Starting phenix.real_space_refine on Mon Mar 18 07:12:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q12_13752/03_2024/7q12_13752_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q12_13752/03_2024/7q12_13752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q12_13752/03_2024/7q12_13752.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q12_13752/03_2024/7q12_13752.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q12_13752/03_2024/7q12_13752_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q12_13752/03_2024/7q12_13752_updated.pdb" } resolution = 3.7 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 108 5.16 5 C 12956 2.51 5 N 3504 2.21 5 O 3672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20244 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4774 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 590, 4758 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Conformer: "B" Number of residues, atoms: 590, 4758 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 bond proxies already assigned to first conformer: 4866 Chain: "E" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 271 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 271 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 271 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 271 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 4774 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 590, 4758 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Conformer: "B" Number of residues, atoms: 590, 4758 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 bond proxies already assigned to first conformer: 4866 Chain: "C" Number of atoms: 4774 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 590, 4758 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Conformer: "B" Number of residues, atoms: 590, 4758 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 bond proxies already assigned to first conformer: 4866 Chain: "D" Number of atoms: 4774 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 590, 4758 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Conformer: "B" Number of residues, atoms: 590, 4758 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 bond proxies already assigned to first conformer: 4866 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.92, per 1000 atoms: 0.89 Number of scatterers: 20244 At special positions: 0 Unit cell: (131.406, 127.062, 131.406, 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 108 16.00 P 4 15.00 O 3672 8.00 N 3504 7.00 C 12956 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: 7.21 Conformation dependent library (CDL) restraints added in 6.1 seconds 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4672 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 12 sheets defined 47.4% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.32 Creating SS restraints... Processing helix chain 'A' and resid 43 through 58 removed outlier: 4.256A pdb=" N LYS A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 89 through 96 Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 146 through 168 Processing helix chain 'A' and resid 184 through 193 removed outlier: 4.068A pdb=" N GLY A 187 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N CYS A 189 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.725A pdb=" N TYR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 290 through 312 removed outlier: 3.997A pdb=" N PHE A 293 " --> pdb=" O MET A 290 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 296 " --> pdb=" O PHE A 293 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN A 299 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER A 300 " --> pdb=" O HIS A 297 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A 301 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU A 306 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG A 309 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 322 No H-bonds generated for 'chain 'A' and resid 320 through 322' Processing helix chain 'A' and resid 339 through 353 Processing helix chain 'A' and resid 377 through 410 Processing helix chain 'A' and resid 424 through 435 Processing helix chain 'A' and resid 455 through 463 Processing helix chain 'A' and resid 493 through 499 Processing helix chain 'A' and resid 515 through 522 Processing helix chain 'A' and resid 533 through 539 Processing helix chain 'A' and resid 560 through 576 Processing helix chain 'A' and resid 579 through 596 removed outlier: 3.650A pdb=" N ARG A 591 " --> pdb=" O ASN A 587 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER A 593 " --> pdb=" O THR A 589 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASP A 594 " --> pdb=" O GLU A 590 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 616 removed outlier: 5.256A pdb=" N ARG A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TYR A 604 " --> pdb=" O TYR A 600 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 321 No H-bonds generated for 'chain 'E' and resid 319 through 321' Processing helix chain 'E' and resid 323 through 325 No H-bonds generated for 'chain 'E' and resid 323 through 325' Processing helix chain 'E' and resid 338 through 348 removed outlier: 4.400A pdb=" N LYS E 344 " --> pdb=" O ASN E 340 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N THR E 347 " --> pdb=" O ARG E 343 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TYR E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 321 No H-bonds generated for 'chain 'F' and resid 319 through 321' Processing helix chain 'F' and resid 323 through 325 No H-bonds generated for 'chain 'F' and resid 323 through 325' Processing helix chain 'F' and resid 338 through 348 removed outlier: 4.400A pdb=" N LYS F 344 " --> pdb=" O ASN F 340 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N THR F 347 " --> pdb=" O ARG F 343 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TYR F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 321 No H-bonds generated for 'chain 'G' and resid 319 through 321' Processing helix chain 'G' and resid 323 through 325 