Starting phenix.real_space_refine on Tue Mar 19 06:34:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t23_25610/03_2024/7t23_25610_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t23_25610/03_2024/7t23_25610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t23_25610/03_2024/7t23_25610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t23_25610/03_2024/7t23_25610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t23_25610/03_2024/7t23_25610_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t23_25610/03_2024/7t23_25610_updated.pdb" } resolution = 4.2 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= 0.003 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: 8 Type Number sf(0) Gaussians Al 5 5.89 5 P 23 5.49 5 Mg 5 5.21 5 S 94 5.16 5 C 14494 2.51 5 N 4149 2.21 5 O 4717 1.98 5 F 20 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23507 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "B" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "C" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "D" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "E" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "F" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3495 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 428} Chain: "G" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1056 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "H" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1056 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "M" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 260 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 12.39, per 1000 atoms: 0.53 Number of scatterers: 23507 At special positions: 0 Unit cell: (160.74, 135.36, 151.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 94 16.00 P 23 15.00 Al 5 13.00 Mg 5 11.99 F 20 9.00 O 4717 8.00 N 4149 7.00 C 14494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS G 568 " distance=2.04 Simple disulfide: pdb=" SG CYS D 103 " - pdb=" SG CYS H 568 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM23496 O3A ADP F1001 .*. O " rejected from bonding due to valence issues. Atom "HETATM23397 O3A ADP C1001 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.73 Conformation dependent library (CDL) restraints added in 4.0 seconds 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5544 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 142 helices and 10 sheets defined 53.4% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.62 Creating SS restraints... Processing helix chain 'A' and resid 31 through 43 Processing helix chain 'A' and resid 46 through 52 removed outlier: 4.103A pdb=" N ASP A 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 52 " --> pdb=" O ASP A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 84 through 93 Processing helix chain 'A' and resid 97 through 100 No H-bonds generated for 'chain 'A' and resid 97 through 100' Processing helix chain 'A' and resid 103 through 112 Processing helix chain 'A' and resid 119 through 147 Processing helix chain 'A' and resid 154 through 173 Processing helix chain 'A' and resid 182 through 198 Processing helix chain 'A' and resid 212 through 218 removed outlier: 3.931A pdb=" N LYS A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 251 removed outlier: 3.569A pdb=" N MET A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 251 " --> pdb=" O ASN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 283 through 286 No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 291 through 297 removed outlier: 4.559A pdb=" N ARG A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 307 Processing helix chain 'A' and resid 320 through 333 removed outlier: 3.508A pdb=" N GLU A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 357 through 375 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 421 through 424 No H-bonds generated for 'chain 'A' and resid 421 through 424' Processing helix chain 'B' and resid 31 through 43 removed outlier: 3.503A pdb=" N LEU B 41 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B 43 " --> pdb=" O GLY B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 63 through 77 Processing helix chain 'B' and resid 84 through 94 Processing helix chain 'B' and resid 97 through 100 No H-bonds generated for 'chain 'B' and resid 97 through 100' Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.566A pdb=" N SER B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 147 removed outlier: 3.714A pdb=" N ILE B 119 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N SER B 120 " --> pdb=" O ALA B 117 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 131 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 172 Processing helix chain 'B' and resid 182 through 198 Processing helix chain 'B' and resid 212 through 218 removed outlier: 3.974A pdb=" N LYS B 217 " --> pdb=" O ASP B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 249 Processing helix chain 'B' and resid 265 through 277 Processing helix chain 'B' and resid 281 through 286 Processing helix chain 'B' and resid 291 through 307 Processing helix chain 'B' and resid 320 through 334 Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 357 through 375 Processing helix chain 'B' and resid 387 through 391 Processing helix chain 'B' and resid 399 through 401 No H-bonds generated for 'chain 'B' and resid 399 through 401' Processing helix chain 'B' and resid 408 through 411 No H-bonds generated for 'chain 'B' and resid 408 through 411' Processing helix chain 'B' and resid 421 through 424 No H-bonds generated for 'chain 'B' and resid 421 through 424' Processing helix chain 'C' and resid 31 through 43 Processing helix chain 'C' and resid 46 through 52 removed