harmonic sigma weight residual 180.00 161.70 18.30 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA ASP B 256 " pdb=" C ASP B 256 " pdb=" N PHE B 257 " pdb=" CA PHE B 257 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 11277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2434 0.070 - 0.140: 258 0.140 - 0.210: 28 0.210 - 0.280: 4 0.280 - 0.350: 8 Chirality restraints: 2732 Sorted by residual: chirality pdb=" C3D NAD C 602 " pdb=" C2D NAD C 602 " pdb=" C4D NAD C 602 " pdb=" O3D NAD C 602 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" C3D NAD B 602 " pdb=" C2D NAD B 602 " pdb=" C4D NAD B 602 " pdb=" O3D NAD B 602 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" C3D NAD D 602 " pdb=" C2D NAD D 602 " pdb=" C4D NAD D 602 " pdb=" O3D NAD D 602 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 2729 not shown) Planarity restraints: 3164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 527 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" C ALA A 527 " -0.028 2.00e-02 2.50e+03 pdb=" O ALA A 527 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 528 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 529 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C LYS B 529 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS B 529 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL B 530 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 529 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C LYS C 529 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS C 529 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL C 530 " 0.009 2.00e-02 2.50e+03 ... (remaining 3161 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 626 2.71 - 3.26: 18525 3.26 - 3.80: 29411 3.80 - 4.35: 38266 4.35 - 4.90: 64854 Nonbonded interactions: 151682 Sorted by model distance: nonbonded pdb=" OE2 GLU B 59 " pdb=" NH2 ARG B 67 " model vdw 2.160 2.520 nonbonded pdb=" OH TYR C 187 " pdb=" OE1 GLN C 253 " model vdw 2.168 2.440 nonbonded pdb=" OH TYR B 187 " pdb=" OE1 GLN B 253 " model vdw 2.168 2.440 nonbonded pdb=" OH TYR A 187 " pdb=" OE1 GLN A 253 " model vdw 2.168 2.440 nonbonded pdb=" OH TYR D 187 " pdb=" OE1 GLN D 253 " model vdw 2.168 2.440 ... (remaining 151677 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=0.00 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: 3.840 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: 12.540 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 47.050 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.100 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:10.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.298 18248 Z= 0.920 Angle : 0.908 13.460 24780 Z= 0.432 Chirality : 0.048 0.350 2732 Planarity : 0.004 0.033 3164 Dihedral : 13.272 75.361 7192 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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 (0.17), residues: 2196 helix: 0.67 (0.15), residues: 1036 sheet: 0.26 (0.41), residues: 184 loop : -0.04 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 342 HIS 0.003 0.001 HIS B 305 PHE 0.021 0.002 PHE C 471 TYR 0.014 0.001 TYR C 552 ARG 0.006 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.208 Fit side-chains REVERT: A 248 ARG cc_start: 0.8128 (tpt170) cc_final: 0.7616 (mmm160) REVERT: A 336 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7004 (tp30) REVERT: A 405 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7461 (mtm180) REVERT: A 539 MET cc_start: 0.8286 (mtp) cc_final: 0.8063 (mtm) REVERT: B 248 ARG cc_start: 0.8113 (tpt170) cc_final: 0.7611 (mmm160) REVERT: B 336 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7004 (tp30) REVERT: B 405 ARG cc_start: 0.7796 (mtm-85) cc_final: 0.7507 (mtm180) REVERT: B 539 MET cc_start: 0.8293 (mtp) cc_final: 0.8057 (mtm) REVERT: C 248 ARG cc_start: 0.8115 (tpt170) cc_final: 0.7620 (mmm160) REVERT: C 336 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7002 (tp30) REVERT: C 405 ARG cc_start: 0.7774 (mtm-85) cc_final: 0.7487 (mtm180) REVERT: C 539 MET cc_start: 0.8297 (mtp) cc_final: 0.8072 (mtm) REVERT: D 248 ARG cc_start: 0.8114 (tpt170) cc_final: 0.7611 (mmm160) REVERT: D 336 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6993 (tp30) REVERT: D 405 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7484 (mtm180) REVERT: D 539 MET cc_start: 0.8296 (mtp) cc_final: 0.8055 (mtm) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 1.2361 time to fit residues: 258.0515 Evaluate side-chains 133 