No H-bonds generated for 'chain 'G' and resid 323 through 325' Processing helix chain 'G' and resid 338 through 348 removed outlier: 4.400A pdb=" N LYS G 344 " --> pdb=" O ASN G 340 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N THR G 347 " --> pdb=" O ARG G 343 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TYR G 348 " --> pdb=" O LYS G 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 321 No H-bonds generated for 'chain 'H' and resid 319 through 321' Processing helix chain 'H' and resid 323 through 325 No H-bonds generated for 'chain 'H' and resid 323 through 325' Processing helix chain 'H' and resid 338 through 348 removed outlier: 4.400A pdb=" N LYS H 344 " --> pdb=" O ASN H 340 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N THR H 347 " --> pdb=" O ARG H 343 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR H 348 " --> pdb=" O LYS H 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 58 removed outlier: 4.255A pdb=" N LYS B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 89 through 96 Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'B' and resid 146 through 168 Processing helix chain 'B' and resid 184 through 193 removed outlier: 4.067A pdb=" N GLY B 187 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N CYS B 189 " --> pdb=" O VAL B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 213 removed outlier: 3.726A pdb=" N TYR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 239 through 251 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 290 through 312 removed outlier: 3.997A pdb=" N PHE B 293 " --> pdb=" O MET B 290 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 296 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN B 299 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 300 " --> pdb=" O HIS B 297 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 301 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU B 306 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG B 309 " --> pdb=" O GLU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 322 No H-bonds generated for 'chain 'B' and resid 320 through 322' Processing helix chain 'B' and resid 339 through 353 Processing helix chain 'B' and resid 377 through 410 Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 455 through 463 Processing helix chain 'B' and resid 493 through 499 Processing helix chain 'B' and resid 515 through 522 Processing helix chain 'B' and resid 533 through 539 Processing helix chain 'B' and resid 560 through 576 Processing helix chain 'B' and resid 579 through 596 removed outlier: 3.650A pdb=" N ARG B 591 " --> pdb=" O ASN B 587 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER B 593 " --> pdb=" O THR B 589 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASP B 594 " --> pdb=" O GLU B 590 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 616 removed outlier: 5.257A pdb=" N ARG B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N TYR B 604 " --> pdb=" O TYR B 600 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 58 removed outlier: 4.255A pdb=" N LYS C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 126 through 133 Processing helix chain 'C' and resid 146 through 168 Processing helix chain 'C' and resid 184 through 193 removed outlier: 4.068A pdb=" N GLY C 187 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N CYS C 189 " --> pdb=" O VAL C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 213 removed outlier: 3.725A pdb=" N TYR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 229 through 234 Processing helix chain 'C' and resid 239 through 251 Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 290 through 312 removed outlier: 3.998A pdb=" N PHE C 293 " --> pdb=" O MET C 290 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 296 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN C 299 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER C 300 " --> pdb=" O HIS C 297 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS C 301 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU C 306 " --> pdb=" O ARG C 303 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG C 309 " --> pdb=" O GLU C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 322 No H-bonds generated for 'chain 'C' and resid 320 through 322' Processing helix chain 'C' and resid 339 through 353 Processing helix chain 'C' and resid 377 through 410 Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 455 through 463 Processing helix chain 'C' and resid 493 through 499 Processing helix chain 'C' and resid 515 through 522 Processing helix chain 'C' and resid 533 through 539 Processing helix chain 'C' and resid 560 through 576 Processing helix chain 'C' and resid 579 through 596 removed outlier: 3.650A pdb=" N ARG C 591 " --> pdb=" O ASN C 587 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU C 592 " --> pdb=" O ARG C 588 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER C 593 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASP C 594 " --> pdb=" O GLU C 590 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LEU C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 616 removed outlier: 5.256A pdb=" N ARG C 603 " --> pdb=" O LYS C 599 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TYR C 604 " --> pdb=" O TYR C 600 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 58 removed outlier: 4.257A pdb=" N LYS D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 89 through 96 Processing helix chain 'D' and resid 126 through 133 Processing helix chain 'D' and resid 146 through 168 Processing helix chain 'D' and resid 184 through 193 removed outlier: 4.068A pdb=" N GLY D 187 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N CYS D 189 " --> pdb=" O VAL D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 213 removed outlier: 3.725A pdb=" N TYR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 223 No H-bonds generated for 'chain 'D' and resid 221 through 223' Processing helix chain 'D' and resid 229 through 234 Processing helix chain 'D' and resid 239 through 251 Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 