Starting phenix.real_space_refine on Thu Dec 14 21:16:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u66_41946/12_2023/8u66_41946_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u66_41946/12_2023/8u66_41946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u66_41946/12_2023/8u66_41946.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u66_41946/12_2023/8u66_41946.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u66_41946/12_2023/8u66_41946_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u66_41946/12_2023/8u66_41946_updated.pdb" } resolution = 2.21 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= -0.001 sd= 0.092 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 128 5.16 5 C 17968 2.51 5 N 5064 2.21 5 O 6181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 29365 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "B" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 125 Classifications: {'water': 125} Link IDs: {None: 124} Chain: "C" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Classifications: {'water': 121} Link IDs: {None: 120} Chain: "E" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 125 Classifications: {'water': 125} Link IDs: {None: 124} Chain: "F" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Classifications: {'water': 121} Link IDs: {None: 120} Chain: "G" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Classifications: {'water': 121} Link IDs: {None: 120} Chain: "H" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Time building chain proxies: 15.95, per 1000 atoms: 0.54 Number of scatterers: 29365 At special positions: 0 Unit cell: (122.85, 122.85, 108.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 128 16.00 P 16 15.00 Mg 8 11.99 O 6181 8.00 N 5064 7.00 C 17968 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: 12.59 Conformation dependent library (CDL) restraints added in 5.2 seconds 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 184 helices and 24 sheets defined 46.7% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.91 Creating SS restraints... Processing helix chain 'A' and resid 13 through 17 removed outlier: 4.105A pdb=" N TYR A 17 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 55 Processing helix chain 'A' and resid 63 through 67 Processing helix chain 'A' and resid 70 through 73 No H-bonds generated for 'chain 'A' and resid 70 through 73' Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 99 through 106 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 128 through 133 removed outlier: 3.905A pdb=" N THR A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 168 through 181 Processing helix chain 'A' and resid 200 through 218 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 255 through 258 No H-bonds generated for 'chain 'A' and resid 255 through 258' Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.872A pdb=" N THR A 288 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 370 through 380 Proline residue: A 374 - end of helix removed outlier: 3.614A pdb=" N TYR A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 393 No H-bonds generated for 'chain 'A' and resid 390 through 393' Processing helix chain 'A' and resid 399 through 418 Processing helix chain 'A' and resid 423 through 437 removed outlier: 5.851A pdb=" N ARG A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 447 Processing helix chain 'B' and resid 13 through 17 removed outlier: 4.104A pdb=" N TYR B 17 " --> pdb=" O ARG B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 55 Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 70 through 73 No H-bonds generated for 'chain 'B' and resid 70 through 73' Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 99 through 106 Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 128 through 133 removed outlier: 3.904A pdb=" N THR B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 148 Processing helix chain 'B' and resid 168 through 181 Processing helix chain 'B' and resid 200 through 218 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 255 through 258 No H-bonds generated for 'chain 'B' and resid 255 through 258' Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 284 through 288 removed outlier: 3.871A pdb=" N THR B 288 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 344 through 346 No H-bonds generated for 'chain 'B' and resid 344 through 346' Processing helix chain 'B' and resid 370 through 380 Proline residue: B 374 - end of helix removed outlier: 3.614A pdb=" N TYR B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 393 No H-bonds generated for 'chain 'B' and resid 390 through 393' Processing helix chain 'B' and resid 399 through 418 Processing helix chain 'B' and resid 423 through 437 removed outlier: 5.851A pdb=" N ARG B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 447 Processing helix chain 'C' and resid 13 through 17 removed outlier: 4.105A pdb=" N TYR C 17 " --> pdb=" O ARG C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 55 Processing helix chain 'C' and resid 63 through 67 Processing helix chain 'C' and resid 70 through 73 No H-bonds generated for 'chain 'C' and resid 70 through 73' Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 99 through 106 Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 128 through 133 removed outlier: 3.905A pdb=" N THR C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 168 through 181 Processing helix chain 'C' and resid 200 through 218 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 