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 104 optimal weight: 0.2980 chunk 128 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN B 43 GLN C 43 GLN D 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.0655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18248 Z= 0.188 Angle : 0.493 5.800 24780 Z= 0.251 Chirality : 0.041 0.194 2732 Planarity : 0.004 0.040 3164 Dihedral : 8.930 52.007 2908 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.12 % Allowed : 4.66 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 0.77 (0.17), residues: 2196 helix: 0.95 (0.16), residues: 1036 sheet: 0.29 (0.41), residues: 184 loop : 0.24 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 558 HIS 0.004 0.001 HIS B 485 PHE 0.018 0.001 PHE D 471 TYR 0.010 0.001 TYR C 552 ARG 0.002 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 1.850 Fit side-chains REVERT: A 248 ARG cc_start: 0.8121 (tpt170) cc_final: 0.7623 (mmm160) REVERT: A 336 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7106 (tp30) REVERT: A 405 ARG cc_start: 0.7898 (mtm-85) cc_final: 0.7427 (mtm-85) REVERT: B 248 ARG cc_start: 0.8130 (tpt170) cc_final: 0.7632 (mmm160) REVERT: B 336 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7061 (tp30) REVERT: B 405 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7470 (mtm-85) REVERT: C 248 ARG cc_start: 0.8126 (tpt170) cc_final: 0.7636 (mmm160) REVERT: C 336 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7060 (tp30) REVERT: C 405 ARG cc_start: 0.7881 (mtm-85) cc_final: 0.7509 (mtm180) REVERT: C 539 MET cc_start: 0.8359 (mtp) cc_final: 0.8045 (mtm) REVERT: D 248 ARG cc_start: 0.8129 (tpt170) cc_final: 0.7632 (mmm160) REVERT: D 336 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7055 (tp30) REVERT: D 405 ARG cc_start: 0.7887 (mtm-85) cc_final: 0.7464 (mtm-85) REVERT: D 539 MET cc_start: 0.8352 (mtp) cc_final: 0.8039 (mtm) outliers start: 21 outliers final: 8 residues processed: 160 average time/residue: 1.2516 time to fit residues: 225.8784 Evaluate side-chains 148 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 504 ASP Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 504 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 166 optimal weight: 0.3980 chunk 136 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 200 optimal weight: 0.0270 chunk 216 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN D 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18248 Z= 0.167 Angle : 0.462 5.846 24780 Z= 0.236 Chirality : 0.040 0.190 2732 Planarity : 0.004 0.031 3164 Dihedral : 7.907 54.768 2908 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.23 % Allowed : 7.12 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 0.89 (0.18), residues: 2196 helix: 1.06 (0.16), residues: 1036 sheet: 0.35 (0.41), residues: 184 loop : 0.29 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 558 HIS 0.003 0.001 HIS C 485 PHE 0.018 0.001 PHE B 471 TYR 0.009 0.001 TYR B 552 ARG 0.002 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 1.911 Fit side-chains REVERT: A 38 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8469 (mtt) REVERT: A 248 ARG cc_start: 0.8113 (tpt170) cc_final: 0.7577 (mmm160) REVERT: A 336 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7104 (tp30) REVERT: A 405 ARG cc_start: 0.7873 (mtm-85) cc_final: 0.7490 (mtm-85) REVERT: A 539 MET cc_start: 0.8213 (mtm) cc_final: 0.8012 (mtm) REVERT: B 219 MET cc_start: 0.7535 (mtm) cc_final: 0.7174 (mtm) REVERT: B 248 ARG cc_start: 0.8105 (tpt170) cc_final: 0.7584 (mmm160) REVERT: B 336 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7093 (tp30) REVERT: B 405 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7416 (mtm-85) REVERT: B 539 MET cc_start: 0.8202 (mtm) cc_final: 0.7998 (mtm) REVERT: C 38 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8467 (mtm) REVERT: C 248 ARG cc_start: 0.8113 (tpt170) cc_final: 0.7589 (mmm160) REVERT: C 336 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7104 (tp30) REVERT: C 405 ARG cc_start: 0.7866 (mtm-85) cc_final: 0.7497 (mtm-85) REVERT: D 38 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8380 (mtm) REVERT: D 219 MET cc_start: 0.7536 (mtm) cc_final: 0.7289 (mtm) REVERT: D 248 ARG cc_start: 0.8106 (tpt170) cc_final: 0.7583 (mmm160) REVERT: D 336 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7101 (tp30) REVERT: D 405 ARG cc_start: 0.7857 (mtm-85) cc_final: 0.7409 (mtm-85) outliers start: 23 outliers final: 12 residues processed: 173 average