290 through 312 removed outlier: 3.998A pdb=" N PHE D 293 " --> pdb=" O MET D 290 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 296 " --> pdb=" O PHE D 293 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN D 299 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER D 300 " --> pdb=" O HIS D 297 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS D 301 " --> pdb=" O ALA D 298 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU D 306 " --> pdb=" O ARG D 303 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG D 309 " --> pdb=" O GLU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 339 through 353 Processing helix chain 'D' and resid 377 through 410 Processing helix chain 'D' and resid 424 through 435 Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 493 through 499 Processing helix chain 'D' and resid 515 through 522 Processing helix chain 'D' and resid 533 through 539 Processing helix chain 'D' and resid 560 through 576 Processing helix chain 'D' and resid 579 through 596 removed outlier: 3.650A pdb=" N ARG D 591 " --> pdb=" O ASN D 587 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU D 592 " --> pdb=" O ARG D 588 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER D 593 " --> pdb=" O THR D 589 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASP D 594 " --> pdb=" O GLU D 590 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LEU D 595 " --> pdb=" O ARG D 591 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 616 removed outlier: 5.256A pdb=" N ARG D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TYR D 604 " --> pdb=" O TYR D 600 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 254 through 256 removed outlier: 7.740A pdb=" N VAL A 175 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N ILE A 201 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA A 177 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N THR A 203 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE A 179 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N PHE A 30 " --> pdb=" O HIS A 178 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE A 63 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N ALA A 33 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL A 65 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 113 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLY A 66 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL A 115 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR A 68 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU A 117 " --> pdb=" O TYR A 68 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 323 through 328 removed outlier: 6.738A pdb=" N THR A 361 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N PHE A 326 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL A 363 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE A 328 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE A 365 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 502 through 504 Processing sheet with id= D, first strand: chain 'B' and resid 254 through 256 removed outlier: 7.740A pdb=" N VAL B 175 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N ILE B 201 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA B 177 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR B 203 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE B 179 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N PHE B 30 " --> pdb=" O HIS B 178 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE B 63 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N ALA B 33 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL B 65 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 113 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N GLY B 66 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL B 115 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR B 68 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU B 117 " --> pdb=" O TYR B 68 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 323 through 328 removed outlier: 6.738A pdb=" N THR B 361 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N PHE B 326 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL B 363 " --> pdb=" O PHE B 326 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE B 328 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE B 365 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 502 through 504 Processing sheet with id= G, first strand: chain 'C' and resid 254 through 256 removed outlier: 7.741A pdb=" N VAL C 175 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N ILE C 201 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA C 177 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR C 203 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE C 179 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N PHE C 30 " --> pdb=" O HIS C 178 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N PHE C 63 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N ALA C 33 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL C 65 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU C 113 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N GLY C 66 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL C 115 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N TYR C 68 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU C 117 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 323 through 328 removed outlier: 6.738A pdb=" N THR C 361 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N PHE C 326 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL C 363 " --> pdb=" O PHE C 326 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ILE C 328 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE C 365 " --> pdb=" O ILE C 328 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 502 through 504 Processing sheet with id= J, first strand: chain 'D' and resid 254 through 256 removed outlier: 7.740A pdb=" N VAL D 175 " --> pdb=" O ALA D 199 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N ILE D 201 