255 through 258 No H-bonds generated for 'chain 'C' and resid 255 through 258' Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 284 through 288 removed outlier: 3.871A pdb=" N THR C 288 " --> pdb=" O ALA C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 307 Processing helix chain 'C' and resid 325 through 336 Processing helix chain 'C' and resid 344 through 346 No H-bonds generated for 'chain 'C' and resid 344 through 346' Processing helix chain 'C' and resid 370 through 380 Proline residue: C 374 - end of helix removed outlier: 3.614A pdb=" N TYR C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 393 No H-bonds generated for 'chain 'C' and resid 390 through 393' Processing helix chain 'C' and resid 399 through 418 Processing helix chain 'C' and resid 423 through 437 removed outlier: 5.850A pdb=" N ARG C 428 " --> pdb=" O LEU C 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR C 437 " --> pdb=" O ASP C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 447 Processing helix chain 'D' and resid 13 through 17 removed outlier: 4.104A pdb=" N TYR D 17 " --> pdb=" O ARG D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 55 Processing helix chain 'D' and resid 63 through 67 Processing helix chain 'D' and resid 70 through 73 No H-bonds generated for 'chain 'D' and resid 70 through 73' Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 99 through 106 Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 128 through 133 removed outlier: 3.905A pdb=" N THR D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 148 Processing helix chain 'D' and resid 168 through 181 Processing helix chain 'D' and resid 200 through 218 Processing helix chain 'D' and resid 233 through 245 Processing helix chain 'D' and resid 255 through 258 No H-bonds generated for 'chain 'D' and resid 255 through 258' Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 284 through 288 removed outlier: 3.871A pdb=" N THR D 288 " --> pdb=" O ALA D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 307 Processing helix chain 'D' and resid 325 through 336 Processing helix chain 'D' and resid 344 through 346 No H-bonds generated for 'chain 'D' and resid 344 through 346' Processing helix chain 'D' and resid 370 through 380 Proline residue: D 374 - end of helix removed outlier: 3.614A pdb=" N TYR D 380 " --> pdb=" O VAL D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 393 No H-bonds generated for 'chain 'D' and resid 390 through 393' Processing helix chain 'D' and resid 399 through 418 Processing helix chain 'D' and resid 423 through 437 removed outlier: 5.851A pdb=" N ARG D 428 " --> pdb=" O LEU D 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN D 429 " --> pdb=" O ALA D 425 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 447 Processing helix chain 'E' and resid 13 through 17 removed outlier: 4.105A pdb=" N TYR E 17 " --> pdb=" O ARG E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 55 Processing helix chain 'E' and resid 63 through 67 Processing helix chain 'E' and resid 70 through 73 No H-bonds generated for 'chain 'E' and resid 70 through 73' Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 99 through 106 Processing helix chain 'E' and resid 110 through 112 No H-bonds generated for 'chain 'E' and resid 110 through 112' Processing helix chain 'E' and resid 128 through 133 removed outlier: 3.904A pdb=" N THR E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 148 Processing helix chain 'E' and resid 168 through 181 Processing helix chain 'E' and resid 200 through 218 Processing helix chain 'E' and resid 233 through 245 Processing helix chain 'E' and resid 255 through 258 No H-bonds generated for 'chain 'E' and resid 255 through 258' Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 284 through 288 removed outlier: 3.871A pdb=" N THR E 288 " --> pdb=" O ALA E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 307 Processing helix chain 'E' and resid 325 through 336 Processing helix chain 'E' and resid 344 through 346 No H-bonds generated for 'chain 'E' and resid 344 through 346' Processing helix chain 'E' and resid 370 through 380 Proline residue: E 374 - end of helix removed outlier: 3.614A pdb=" N TYR E 380 " --> pdb=" O VAL E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 393 No H-bonds generated for 'chain 'E' and resid 390 through 393' Processing helix chain 'E' and resid 399 through 418 Processing helix chain 'E' and resid 423 through 437 removed outlier: 5.850A pdb=" N ARG E 428 " --> pdb=" O LEU E 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN E 429 " --> pdb=" O ALA E 425 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR E 437 " --> pdb=" O ASP E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 447 Processing helix chain 'F' and resid 13 through 17 removed outlier: 4.106A pdb=" N TYR F 17 " --> pdb=" O ARG F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 55 Processing helix chain 'F' and resid 63 through 67 Processing helix chain 'F' and resid 70 through 73 No H-bonds generated for 'chain 'F' and resid 70 through 73' Processing helix chain 'F' and resid 91 through 93 No H-bonds generated for 'chain 'F' and resid 91 through 93' Processing helix chain 'F' and resid 99 through 106 Processing helix chain 'F' and resid 110 through 112 No H-bonds generated for 'chain 'F' and resid 110 through 112' Processing helix chain 'F' and resid 128 through 133 removed outlier: 3.905A pdb=" N THR F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 148 Processing helix chain 