time/residue: 1.2286 time to fit residues: 239.9139 Evaluate side-chains 155 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 504 ASP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain D residue 504 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 134 optimal weight: 0.0870 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 chunk 104 optimal weight: 0.0270 chunk 190 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.4020 ------------------------------------------------------------------------------- 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: 0.7825 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18248 Z= 0.291 Angle : 0.511 6.879 24780 Z= 0.261 Chirality : 0.042 0.208 2732 Planarity : 0.004 0.030 3164 Dihedral : 7.601 55.862 2908 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.34 % Allowed : 8.67 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 0.71 (0.17), residues: 2196 helix: 0.94 (0.16), residues: 1036 sheet: 0.19 (0.41), residues: 184 loop : 0.17 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 558 HIS 0.002 0.001 HIS A 125 PHE 0.022 0.002 PHE B 471 TYR 0.015 0.001 TYR D 552 ARG 0.002 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 2.117 Fit side-chains REVERT: A 125 HIS cc_start: 0.7465 (t-90) cc_final: 0.7255 (t-90) REVERT: A 248 ARG cc_start: 0.8141 (tpt170) cc_final: 0.7588 (mmm160) REVERT: A 336 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7112 (tp30) REVERT: A 405 ARG cc_start: 0.7873 (mtm-85) cc_final: 0.7320 (mtm-85) REVERT: B 248 ARG cc_start: 0.8145 (tpt170) cc_final: 0.7592 (mmm160) REVERT: B 336 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7117 (tp30) REVERT: B 405 ARG cc_start: 0.7873 (mtm-85) cc_final: 0.7362 (mtm-85) REVERT: C 248 ARG cc_start: 0.8142 (tpt170) cc_final: 0.7597 (mmm160) REVERT: C 336 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7116 (tp30) REVERT: C 405 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7359 (mtm-85) REVERT: D 248 ARG cc_start: 0.8146 (tpt170) cc_final: 0.7593 (mmm160) REVERT: D 336 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7121 (tp30) REVERT: D 405 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7360 (mtm-85) outliers start: 25 outliers final: 15 residues processed: 167 average time/residue: 1.2509 time to fit residues: 236.1332 Evaluate side-chains 156 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 504 ASP Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain D residue 504 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 3 optimal weight: 0.0270 chunk 158 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 181 optimal weight: 0.6980 chunk 146 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN C 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18248 Z= 0.170 Angle : 0.452 5.968 24780 Z= 0.233 Chirality : 0.040 0.189 2732 Planarity : 0.004 0.033 3164 Dihedral : 7.338 59.121 2908 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.12 % Allowed : 10.22 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 0.82 (0.18), residues: 2196 helix: 1.04 (0.16), residues: 1036 sheet: 0.18 (0.41), residues: 184 loop : 0.23 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 558 HIS 0.002 0.001 HIS C 485 PHE 0.018 0.001 PHE B 471 TYR 0.009 0.001 TYR D 552 ARG 0.002 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 1.683 Fit side-chains REVERT: A 248 ARG cc_start: 0.8101 (tpt170) cc_final: 0.7573 (mmm160) REVERT: A 336 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7065 (tp30) REVERT: A 405 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7377 (mtm-85) REVERT: B 248 ARG cc_start: 0.8095 (tpt170) cc_final: 0.7582 (mmm160) REVERT: B 336 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7085 (tp30) REVERT: B 405 ARG cc_start: 0.7878 (mtm-85) cc_final: 0.7393 (mtm-85) REVERT: C 248 ARG cc_start: 0.8090 (tpt170) cc_final: 0.7584 (mmm160) REVERT: C 336 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7086 (tp30) REVERT: C 405 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7366 (mtm-85) REVERT: D 248 ARG cc_start: 0.8095 (tpt170) cc_final: 0.7582 (mmm160) REVERT: D 336 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7049 (tp30) REVERT: D 405 ARG cc_start: 0.7852 (mtm-85) cc_final: 0.7367 (mtm-85) outliers start: 21 outliers final: 15 residues processed: 160 average time/residue: 1.3031 time to fit residues: 234.6673 Evaluate side-chains 153 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 504 