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA D 177 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N THR D 203 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE D 179 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N PHE D 30 " --> pdb=" O HIS D 178 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N PHE D 63 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N ALA D 33 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL D 65 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU D 113 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLY D 66 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL D 115 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR D 68 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU D 117 " --> pdb=" O TYR D 68 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 323 through 328 removed outlier: 6.738A pdb=" N THR D 361 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N PHE D 326 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL D 363 " --> pdb=" O PHE D 326 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE D 328 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE D 365 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 502 through 504 760 hydrogen bonds defined for protein. 2048 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: 6.07 Time building geometry restraints manager: 7.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6568 1.34 - 1.46: 5178 1.46 - 1.58: 8858 1.58 - 1.70: 4 1.70 - 1.81: 164 Bond restraints: 20772 Sorted by residual: bond pdb=" O6 G6P B 801 " pdb=" P G6P B 801 " ideal model delta sigma weight residual 1.722 1.646 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" O6 G6P A 801 " pdb=" P G6P A 801 " ideal model delta sigma weight residual 1.722 1.646 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" O6 G6P D 801 " pdb=" P G6P D 801 " ideal model delta sigma weight residual 1.722 1.646 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" O6 G6P C 801 " pdb=" P G6P C 801 " ideal model delta sigma weight residual 1.722 1.647 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C2 G6P C 801 " pdb=" C3 G6P C 801 " ideal model delta sigma weight residual 1.523 1.461 0.062 2.00e-02 2.50e+03 9.61e+00 ... (remaining 20767 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.65: 507 106.65 - 113.50: 11011 113.50 - 120.35: 7962 120.35 - 127.20: 8421 127.20 - 134.04: 243 Bond angle restraints: 28144 Sorted by residual: angle pdb=" N ILE A 238 " pdb=" CA ILE A 238 " pdb=" C ILE A 238 " ideal model delta sigma weight residual 111.88 107.82 4.06 1.06e+00 8.90e-01 1.47e+01 angle pdb=" N ILE D 238 " pdb=" CA ILE D 238 " pdb=" C ILE D 238 " ideal model delta sigma weight residual 111.88 107.82 4.06 1.06e+00 8.90e-01 1.47e+01 angle pdb=" N ILE C 238 " pdb=" CA ILE C 238 " pdb=" C ILE C 238 " ideal model delta sigma weight residual 111.88 107.83 4.05 1.06e+00 8.90e-01 1.46e+01 angle pdb=" N ILE B 238 " pdb=" CA ILE B 238 " pdb=" C ILE B 238 " ideal model delta sigma weight residual 111.88 107.83 4.05 1.06e+00 8.90e-01 1.46e+01 angle pdb=" C THR A 136 " pdb=" N CYS A 137 " pdb=" CA CYS A 137 " ideal model delta sigma weight residual 121.54 127.81 -6.27 1.91e+00 2.74e-01 1.08e+01 ... (remaining 28139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.43: 11776 28.43 - 56.86: 448 56.86 - 85.29: 36 85.29 - 113.72: 32 113.72 - 142.15: 24 Dihedral angle restraints: 12316 sinusoidal: 5044 harmonic: 7272 Sorted by residual: dihedral pdb=" C3 G6P B 801 " pdb=" C1 G6P B 801 " pdb=" C2 G6P B 801 " pdb=" O1 G6P B 801 " ideal model delta sinusoidal sigma weight residual 74.65 -67.50 142.15 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C3 G6P A 801 " pdb=" C1 G6P A 801 " pdb=" C2 G6P A 801 " pdb=" O1 G6P A 801 " ideal model delta sinusoidal sigma weight residual 74.65 -67.49 142.14 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C3 G6P D 801 " pdb=" C1 G6P D 801 " pdb=" C2 G6P D 801 " pdb=" O1 G6P D 801 " ideal model delta sinusoidal sigma weight residual 74.65 -67.46 142.11 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 12313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.016: 2992 1.016 - 2.033: 0 2.033 - 3.049: 0 3.049 - 4.065: 0 4.065 - 5.081: 16 Chirality restraints: 3008 Sorted by residual: chirality pdb=" C5 G6P B 801 " pdb=" C4 G6P B 801 " pdb=" C6 G6P B 801 " pdb=" O5 G6P B 801 " both_signs ideal model delta sigma weight residual False -2.51 2.57 -5.08 2.00e-01 2.50e+01 6.46e+02 chirality pdb=" C5 G6P C 801 " pdb=" C4 G6P C 801 " pdb=" C6 G6P C 801 " pdb=" O5 G6P C 801 " both_signs ideal model delta sigma weight residual False -2.51 2.57 -5.08 2.00e-01 2.50e+01 6.46e+02 chirality pdb=" C5 G6P A 801 " pdb=" C4 G6P A 801 " pdb=" C6 G6P A 801 " pdb=" O5 G6P A 801 " both_signs ideal model delta sigma weight residual False -2.51 2.57 -5.08 2.00e-01 2.50e+01 6.45e+02 ... (remaining 3005 not shown) Planarity restraints: 3616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 141 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO C 142 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 142 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 142 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 141 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO A 142 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 141 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.16e+00 pdb=" N PRO B 142 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 142 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 142 " 0.025 5.00e-02 4.00e+02 ... (remaining 3613 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4057 2.77 - 3.30: 20011 3.30 - 3.84: 33822 3.84 - 4.37: 38879 4.37 - 4.90: 65940 Nonbonded interactions: 162709 Sorted by model distance: nonbonded pdb=" OD2 ASP A 317 " pdb=" OG SER A 469 " model vdw 2.241 2.440 nonbonded pdb=" OD2 ASP D 317 " pdb=" OG SER D 469 " model vdw 2.241 2.440 nonbonded pdb=" OD2 ASP C 317 " pdb=" OG SER C 469 " model vdw 2.241 2.440 nonbonded pdb=" OD2 ASP B 317 " pdb=" OG SER B 469 " model vdw 2.241 2.440 nonbonded pdb=" O