'F' and resid 168 through 181 Processing helix chain 'F' and resid 200 through 218 Processing helix chain 'F' and resid 233 through 245 Processing helix chain 'F' and resid 255 through 258 No H-bonds generated for 'chain 'F' and resid 255 through 258' Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 284 through 288 removed outlier: 3.871A pdb=" N THR F 288 " --> pdb=" O ALA F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 307 Processing helix chain 'F' and resid 325 through 336 Processing helix chain 'F' and resid 344 through 346 No H-bonds generated for 'chain 'F' and resid 344 through 346' Processing helix chain 'F' and resid 370 through 380 Proline residue: F 374 - end of helix removed outlier: 3.615A pdb=" N TYR F 380 " --> pdb=" O VAL F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 393 No H-bonds generated for 'chain 'F' and resid 390 through 393' Processing helix chain 'F' and resid 399 through 418 Processing helix chain 'F' and resid 423 through 437 removed outlier: 5.850A pdb=" N ARG F 428 " --> pdb=" O LEU F 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN F 429 " --> pdb=" O ALA F 425 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR F 437 " --> pdb=" O ASP F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 447 Processing helix chain 'G' and resid 13 through 17 removed outlier: 4.105A pdb=" N TYR G 17 " --> pdb=" O ARG G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 55 Processing helix chain 'G' and resid 63 through 67 Processing helix chain 'G' and resid 70 through 73 No H-bonds generated for 'chain 'G' and resid 70 through 73' Processing helix chain 'G' and resid 91 through 93 No H-bonds generated for 'chain 'G' and resid 91 through 93' Processing helix chain 'G' and resid 99 through 106 Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 128 through 133 removed outlier: 3.904A pdb=" N THR G 133 " --> pdb=" O ALA G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 148 Processing helix chain 'G' and resid 168 through 181 Processing helix chain 'G' and resid 200 through 218 Processing helix chain 'G' and resid 233 through 245 Processing helix chain 'G' and resid 255 through 258 No H-bonds generated for 'chain 'G' and resid 255 through 258' Processing helix chain 'G' and resid 260 through 273 Processing helix chain 'G' and resid 284 through 288 removed outlier: 3.871A pdb=" N THR G 288 " --> pdb=" O ALA G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 307 Processing helix chain 'G' and resid 325 through 336 Processing helix chain 'G' and resid 344 through 346 No H-bonds generated for 'chain 'G' and resid 344 through 346' Processing helix chain 'G' and resid 370 through 380 Proline residue: G 374 - end of helix removed outlier: 3.613A pdb=" N TYR G 380 " --> pdb=" O VAL G 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 393 No H-bonds generated for 'chain 'G' and resid 390 through 393' Processing helix chain 'G' and resid 399 through 418 Processing helix chain 'G' and resid 423 through 437 removed outlier: 5.850A pdb=" N ARG G 428 " --> pdb=" O LEU G 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN G 429 " --> pdb=" O ALA G 425 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR G 437 " --> pdb=" O ASP G 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 447 Processing helix chain 'H' and resid 13 through 17 removed outlier: 4.106A pdb=" N TYR H 17 " --> pdb=" O ARG H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 55 Processing helix chain 'H' and resid 63 through 67 Processing helix chain 'H' and resid 70 through 73 No H-bonds generated for 'chain 'H' and resid 70 through 73' Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'H' and resid 99 through 106 Processing helix chain 'H' and resid 110 through 112 No H-bonds generated for 'chain 'H' and resid 110 through 112' Processing helix chain 'H' and resid 128 through 133 removed outlier: 3.905A pdb=" N THR H 133 " --> pdb=" O ALA H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 148 Processing helix chain 'H' and resid 168 through 181 Processing helix chain 'H' and resid 200 through 218 Processing helix chain 'H' and resid 233 through 245 Processing helix chain 'H' and resid 255 through 258 No H-bonds generated for 'chain 'H' and resid 255 through 258' Processing helix chain 'H' and resid 260 through 273 Processing helix chain 'H' and resid 284 through 288 removed outlier: 3.871A pdb=" N THR H 288 " --> pdb=" O ALA H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 307 Processing helix chain 'H' and resid 325 through 336 Processing helix chain 'H' and resid 344 through 346 No H-bonds generated for 'chain 'H' and resid 344 through 346' Processing helix chain 'H' and resid 370 through 380 Proline residue: H 374 - end of helix removed outlier: 3.614A pdb=" N TYR H 380 " --> pdb=" O VAL H 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 390 through 393 No H-bonds generated for 'chain 'H' and resid 390 through 393' Processing helix chain 'H' and resid 399 through 418 Processing helix chain 'H' and resid 423 through 437 removed outlier: 5.850A pdb=" N ARG H 428 " --> pdb=" O LEU H 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN H 429 " --> pdb=" O ALA H 425 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR H 437 " --> pdb=" O ASP H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 439 through 447 Processing sheet with id= A, first strand: chain 'A' and resid 118 through 125 removed outlier: 6.769A pdb=" N ALA A 32 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET A 124 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU A 30 " --> pdb=" O MET A 124 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 79 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA A 88 " --> pdb=" O CYS A 77 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N CYS A 77 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 155 through 157 removed outlier: 7.701A pdb=" N LEU A 387 " --> pdb=" O PRO A 362 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA A 364 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 250 through 254 removed outlier: 5.949A pdb=" N MET A 276 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL A 253 " --> pdb=" O MET A 276 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N HIS A 278 " --> pdb=" O VAL A 253 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 118 through 125 removed outlier: 6.768A pdb=" N ALA B 32 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET B 124 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU B 30 " --> pdb=" O MET B 124 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 79 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA B 88 " --> pdb=" O CYS B 77 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N CYS B 77 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 155 through 157 removed outlier: 7.701A pdb=" N LEU B 387 " --> pdb=" O PRO B 362 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA B 364 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 250 through 254 removed outlier: 5.949A pdb=" N MET B 276 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL B 253 " --> pdb=" O MET B 276 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N HIS B 278 " --> pdb=" O VAL B 253 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 118 through 125 removed outlier: 6.767A pdb=" N ALA C 32 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET C 124 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU C 30 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA C 79 " --> pdb=" O TYR C 86 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA C 88 " --> pdb=" O CYS C 77 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N CYS C 77 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 155 through 157 removed outlier: 7.701A pdb=" N LEU C 387 " --> pdb=" O PRO C 362 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA C 364 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 250 through 254 removed outlier: 5.950A pdb=" N MET C 276 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL C 253 " --> pdb=" O MET C 276 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N HIS C 278 " --> pdb=" O VAL C 253 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 118 through 125 removed outlier: 6.767A pdb=" N ALA D 32 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N MET D 124 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU D 30 " --> pdb=" O MET D 124 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA D 79 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA D 88 " --> pdb=" O CYS D 77 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N CYS D 77 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 155 through 157 removed outlier: 7.701A pdb=" N LEU D 387 " --> pdb=" O PRO D 362 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA D 364 " --> pdb=" O LEU D 387 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 250 through 254 removed outlier: 5.949A pdb=" N MET D 276 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL D 253 " --> pdb=" O MET D 276 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N HIS D 278 " --> pdb=" O VAL D 253 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 118 through 125 removed outlier: 6.767A pdb=" N ALA E 32 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET E 124 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU E 30 " --> pdb=" O MET E 124 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA E 79 " --> pdb=" O TYR E 86 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA E 88 " --> pdb=" O CYS E 77 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N CYS E 77 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 155 through 157 removed outlier: 7.701A pdb=" N LEU E 387 " --> pdb=" O PRO E 362 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA E 364 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 250 through 254 removed outlier: 5.949A pdb=" N MET E 276 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL E 253 " --> pdb=" O MET E 276 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N HIS E 278 " --> pdb=" O VAL E 253 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'F' and resid 118 through 125 removed outlier: 6.768A pdb=" N ALA F 32 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET F 124 " --> pdb=" O LEU F 30 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU F 30 " --> pdb=" O MET F 124 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA F 79 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA F 88 " --> pdb=" O CYS F 77 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N CYS F 77 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 155 through 157 removed outlier: 7.702A pdb=" N LEU F 387 " --> pdb=" O PRO F 362 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA F 364 " --> pdb=" O LEU F 387 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 250 through 254 removed outlier: 5.949A pdb=" N MET F 276 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL F 