ASP Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain D residue 504 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 212 optimal weight: 0.7980 chunk 176 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.7818 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18248 Z= 0.259 Angle : 0.486 6.317 24780 Z= 0.249 Chirality : 0.041 0.204 2732 Planarity : 0.004 0.032 3164 Dihedral : 7.219 59.510 2908 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.45 % Allowed : 10.76 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 0.69 (0.17), residues: 2196 helix: 0.93 (0.16), residues: 1036 sheet: 0.07 (0.41), residues: 184 loop : 0.18 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 558 HIS 0.002 0.001 HIS A 69 PHE 0.021 0.002 PHE B 471 TYR 0.013 0.001 TYR A 552 ARG 0.002 0.000 ARG D 270 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 ARG cc_start: 0.8088 (tpt170) cc_final: 0.7637 (mmm160) REVERT: B 239 MET cc_start: 0.7670 (mmm) cc_final: 0.7460 (mtm) REVERT: B 248 ARG cc_start: 0.8095 (tpt170) cc_final: 0.7638 (mmm160) REVERT: C 239 MET cc_start: 0.7672 (mmm) cc_final: 0.7460 (mtm) REVERT: C 248 ARG cc_start: 0.8090 (tpt170) cc_final: 0.7640 (mmm160) REVERT: D 239 MET cc_start: 0.7677 (mmm) cc_final: 0.7465 (mtm) REVERT: D 248 ARG cc_start: 0.8099 (tpt170) cc_final: 0.7641 (mmm160) outliers start: 27 outliers final: 18 residues processed: 158 average time/residue: 1.2236 time to fit residues: 220.0535 Evaluate side-chains 150 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 504 ASP Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain D residue 504 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 120 optimal weight: 0.5980 chunk 179 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 212 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 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: 0.7793 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18248 Z= 0.177 Angle : 0.458 5.981 24780 Z= 0.234 Chirality : 0.040 0.191 2732 Planarity : 0.004 0.032 3164 Dihedral : 7.033 59.022 2908 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.66 % Allowed : 10.60 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 0.77 (0.18), residues: 2196 helix: 1.03 (0.16), residues: 1036 sheet: 0.11 (0.41), residues: 184 loop : 0.18 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 558 HIS 0.002 0.001 HIS C 485 PHE 0.019 0.001 PHE D 471 TYR 0.009 0.001 TYR D 552 ARG 0.001 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 ARG cc_start: 0.8081 (tpt170) cc_final: 0.7631 (mmm160) REVERT: A 405 ARG cc_start: 0.7917 (mtm-85) cc_final: 0.7324 (mtm-85) REVERT: B 248 ARG cc_start: 0.8087 (tpt170) cc_final: 0.7644 (mmm160) REVERT: C 248 ARG cc_start: 0.8081 (tpt170) cc_final: 0.7644 (mmm160) REVERT: D 248 ARG cc_start: 0.8088 (tpt170) cc_final: 0.7644 (mmm160) outliers start: 31 outliers final: 19 residues processed: 157 average time/residue: 1.2043 time to fit residues: 214.9502 Evaluate side-chains 146 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 504 ASP Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain D residue 504 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.4980 chunk 84 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 104 optimal weight: 0.0060 chunk 19 optimal weight: 2.9990 chunk 166 optimal weight: 0.3980 chunk 192 optimal weight: 0.1980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN B 305 HIS B 335 GLN C 335 GLN D 305 HIS D 335 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18248 Z= 0.137 Angle : 0.435 5.955 24780 Z= 0.224 Chirality : 0.039 0.181 2732 Planarity : 0.004 0.031 3164 Dihedral : 6.786 57.426 2908 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.23 % Allowed : 10.92 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 0.85 (0.18), residues: 2196 helix: 1.12 (0.17), residues: 1036 sheet: 0.26 (0.41), residues: 184 loop : 0.15 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 342 HIS 0.002 0.001 HIS D 485 PHE 0.016 0.001 PHE A 471 TYR 0.006 0.001 TYR D 231 ARG 0.001 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 2.146 Fit side-chains REVERT: A 248 ARG cc_start: 0.8074 (tpt170) cc_final: 0.7639 (mmm160) REVERT: A 405 ARG cc_start: 0.7900 (mtm-85) cc_final: 0.7405 (mtm-85) REVERT: B 103 ASP cc_start: 0.7651 (t0) cc_final: 0.7312 (t0) REVERT: B 248 ARG cc_start: 0.8069 (tpt170) cc_final: 0.7638 (mmm160) REVERT: C 248 ARG cc_start: 0.8069 (tpt170) cc_final: 0.7640 (mmm160) REVERT: D 248 ARG cc_start: 0.8070 (tpt170) cc_final: 0.7639 (mmm160) outliers start: 23 outliers final: 18 residues processed: 160 average time/residue: 1.3106 time to fit residues: 236.8024 Evaluate side-chains 141 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 504 ASP Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 467 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 0.8980 chunk 185 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS B 43 GLN B 305 HIS C 305 HIS D 305 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18248 Z= 0.196 Angle : 0.457 5.995 24780 Z= 0.234 Chirality : 0.040 0.193 2732 Planarity : 0.004 0.031 3164 Dihedral : 6.711 57.729 2908 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.28 % Allowed : 11.24 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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 (0.18), residues: 2196 helix: 1.08 (0.16), residues: 1036 sheet: 0.15 (0.41), residues: 184 loop : 0.13 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 558 HIS 0.002 0.001 HIS C 485 PHE 0.019 0.001 PHE D 471 TYR 0.010 0.001 TYR D 552 ARG 0.001 0.000 ARG D 556 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 2.235 Fit side-chains REVERT: A 248 ARG cc_start: 0.8081 (tpt170) cc_final: 0.7646 (mmm160) REVERT: B 248 ARG cc_start: 0.8071 (tpt170) cc_final: 0.7641 (mmm160) REVERT: C 248 ARG cc_start: 0.8069 (tpt170) cc_final: 0.7644 (mmm160) REVERT: D 248 ARG cc_start: 0.8073 (tpt170) cc_final: 0.7642 (mmm160) outliers start: 24 outliers final: 18 residues processed: 147 average time/residue: 1.1749 time to fit residues: 196.9592 Evaluate side-chains 144 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 504 ASP Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 467 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 9.9990 chunk 127 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 145 optimal weight: 0.0070 chunk 219 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS B 305 HIS C 305 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18248 Z= 0.171 Angle : 0.450 5.979 24780 Z= 0.231 Chirality : 0.040 0.189 2732 Planarity : 0.004 0.030 3164 Dihedral : 6.618 57.316 2908 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.07 % Allowed : 11.72 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 0.83 (0.18), residues: 2196 helix: 1.09 (0.17), residues: 1036 sheet: 0.21 (0.41), residues: 184 loop : 0.17 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 342 HIS 0.002 0.001 HIS B 485 PHE 0.018 0.001 PHE A 471 TYR 0.008 0.001 TYR B 552 ARG 0.001 0.000 ARG D 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 2.013 Fit side-chains REVERT: A 248 ARG cc_start: 0.8078 (tpt170) cc_final: 0.7641 (mmm160) REVERT: B 103 ASP cc_start: 0.7653 (t0) cc_final: 0.7312 (t0) REVERT: B 248 ARG cc_start: 0.8067 (tpt170) cc_final: 0.7645 (mmm160) REVERT: C 248 ARG cc_start: 0.8066 (tpt170) cc_final: 0.7643 (mmm160) REVERT: D 248 ARG cc_start: 0.8069 (tpt170) cc_final: 0.7643 (mmm160) outliers start: 20 outliers final: 19 residues processed: 151 average time/residue: 1.1430 time to fit residues: 197.4551 Evaluate side-chains 146 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 504 ASP Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain D residue 504 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 160 optimal weight: 0.4980 chunk 25 optimal weight: 0.0470 chunk 48 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 chunk 73 optimal weight: 0.2980 chunk 179 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS B 335 GLN C 305 HIS C 335 GLN D 335 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.149154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.110699 restraints weight = 21719.557| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.85 r_work: 0.3311 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18248 Z= 0.147 Angle : 0.438 5.960 24780 Z= 0.226 Chirality : 0.039 0.183 2732 Planarity : 0.004 0.030 3164 Dihedral : 6.504 56.763 2908 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.23 % Allowed : 12.21 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 0.87 (0.18), residues: 2196 helix: 1.14 (0.17), residues: 1036 sheet: 0.26 (0.41), residues: 184 loop : 0.16 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 342 HIS 0.002 0.001 HIS C 305 PHE 0.017 0.001 PHE A 471 TYR 0.008 0.001 TYR C 123 ARG 0.001 0.000 ARG D 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4995.37 seconds wall clock time: 89 minutes 51.97 seconds (5391.97 seconds total)