PHE D 165 " pdb=" OG SER D 169 " model vdw 2.250 2.440 ... (remaining 162704 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 29 through 579 or resid 581 through 587 or resid 589 throu \ gh 618 or resid 801)) selection = (chain 'B' and (resid 29 through 579 or resid 581 through 587 or resid 589 throu \ gh 618 or resid 801)) selection = (chain 'C' and (resid 29 through 579 or resid 581 through 587 or resid 589 throu \ gh 618 or resid 801)) selection = (chain 'D' and (resid 29 through 579 or resid 581 through 587 or resid 589 throu \ gh 618 or resid 801)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.300 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 61.880 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 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 0.076 20772 Z= 0.189 Angle : 0.581 8.352 28144 Z= 0.283 Chirality : 0.351 5.081 3008 Planarity : 0.003 0.045 3616 Dihedral : 17.596 142.147 7644 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: 0.25 (0.18), residues: 2480 helix: 0.95 (0.15), residues: 1240 sheet: 0.37 (0.37), residues: 216 loop : -0.79 (0.21), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 325 HIS 0.002 0.001 HIS D 297 PHE 0.008 0.001 PHE C 425 TYR 0.006 0.001 TYR C 221 ARG 0.003 0.000 ARG D 371 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 2.264 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU F 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU G 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.8840 (ppt170) cc_final: 0.8491 (ppt170) REVERT: A 209 LEU cc_start: 0.7621 (tt) cc_final: 0.7217 (tp) REVERT: A 244 MET cc_start: 0.9180 (pmm) cc_final: 0.8955 (pmm) REVERT: A 271 LYS cc_start: 0.9053 (mmpt) cc_final: 0.8726 (mmmt) REVERT: A 306 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7161 (mp0) REVERT: B 146 ARG cc_start: 0.8885 (ppt170) cc_final: 0.8563 (ppt170) REVERT: B 209 LEU cc_start: 0.7437 (tt) cc_final: 0.6991 (tp) REVERT: B 244 MET cc_start: 0.9151 (pmm) cc_final: 0.8908 (pmm) REVERT: B 271 LYS cc_start: 0.9018 (mmpt) cc_final: 0.8693 (mmmt) REVERT: B 306 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7121 (mp0) REVERT: C 146 ARG cc_start: 0.8904 (ppt170) cc_final: 0.8554 (ppt170) REVERT: C 209 LEU cc_start: 0.7503 (tt) cc_final: 0.7081 (tp) REVERT: C 240 HIS cc_start: 0.9308 (p90) cc_final: 0.8639 (p90) REVERT: C 244 MET cc_start: 0.9151 (pmm) cc_final: 0.8897 (pmm) REVERT: C 271 LYS cc_start: 0.8995 (mmpt) cc_final: 0.8625 (mmmt) REVERT: C 306 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7144 (mp0) REVERT: D 146 ARG cc_start: 0.8764 (ppt170) cc_final: 0.8404 (ppt170) REVERT: D 209 LEU cc_start: 0.7456 (tt) cc_final: 0.7018 (tp) REVERT: D 244 MET cc_start: 0.9120 (pmm) cc_final: 0.8872 (pmm) REVERT: D 271 LYS cc_start: 0.9057 (mmpt) cc_final: 0.8714 (mmmt) REVERT: D 306 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7070 (mp0) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.2964 time to fit residues: 136.9159 Evaluate side-chains 227 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 126 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 194 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 144 optimal weight: 9.9990 chunk 225 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS A 587 ASN B 291 HIS B 587 ASN C 291 HIS C 587 ASN D 291 HIS D 587 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20772 Z= 0.183 Angle : 0.558 8.055 28144 Z= 0.270 Chirality : 0.043 0.287 3008 Planarity : 0.003 0.043 3616 Dihedral : 6.906 56.386 2864 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.49 % Allowed : 8.38 % Favored : 90.13 % 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: 0.17 (0.17), residues: 2480 helix: 0.87 (0.15), residues: 1232 sheet: 0.29 (0.37), residues: 216 loop : -0.80 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 325 HIS 0.012 0.001 HIS C 250 PHE 0.035 0.002 PHE D 400 TYR 0.009 0.001 TYR B 212 ARG 0.002 0.000 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 236 time to evaluate : 2.218 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU F 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU G 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 271 LYS cc_start: 0.9073 (mmpt) cc_final: 0.8724 (mmmt) REVERT: A 306 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7206 (mp0) REVERT: F 342 LYS cc_start: 0.8322 (mmtt) cc_final: 0.7888 (mttm) REVERT: B 250 HIS cc_start: 0.8644 (t-170) cc_final: 0.8386 (t-170) REVERT: B 271 LYS cc_start: 0.9040 (mmpt) cc_final: 0.8700 (mmmt) REVERT: B 306 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7169 (mp0) REVERT: C 240 HIS cc_start: 0.9315 (p90) cc_final: 0.8708 (p90) REVERT: C 271 LYS cc_start: 0.9014 (mmpt) cc_final: 0.8636 (mmmt) REVERT: C 306 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7145 (mp0) REVERT: D 271 LYS cc_start: 0.9071 (mmpt) cc_final: 0.8723 (mmmt) REVERT: D 306 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7127 (mp0) outliers start: 32 outliers final: 13 residues processed: 251 average time/residue: 0.3070 time to fit residues: 119.4767 Evaluate side-chains 235 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 222 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain G residue 337 SER Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 290 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 0.0870 chunk 187 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 225 optimal weight: 0.5980 chunk 243 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 180 optimal weight: 0.7980 overall best weight: 1.0962 ------------------------------------------------------------------------------- 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: 0.7914 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20772 Z= 0.191 Angle : 0.552 9.864 28144 Z= 0.273 Chirality : 0.042 0.290 3008 Planarity : 0.003 0.036 3616 Dihedral : 4.779 59.612 2864 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.26 % Allowed : 10.66 % Favored : 88.08 % 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: 0.05 (0.17), residues: 2480 helix: 0.75 (0.15), residues: 