253 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N HIS F 278 " --> pdb=" O VAL F 253 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'G' and resid 118 through 125 removed outlier: 6.767A pdb=" N ALA G 32 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET G 124 " --> pdb=" O LEU G 30 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU G 30 " --> pdb=" O MET G 124 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA G 79 " --> pdb=" O TYR G 86 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA G 88 " --> pdb=" O CYS G 77 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N CYS G 77 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 155 through 157 removed outlier: 7.701A pdb=" N LEU G 387 " --> pdb=" O PRO G 362 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA G 364 " --> pdb=" O LEU G 387 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 250 through 254 removed outlier: 5.949A pdb=" N MET G 276 " --> pdb=" O ILE G 251 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL G 253 " --> pdb=" O MET G 276 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N HIS G 278 " --> pdb=" O VAL G 253 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'H' and resid 118 through 125 removed outlier: 6.768A pdb=" N ALA H 32 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N MET H 124 " --> pdb=" O LEU H 30 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU H 30 " --> pdb=" O MET H 124 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA H 79 " --> pdb=" O TYR H 86 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA H 88 " --> pdb=" O CYS H 77 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N CYS H 77 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 155 through 157 removed outlier: 7.701A pdb=" N LEU H 387 " --> pdb=" O PRO H 362 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA H 364 " --> pdb=" O LEU H 387 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 250 through 254 removed outlier: 5.948A pdb=" N MET H 276 " --> pdb=" O ILE H 251 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL H 253 " --> pdb=" O MET H 276 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N HIS H 278 " --> pdb=" O VAL H 253 " (cutoff:3.500A) No H-bonds generated for sheet with id= X 1064 hydrogen bonds defined for protein. 2904 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: 10.64 Time building geometry restraints manager: 13.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4693 1.32 - 1.44: 8100 1.44 - 1.56: 16079 1.56 - 1.68: 16 1.68 - 1.81: 208 Bond restraints: 29096 Sorted by residual: bond pdb=" NZ KCX E 187 " pdb=" CX KCX E 187 " ideal model delta sigma weight residual 1.411 1.329 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" NZ KCX F 187 " pdb=" CX KCX F 187 " ideal model delta sigma weight residual 1.411 1.331 0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" NZ KCX D 187 " pdb=" CX KCX D 187 " ideal model delta sigma weight residual 1.411 1.332 0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" NZ KCX H 187 " pdb=" CX KCX H 187 " ideal model delta sigma weight residual 1.411 1.334 0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" NZ KCX C 187 " pdb=" CX KCX C 187 " ideal model delta sigma weight residual 1.411 1.334 0.077 2.00e-02 2.50e+03 1.47e+01 ... (remaining 29091 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.82: 969 106.82 - 113.62: 15435 113.62 - 120.42: 11103 120.42 - 127.21: 11516 127.21 - 134.01: 449 Bond angle restraints: 39472 Sorted by residual: angle pdb=" C3 CAP H 502 " pdb=" C4 CAP H 502 " pdb=" C5 CAP H 502 " ideal model delta sigma weight residual 111.00 124.20 -13.20 3.00e+00 1.11e-01 1.94e+01 angle pdb=" C3 CAP E 502 " pdb=" C4 CAP E 502 " pdb=" C5 CAP E 502 " ideal model delta sigma weight residual 111.00 124.18 -13.18 3.00e+00 1.11e-01 1.93e+01 angle pdb=" C3 CAP G 502 " pdb=" C4 CAP G 502 " pdb=" C5 CAP G 502 " ideal model delta sigma weight residual 111.00 124.18 -13.18 3.00e+00 1.11e-01 1.93e+01 angle pdb=" C3 CAP D 502 " pdb=" C4 CAP D 502 " pdb=" C5 CAP D 502 " ideal model delta sigma weight residual 111.00 124.18 -13.18 3.00e+00 1.11e-01 1.93e+01 angle pdb=" C3 CAP B 502 " pdb=" C4 CAP B 502 " pdb=" C5 CAP B 502 " ideal model delta sigma weight residual 111.00 124.16 -13.16 3.00e+00 1.11e-01 1.92e+01 ... (remaining 39467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.78: 16529 34.78 - 69.56: 507 69.56 - 104.34: 84 104.34 - 139.12: 4 139.12 - 173.90: 4 Dihedral angle restraints: 17128 sinusoidal: 6952 harmonic: 10176 Sorted by residual: dihedral pdb=" C3 CAP H 502 " pdb=" C CAP H 502 " pdb=" C2 CAP H 502 " pdb=" O6 CAP H 502 " ideal model delta sinusoidal sigma weight residual 81.86 -92.04 173.90 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C3 CAP D 502 " pdb=" C CAP D 502 " pdb=" C2 CAP D 502 " pdb=" O6 CAP D 502 " ideal model delta sinusoidal sigma weight residual 81.86 -92.04 173.90 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C3 CAP E 502 " pdb=" C CAP E 502 " pdb=" C2 CAP E 502 " pdb=" O6 CAP E 502 " ideal model delta sinusoidal sigma weight residual 81.86 -92.03 173.89 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 17125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.350: 4144 0.350 - 0.700: 0 0.700 - 1.050: 0 1.050 - 1.400: 0 1.400 - 1.750: 8 Chirality restraints: 4152 Sorted by residual: chirality pdb=" C4 CAP B 502 " pdb=" C3 CAP B 502 " pdb=" C5 CAP B 502 " pdb=" O4 CAP B 502 " both_signs ideal model delta sigma weight residual False -2.47 -0.72 -1.75 2.00e-01 2.50e+01 7.66e+01 chirality pdb=" C4 CAP H 502 " pdb=" C3 CAP H 502 " pdb=" C5 CAP H 502 " pdb=" O4 CAP H 502 " both_signs ideal model delta sigma weight residual False -2.47 -0.72 -1.75 2.00e-01 2.50e+01 7.63e+01 chirality pdb=" C4 CAP G 502 " pdb=" C3 CAP G 502 " pdb=" C5 CAP G 502 " pdb=" O4 CAP G 502 " both_signs ideal model delta sigma weight residual False -2.47 -0.72 -1.75 2.00e-01 2.50e+01 7.63e+01 ... (remaining 4149 not shown) Planarity restraints: 5168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA KCX F 187 " -0.009 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C KCX F 187 " 0.033 2.00e-02 2.50e+03 pdb=" O KCX F 187 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP F 188 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA KCX A 187 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C KCX A 187 " 0.033 2.00e-02 2.50e+03 pdb=" O KCX A 187 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP A 188 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA KCX B 187 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C KCX B 187 " -0.033 2.00e-02 2.50e+03 pdb=" O KCX B 187 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP B 188 " 0.011 2.00e-02 2.50e+03 ... (remaining 5165 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 196 2.48 - 3.08: 21276 3.08 - 3.69: 51881 3.69 - 4.29: 84576 4.29 - 4.90: 129204 Nonbonded interactions: 287133 Sorted by model distance: nonbonded pdb=" OD1 ASP E 189 " pdb="MG MG E 501 " model vdw 1.869 2.170 nonbonded pdb=" OD1 ASP G 189 " pdb="MG MG G 501 " model vdw 1.870 2.170 nonbonded pdb=" OD1 ASP C 189 " pdb="MG MG C 501 " model vdw 1.871 2.170 nonbonded pdb=" OD1 ASP H 189 " pdb="MG MG H 501 " model vdw 1.871 2.170 nonbonded pdb=" OD1 ASP B 189 " pdb="MG MG B 501 " model vdw 1.872 2.170 ... (remaining 287128 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 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: 7.810 Check model and map are aligned: 0.490 Set scattering table: 0.290 Process input model: 79.350 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.220 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:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 : 0.004 0.082 29096 Z= 0.235 Angle : 0.561 13.198 39472 Z= 0.263 Chirality : 0.085 1.750 4152 Planarity : 0.003 0.022 5168 Dihedral : 16.747 173.903 10664 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.28 % Allowed : 11.41 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.01 (0.15), residues: 3544 helix: 1.76 (0.13), residues: 1664 sheet: 0.50 (0.25), residues: 424 loop : 1.32 (0.18), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 354 HIS 0.003 0.001 HIS E 311 PHE 0.012 0.001 PHE E 297 TYR 0.016 0.001 TYR C 263 ARG 0.001 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 441 time to evaluate : 3.356 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 441 average time/residue: 2.2345 time to fit residues: 1105.0969 Evaluate side-chains 413 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 405 time to evaluate : 3.920 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4901 time to fit residues: 11.0809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 179 optimal weight: 0.0370 chunk 142 optimal weight: 6.9990 chunk 275 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 319 optimal weight: 7.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN D 193 ASN ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 ASN ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 ASN ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 ASN ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 29096 Z= 0.402 Angle : 0.684 8.098 39472 Z= 0.357 Chirality : 0.047 0.151 4152 Planarity : 0.005 0.044 5168 Dihedral : 9.711 173.266 4128 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.08 % Allowed : 11.37 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.14), residues: 3544 helix: 1.22 (0.13), residues: 1608 sheet: 0.26 (0.21), residues: 536 loop : 1.26 (0.18), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP F 354 HIS 0.007 0.002 HIS A 311 PHE 0.022 0.003 PHE A 297 TYR 0.031 0.003 TYR G 263 ARG 0.005 0.001 ARG E 238 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 414 time to evaluate : 3.441 Fit side-chains outliers start: 59 outliers final: 24 residues processed: 460 average time/residue: 2.1428 time to fit residues: 1101.2393 Evaluate side-chains 435 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 411 time to evaluate : 3.367 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 16 residues processed: 8 average time/residue: 1.9861 time to fit residues: 22.2584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 217 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 320 optimal weight: 1.9990 chunk 345 optimal weight: 0.8980 chunk 285 optimal weight: 3.9990 chunk 317 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 256 optimal weight: 0.4980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 29096 Z= 0.209 Angle : 0.549 6.687 39472 Z= 0.285 Chirality : 0.041 0.130 4152 Planarity : 0.004 0.060 5168 Dihedral : 9.242 173.595 4128 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.05 % Allowed : 11.05 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.14), residues: 3544 helix: 1.25 (0.13), residues: 1616 sheet: 0.22 (0.22), residues: 520 loop : 1.23 (0.18), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 354 HIS 0.005 0.001 HIS D 311 PHE 0.016 0.002 PHE F 297 TYR 0.024 0.002 TYR F 263 ARG 0.004 