1224 sheet: 0.21 (0.37), residues: 216 loop : -0.80 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 134 HIS 0.011 0.001 HIS D 250 PHE 0.027 0.001 PHE D 400 TYR 0.008 0.001 TYR C 212 ARG 0.003 0.000 ARG C 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 227 time to evaluate : 2.662 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU F 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU G 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. REVERT: A 271 LYS cc_start: 0.9079 (mmpt) cc_final: 0.8744 (mmmt) REVERT: A 306 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7198 (mp0) REVERT: F 342 LYS cc_start: 0.8410 (mmtt) cc_final: 0.7930 (mttm) REVERT: B 250 HIS cc_start: 0.8634 (t-170) cc_final: 0.8369 (t-170) REVERT: B 271 LYS cc_start: 0.9052 (mmpt) cc_final: 0.8735 (mmmt) REVERT: B 306 GLU cc_start: 0.7317 (mm-30) cc_final: 0.7089 (mp0) REVERT: C 271 LYS cc_start: 0.9034 (mmpt) cc_final: 0.8654 (mmmt) REVERT: D 271 LYS cc_start: 0.9074 (mmpt) cc_final: 0.8726 (mmmt) REVERT: D 306 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7090 (mp0) outliers start: 27 outliers final: 18 residues processed: 236 average time/residue: 0.2959 time to fit residues: 110.8789 Evaluate side-chains 231 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 213 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain G residue 337 SER Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 344 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 0.9980 chunk 169 optimal weight: 0.0870 chunk 117 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 226 optimal weight: 0.9980 chunk 239 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS B 253 HIS ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 HIS D 253 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20772 Z= 0.154 Angle : 0.526 10.323 28144 Z= 0.257 Chirality : 0.041 0.351 3008 Planarity : 0.003 0.034 3616 Dihedral : 4.671 59.422 2864 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.21 % Allowed : 11.50 % Favored : 87.29 % 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: 0.02 (0.17), residues: 2480 helix: 0.74 (0.15), residues: 1228 sheet: 0.22 (0.37), residues: 216 loop : -0.85 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 182 HIS 0.012 0.001 HIS A 250 PHE 0.030 0.001 PHE B 165 TYR 0.009 0.001 TYR C 212 ARG 0.001 0.000 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 234 time to evaluate : 2.468 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU F 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU G 349 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. REVERT: A 244 MET cc_start: 0.9209 (pmm) cc_final: 0.8982 (pmm) REVERT: A 271 LYS cc_start: 0.9075 (mmpt) cc_final: 0.8741 (mmmt) REVERT: A 306 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7201 (mp0) REVERT: F 342 LYS cc_start: 0.8354 (mmtt) cc_final: 0.7962 (mttm) REVERT: B 244 MET cc_start: 0.9210 (pmm) cc_final: 0.8981 (pmm) REVERT: B 250 HIS cc_start: 0.8657 (t-170) cc_final: 0.8373 (t-170) REVERT: B 271 LYS cc_start: 0.9047 (mmpt) cc_final: 0.8727 (mmmt) REVERT: B 306 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7117 (mp0) REVERT: C 244 MET cc_start: 0.9206 (pmm) cc_final: 0.8974 (pmm) REVERT: C 271 LYS cc_start: 0.9035 (mmpt) cc_final: 0.8669 (mmmt) REVERT: D 244 MET cc_start: 0.9187 (pmm) cc_final: 0.8880 (pmm) REVERT: D 271 LYS cc_start: 0.9075 (mmpt) cc_final: 0.8726 (mmmt) REVERT: D 306 GLU cc_start: 0.7295 (mm-30) cc_final: 0.7078 (mp0) outliers start: 26 outliers final: 16 residues processed: 246 average time/residue: 0.3043 time to fit residues: 117.5972 Evaluate side-chains 228 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 212 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain G residue 337 SER Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 344 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 0.5980 chunk 136 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 178 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20772 Z= 0.170 Angle : 0.527 11.997 28144 Z= 0.259 Chirality : 0.041 0.361 3008 Planarity : 0.003 0.033 3616 Dihedral : 4.601 57.895 2864 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.93 % Allowed : 12.38 % Favored : 86.69 % 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: 0.02 (0.17), residues: 2480 helix: 0.74 (0.15), residues: 1224 sheet: 0.20 (0.37), residues: 216 loop : -0.85 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 182 HIS 0.013 0.001 HIS A 250 PHE 0.029 0.001 PHE A 165 TYR 0.008 0.001 TYR C 212 ARG 0.002 0.000 ARG C 556 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 221 time to evaluate : 2.453 Fit side-chains TARDY: cannot create tardy model for: "LEU E 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU F 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU G 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. REVERT: A 271 LYS cc_start: 0.9120 (mmpt) cc_final: 0.8780 (mmmt) REVERT: A 306 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7186 (mp0) REVERT: F 342 LYS cc_start: 0.8274 (mmtt) cc_final: 0.7789 (mttm) REVERT: B 250 HIS cc_start: 0.8635 (t-170) cc_final: 0.8338 (t-170) REVERT: B 271 LYS cc_start: 0.9094 (mmpt) cc_final: 0.8774 (mmmt) REVERT: B 306 GLU cc_start: 0.7291 (mm-30) cc_final: 0.7083 (mp0) REVERT: C 271 LYS cc_start: 0.9046 (mmpt) cc_final: 0.8685 (mmmt) REVERT: D 271 LYS cc_start: 0.9082 (mmpt) cc_final: 0.8740 (mmmt) REVERT: D 306 GLU cc_start: 0.7285 (mm-30) cc_final: 0.7081 (mp0) outliers start: 20 outliers final: 11 residues processed: 235 average time/residue: 0.2927 time to fit residues: 110.0589 Evaluate side-chains 220 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 209 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 344 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 140 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 239 optimal weight: 0.9990 chunk 199 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 79 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20772 Z= 0.200 Angle : 0.571 12.158 28144 Z= 0.283 Chirality : 0.043 0.358 3008 Planarity : 