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 435 time to evaluate : 3.531 Fit side-chains outliers start: 58 outliers final: 33 residues processed: 475 average time/residue: 2.0885 time to fit residues: 1112.6966 Evaluate side-chains 439 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 406 time to evaluate : 3.210 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 32 residues processed: 1 average time/residue: 1.8520 time to fit residues: 6.4219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 4.9990 chunk 240 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 215 optimal weight: 0.2980 chunk 321 optimal weight: 0.0980 chunk 340 optimal weight: 3.9990 chunk 167 optimal weight: 0.5980 chunk 304 optimal weight: 5.9990 chunk 91 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 65 GLN ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 29096 Z= 0.200 Angle : 0.537 6.353 39472 Z= 0.279 Chirality : 0.040 0.128 4152 Planarity : 0.004 0.056 5168 Dihedral : 9.066 171.569 4128 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.00 % Allowed : 11.05 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.14), residues: 3544 helix: 1.20 (0.13), residues: 1616 sheet: 0.15 (0.22), residues: 520 loop : 1.19 (0.18), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 354 HIS 0.005 0.001 HIS B 311 PHE 0.016 0.002 PHE B 297 TYR 0.025 0.002 TYR A 263 ARG 0.004 0.000 ARG E 442 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 420 time to evaluate : 3.466 Fit side-chains outliers start: 85 outliers final: 42 residues processed: 482 average time/residue: 2.2507 time to fit residues: 1211.9045 Evaluate side-chains 461 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 419 time to evaluate : 3.211 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 40 residues processed: 2 average time/residue: 1.8938 time to fit residues: 8.3925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 7.9990 chunk 193 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 253 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 290 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 0.5980 chunk 305 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 29096 Z= 0.327 Angle : 0.638 7.944 39472 Z= 0.332 Chirality : 0.044 0.144 4152 Planarity : 0.005 0.064 5168 Dihedral : 9.521 170.482 4128 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.61 % Allowed : 11.97 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.14), residues: 3544 helix: 0.95 (0.13), residues: 1616 sheet: -0.07 (0.21), residues: 536 loop : 1.16 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 354 HIS 0.008 0.002 HIS D 311 PHE 0.022 0.003 PHE F 297 TYR 0.032 0.003 TYR A 263 ARG 0.005 0.001 ARG C 173 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 427 time to evaluate : 3.479 Fit side-chains outliers start: 74 outliers final: 46 residues processed: 476 average time/residue: 2.2729 time to fit residues: 1207.8852 Evaluate side-chains 476 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 430 time to evaluate : 3.792 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 40 residues processed: 6 average time/residue: 1.9537 time to fit residues: 17.7991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 10.0000 chunk 306 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 340 optimal weight: 1.9990 chunk 282 optimal weight: 0.5980 chunk 157 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 112 optimal weight: 0.4980 chunk 178 optimal weight: 0.1980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 29096 Z= 0.177 Angle : 0.523 6.026 39472 Z= 0.271 Chirality : 0.039 0.128 4152 Planarity : 0.004 0.044 5168 Dihedral : 9.135 170.439 4128 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.15 % Allowed : 12.36 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.14), residues: 3544 helix: 1.17 (0.13), residues: 1616 sheet: 0.04 (0.24), residues: 464 loop : 1.08 (0.18), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 354 HIS 0.004 0.001 HIS G 311 PHE 0.014 0.002 PHE B 297 TYR 0.021 0.001 TYR B 263 ARG 0.004 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 424 time to evaluate : 3.582 Fit side-chains outliers start: 61 outliers final: 40 residues processed: 472 average time/residue: 2.1564 time to fit residues: 1139.1177 Evaluate side-chains 462 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 422 time to evaluate : 3.357 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 40 residues processed: 0 time to fit residues: 4.4397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 286 optimal weight: 6.9990 chunk 190 optimal weight: 0.9990 chunk 339 optimal weight: 8.9990 chunk 212 optimal weight: 0.6980 chunk 206 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 29096 Z= 0.230 Angle : 0.567 6.634 39472 Z= 0.294 Chirality : 0.041 0.130 4152 Planarity : 0.004 0.052 5168 Dihedral : 9.263 169.631 4128 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.08 % Allowed : 12.99 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.14), residues: 3544 helix: 1.09 (0.13), residues: 1616 sheet: -0.06 (0.22), residues: 536 loop : 1.16 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 354 HIS 0.006 0.001 HIS D 311 PHE 0.018 0.002 PHE G 297 TYR 0.027 0.002 TYR A 263 ARG 0.005 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 428 time to evaluate : 3.800 Fit side-chains outliers start: 59 outliers final: 44 residues processed: 469 average time/residue: 2.2015 time to fit residues: 1156.1075 Evaluate side-chains 469 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 425 time to evaluate : 3.651 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 40 residues processed: 4 average time/residue: 1.8117 time to fit residues: 12.4211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 215 optimal weight: 0.0070 chunk 231 optimal weight: 8.9990 chunk 167 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 266 optimal weight: 6.