0.003 0.032 3616 Dihedral : 4.576 55.661 2864 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.98 % Allowed : 12.43 % Favored : 86.59 % 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: -0.06 (0.17), residues: 2480 helix: 0.71 (0.15), residues: 1216 sheet: 0.16 (0.37), residues: 216 loop : -0.91 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 182 HIS 0.012 0.001 HIS D 250 PHE 0.030 0.001 PHE B 165 TYR 0.024 0.001 TYR H 332 ARG 0.002 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 216 time to evaluate : 2.171 Fit side-chains TARDY: cannot create tardy model for: "LEU E 349 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU F 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU G 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. REVERT: A 271 LYS cc_start: 0.9128 (mmpt) cc_final: 0.8795 (mmmt) REVERT: A 306 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7210 (mp0) REVERT: H 342 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7929 (mmtt) REVERT: B 271 LYS cc_start: 0.9106 (mmpt) cc_final: 0.8788 (mmmt) REVERT: C 271 LYS cc_start: 0.9097 (mmpt) cc_final: 0.8732 (mmmt) REVERT: D 271 LYS cc_start: 0.9088 (mmpt) cc_final: 0.8762 (mmmt) REVERT: D 306 GLU cc_start: 0.7240 (mm-30) cc_final: 0.7026 (mp0) outliers start: 21 outliers final: 13 residues processed: 228 average time/residue: 0.2956 time to fit residues: 107.3480 Evaluate side-chains 222 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 209 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 344 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 175 optimal weight: 0.0570 chunk 135 optimal weight: 20.0000 chunk 201 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 239 optimal weight: 0.7980 chunk 149 optimal weight: 0.3980 chunk 145 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20772 Z= 0.155 Angle : 0.564 12.737 28144 Z= 0.274 Chirality : 0.042 0.368 3008 Planarity : 0.003 0.038 3616 Dihedral : 4.506 54.226 2864 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.40 % Allowed : 12.20 % Favored : 86.41 % 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: -0.05 (0.17), residues: 2480 helix: 0.73 (0.15), residues: 1216 sheet: 0.20 (0.37), residues: 216 loop : -0.93 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 160 HIS 0.012 0.001 HIS D 250 PHE 0.027 0.001 PHE A 165 TYR 0.012 0.001 TYR C 212 ARG 0.004 0.000 ARG D 241 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 219 time to evaluate : 2.252 Fit side-chains TARDY: cannot create tardy model for: "LEU E 349 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU F 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU G 349 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. REVERT: A 271 LYS cc_start: 0.9116 (mmpt) cc_final: 0.8788 (mmmt) REVERT: A 306 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7209 (mp0) REVERT: E 342 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7930 (mmtt) REVERT: H 342 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7943 (mmtt) REVERT: B 271 LYS cc_start: 0.9084 (mmpt) cc_final: 0.8762 (mmmt) REVERT: C 271 LYS cc_start: 0.9075 (mmpt) cc_final: 0.8715 (mmmt) REVERT: D 271 LYS cc_start: 0.9118 (mmpt) cc_final: 0.8778 (mmmt) REVERT: D 306 GLU cc_start: 0.7218 (mm-30) cc_final: 0.7009 (mp0) outliers start: 30 outliers final: 21 residues processed: 230 average time/residue: 0.3035 time to fit residues: 110.4973 Evaluate side-chains 230 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 209 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain G residue 337 SER Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 344 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 10.0000 chunk 95 optimal weight: 0.2980 chunk 142 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 chunk 151 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 217 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 174 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20772 Z= 0.153 Angle : 0.567 12.831 28144 Z= 0.273 Chirality : 0.042 0.372 3008 Planarity : 0.003 0.032 3616 Dihedral : 4.440 52.870 2864 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.30 % Allowed : 12.52 % Favored : 86.17 % 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: -0.01 (0.17), residues: 2480 helix: 0.80 (0.15), residues: 1196 sheet: -0.13 (0.38), residues: 192 loop : -0.84 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 182 HIS 0.012 0.001 HIS D 250 PHE 0.026 0.001 PHE B 165 TYR 0.012 0.001 TYR B 212 ARG 0.003 0.000 ARG B 241 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 213 time to evaluate : 2.290 Fit side-chains TARDY: cannot create tardy model for: "LEU E 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU F 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU G 349 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. REVERT: A 271 LYS cc_start: 0.9123 (mmpt) cc_final: 0.8778 (mmmt) REVERT: A 306 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7193 (mp0) REVERT: E 342 LYS cc_start: 0.8222 (mmtt) cc_final: 0.7951 (mmtt) REVERT: F 342 LYS cc_start: 0.8131 (mmtt) cc_final: 0.7889 (mmtt) REVERT: H 342 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7930 (mmtt) REVERT: B 271 LYS cc_start: 0.9095 (mmpt) cc_final: 0.8775 (mmmt) REVERT: C 271 LYS cc_start: 0.9066 (mmpt) cc_final: 0.8708 (mmmt) REVERT: D 271 LYS cc_start: 0.9128 (mmpt) cc_final: 0.8779 (mmmt) REVERT: D 306 GLU cc_start: 0.7251 (mm-30) cc_final: 0.7043 (mp0) outliers start: 28 outliers final: 21 residues processed: 227 average time/residue: 0.2984 time to fit residues: 107.1810 Evaluate side-chains 236 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 215 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain G residue 332 TYR Chi-restraints excluded: chain G residue 337 SER Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 344 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 134 optimal weight: 0.0980 chunk 97 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 68 optimal weight: 0.0470 chunk 201 optimal weight: 0.9990 chunk 210 optimal weight: 6.9990 chunk 221 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 overall best weight: 0.8282 ------------------------------------------------------------------------------- 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: 0.7913 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20772 Z= 0.171 Angle : 0.587 13.130 28144 Z= 0.281 Chirality : 0.043 0.388 3008 Planarity : 0.003 0.031 3616 Dihedral : 4.396 51.240 2864 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.12 % Allowed : 12.90 % Favored : 85.99 % 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: -0.08 (0.17), residues: 2480 helix: 0.70 (0.15), residues: 1220 sheet: 0.18 (0.37), residues: 216 loop : -0.95 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 182 HIS 0.013 0.001 HIS B 250 PHE 0.026 0.001 PHE A 165 TYR 0.013 0.001 TYR C 212 ARG 0.001 0.000 ARG G 321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 219 time to evaluate : 2.234 Fit side-chains TARDY: cannot create tardy model for: "LEU E 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU F 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU G 349 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. REVERT: A 271 LYS cc_start: 0.9122 (mmpt) cc_final: 0.8777 (mmmt) REVERT: A 306 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7227 (mp0) REVERT: E 342 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7955 (mmtt) REVERT: F 342 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7885 (mmtt) REVERT: H 342 LYS cc_start: 0.8222 (mmtt) cc_final: 0.7941 (mmtt) REVERT: B 271 LYS cc_start: 0.9099 (mmpt) cc_final: 0.8776 (mmmt) REVERT: C 271 LYS cc_start: 0.9069 (mmpt) cc_final: 0.8714 (mmmt) REVERT: D 271 LYS cc_start: 0.9130 (mmpt) cc_final: 0.8779 (mmmt) outliers start: 24 outliers final: 19 residues processed: 229 average time/residue: 0.2863 time to fit residues: 104.4651 Evaluate side-chains 231 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 212 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain G residue 332 TYR Chi-restraints excluded: chain G residue 345 LEU Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 344 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 163 optimal weight: 0.9980 chunk 247 optimal weight: 9.9990 chunk 227 optimal weight: 0.0670 chunk 196 optimal weight: 0.0370 chunk 20 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 156 optimal weight: 0.0670 overall best weight: 0.3134 ------------------------------------------------------------------------------- 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: 0.7872 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20772 Z= 0.142 Angle : 0.592 13.712 28144 Z= 0.280 Chirality : 0.042 0.379 3008 Planarity : 0.003 0.032 3616 Dihedral : 4.293 49.394 2864 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.98 % Allowed : 13.04 % Favored : 85.99 % 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: -0.07 (0.17), residues: 2480 helix: 0.75 (0.15), residues: 1208 sheet: -0.02 (0.38), residues: 192 loop : -0.91 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 160 HIS 0.013 0.001 HIS B 250 PHE 0.023 0.001 PHE A 154 TYR 0.014 0.001 TYR C 212 ARG 0.002 0.000 ARG B 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 230 time to evaluate : 2.427 Fit side-chains TARDY: cannot create tardy model for: "LEU E 349 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU F 349 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU G 349 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU H 349 " (corrupted residue). Skipping it. REVERT: A 271 LYS cc_start: 0.9093 (mmpt) cc_final: 0.8752 (mmmt) REVERT: A 306 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7227 (mp0) REVERT: E 342 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7976 (mmtt) REVERT: F 342 LYS cc_start: 0.8188 (mmtt) cc_final: 0.7955 (mmtt) REVERT: H 342 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7936 (mmtt) REVERT: B 271 LYS cc_start: 0.9061 (mmpt) cc_final: 0.8741 (mmmt) REVERT: B 290 MET cc_start: 0.8287 (mpp) cc_final: 0.8002 (mpp) REVERT: C 271 LYS cc_start: 0.9064 (mmpt) cc_final: 0.8684 (mmmt) REVERT: C 290 MET cc_start: 0.8284 (mpp) cc_final: 0.8074 (mpp) REVERT: D 271 LYS cc_start: 0.9098 (mmpt) cc_final: 0.8737 (mmmt) outliers start: 21 outliers final: 18 residues processed: 238 average time/residue: 0.2915 time to fit residues: 111.0666 Evaluate side-chains 233 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 215 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain E residue 332 TYR Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain G residue 332 TYR Chi-restraints excluded: chain G residue 337 SER Chi-restraints excluded: chain H residue 332 TYR Chi-restraints excluded: chain H residue 345 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 344 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 181 optimal weight: 0.0670 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 197 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 202 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 173 optimal weight: 0.0070 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.133083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.094173 restraints weight = 103254.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.094158 restraints weight = 42247.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.094990 restraints weight = 31481.895| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20772 Z= 0.169 Angle : 0.595 13.842 28144 Z= 0.283 Chirality : 0.043 0.382 3008 Planarity : 0.003 0.035 3616 Dihedral : 4.227 47.011 2864 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.88 % Allowed : 13.59 % Favored : 85.52 % 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: 0.00 (0.18), residues: 2480 helix: 0.80 (0.15), residues: 1204 sheet: 0.13 (0.38), residues: 216 loop : -0.91 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 182 HIS 0.013 0.001 HIS A 250 PHE 0.029 0.001 PHE A 154 TYR 0.012 0.001 TYR C 212 ARG 0.001 0.000 ARG G 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3541.74 seconds wall clock time: 65 minutes 31.51 seconds (3931.51 seconds total)