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 29096 Z= 0.213 Angle : 0.555 6.547 39472 Z= 0.287 Chirality : 0.040 0.127 4152 Planarity : 0.004 0.048 5168 Dihedral : 9.215 169.465 4128 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.05 % Allowed : 13.31 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.14), residues: 3544 helix: 1.10 (0.13), residues: 1616 sheet: -0.07 (0.22), residues: 536 loop : 1.16 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 354 HIS 0.005 0.001 HIS A 311 PHE 0.017 0.002 PHE G 297 TYR 0.025 0.002 TYR A 263 ARG 0.006 0.000 ARG G 442 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 427 time to evaluate : 3.646 Fit side-chains outliers start: 58 outliers final: 41 residues processed: 471 average time/residue: 2.2189 time to fit residues: 1170.8651 Evaluate side-chains 465 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 424 time to evaluate : 3.466 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 40 residues processed: 1 average time/residue: 1.9148 time to fit residues: 6.5931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 5.9990 chunk 325 optimal weight: 5.9990 chunk 296 optimal weight: 0.8980 chunk 316 optimal weight: 4.9990 chunk 324 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 137 optimal weight: 8.9990 chunk 248 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 299 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 29096 Z= 0.291 Angle : 0.621 7.597 39472 Z= 0.321 Chirality : 0.043 0.139 4152 Planarity : 0.005 0.054 5168 Dihedral : 9.452 168.982 4128 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.66 % Allowed : 13.88 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.14), residues: 3544 helix: 0.95 (0.13), residues: 1616 sheet: -0.15 (0.21), residues: 536 loop : 1.15 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 354 HIS 0.007 0.002 HIS G 311 PHE 0.021 0.003 PHE G 297 TYR 0.030 0.002 TYR D 263 ARG 0.007 0.001 ARG G 442 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 419 time to evaluate : 3.635 Fit side-chains outliers start: 47 outliers final: 41 residues processed: 459 average time/residue: 2.2148 time to fit residues: 1134.7183 Evaluate side-chains 458 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 417 time to evaluate : 3.564 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 40 residues processed: 1 average time/residue: 1.9071 time to fit residues: 6.8810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 334 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 232 optimal weight: 7.9990 chunk 350 optimal weight: 3.9990 chunk 322 optimal weight: 0.8980 chunk 279 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 215 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 29096 Z= 0.196 Angle : 0.548 6.374 39472 Z= 0.284 Chirality : 0.040 0.128 4152 Planarity : 0.004 0.045 5168 Dihedral : 9.189 169.260 4128 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.62 % Allowed : 14.09 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.14), residues: 3544 helix: 1.09 (0.13), residues: 1616 sheet: -0.17 (0.21), residues: 536 loop : 1.17 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 354 HIS 0.005 0.001 HIS G 311 PHE 0.016 0.002 PHE G 297 TYR 0.024 0.002 TYR B 263 ARG 0.008 0.000 ARG D 442 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 423 time to evaluate : 3.839 Fit side-chains outliers start: 46 outliers final: 41 residues processed: 463 average time/residue: 2.2091 time to fit residues: 1146.7870 Evaluate side-chains 465 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 424 time to evaluate : 3.437 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 40 residues processed: 1 average time/residue: 2.0205 time to fit residues: 6.6337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 5.9990 chunk 221 optimal weight: 0.8980 chunk 297 optimal weight: 0.0020 chunk 85 optimal weight: 0.4980 chunk 257 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 279 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 287 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 429 GLN ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 429 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.132044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.118985 restraints weight = 26269.356| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 0.80 r_work: 0.3260 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 29096 Z= 0.155 Angle : 0.505 5.934 39472 Z= 0.261 Chirality : 0.039 0.126 4152 Planarity : 0.004 0.032 5168 Dihedral : 8.886 168.205 4128 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.62 % Allowed : 14.16 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.14), residues: 3544 helix: 1.28 (0.13), residues: 1616 sheet: 0.24 (0.25), residues: 424 loop : 0.95 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 354 HIS 0.004 0.001 HIS A 311 PHE 0.012 0.002 PHE H 297 TYR 0.019 0.001 TYR A 263 ARG 0.008 0.000 ARG H 442 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14951.29 seconds wall clock time: 264 minutes 33.59 seconds (15873.59 seconds total)