outlier: 4.079A pdb=" N ASP C 49 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA C 52 " --> pdb=" O ASP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 63 through 77 Processing helix chain 'C' and resid 84 through 93 Processing helix chain 'C' and resid 97 through 100 No H-bonds generated for 'chain 'C' and resid 97 through 100' Processing helix chain 'C' and resid 102 through 112 removed outlier: 3.597A pdb=" N LEU C 109 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 147 Processing helix chain 'C' and resid 154 through 176 removed outlier: 5.304A pdb=" N LYS C 175 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASP C 176 " --> pdb=" O ARG C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 198 Processing helix chain 'C' and resid 212 through 218 removed outlier: 3.835A pdb=" N LYS C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 249 Processing helix chain 'C' and resid 265 through 277 Processing helix chain 'C' and resid 281 through 286 Processing helix chain 'C' and resid 291 through 307 Processing helix chain 'C' and resid 320 through 334 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 357 through 375 Processing helix chain 'C' and resid 388 through 391 No H-bonds generated for 'chain 'C' and resid 388 through 391' Processing helix chain 'C' and resid 399 through 401 No H-bonds generated for 'chain 'C' and resid 399 through 401' Processing helix chain 'C' and resid 408 through 411 No H-bonds generated for 'chain 'C' and resid 408 through 411' Processing helix chain 'C' and resid 421 through 424 No H-bonds generated for 'chain 'C' and resid 421 through 424' Processing helix chain 'D' and resid 31 through 43 removed outlier: 3.697A pdb=" N LEU D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU D 43 " --> pdb=" O GLY D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 63 through 77 Processing helix chain 'D' and resid 84 through 94 Processing helix chain 'D' and resid 97 through 100 No H-bonds generated for 'chain 'D' and resid 97 through 100' Processing helix chain 'D' and resid 103 through 112 removed outlier: 3.699A pdb=" N SER D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 147 removed outlier: 4.704A pdb=" N SER D 120 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 171 Processing helix chain 'D' and resid 182 through 197 Processing helix chain 'D' and resid 212 through 218 removed outlier: 4.026A pdb=" N LYS D 217 " --> pdb=" O ASP D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 Processing helix chain 'D' and resid 265 through 277 Processing helix chain 'D' and resid 281 through 286 Processing helix chain 'D' and resid 291 through 307 Processing helix chain 'D' and resid 320 through 334 Processing helix chain 'D' and resid 345 through 347 No H-bonds generated for 'chain 'D' and resid 345 through 347' Processing helix chain 'D' and resid 357 through 375 Processing helix chain 'D' and resid 387 through 389 No H-bonds generated for 'chain 'D' and resid 387 through 389' Processing helix chain 'D' and resid 399 through 401 No H-bonds generated for 'chain 'D' and resid 399 through 401' Processing helix chain 'D' and resid 408 through 411 No H-bonds generated for 'chain 'D' and resid 408 through 411' Processing helix chain 'D' and resid 421 through 424 No H-bonds generated for 'chain 'D' and resid 421 through 424' Processing helix chain 'E' and resid 31 through 43 Processing helix chain 'E' and resid 46 through 52 removed outlier: 3.917A pdb=" N ASP E 49 " --> pdb=" O GLU E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 Processing helix chain 'E' and resid 84 through 94 removed outlier: 3.502A pdb=" N ALA E 88 " --> pdb=" O LEU E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 119 through 147 Processing helix chain 'E' and resid 154 through 171 removed outlier: 3.738A pdb=" N SER E 171 " --> pdb=" O LYS E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 Processing helix chain 'E' and resid 212 through 218 removed outlier: 3.997A pdb=" N LYS E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 251 Processing helix chain 'E' and resid 265 through 277 Processing helix chain 'E' and resid 281 through 286 Processing helix chain 'E' and resid 291 through 307 Processing helix chain 'E' and resid 320 through 334 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 357 through 375 Processing helix chain 'E' and resid 387 through 389 No H-bonds generated for 'chain 'E' and resid 387 through 389' Processing helix chain 'E' and resid 399 through 401 No H-bonds generated for 'chain 'E' and resid 399 through 401' Processing helix chain 'E' and resid 408 through 411 No H-bonds generated for 'chain 'E' and resid 408 through 411' Processing helix chain 'E' and resid 421 through 424 No H-bonds generated for 'chain 'E' and resid 421 through 424' Processing helix chain 'F' and resid 31 through 43 removed outlier: 3.567A pdb=" N MET F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU F 43 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 54 Processing helix chain 'F' and resid 57 through 59 No H-bonds generated for 'chain 'F' and resid 57 through 59' Processing helix chain 'F' and resid 63 through 78 Processing helix chain 'F' and resid 84 through 94 Processing helix chain 'F' and resid 103 through 112 removed outlier: 3.631A pdb=" N SER F 110 " --> pdb=" O LEU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 147 Processing helix chain 'F' and resid 154 through 170 Processing helix chain 'F' and resid 182 through 196 Processing helix chain 'F' and resid 212 through 218 removed outlier: 4.020A pdb=" N LYS F 216 " --> pdb=" O ASP F 212 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 249 Processing helix chain 'F' and resid 265 through 277 Processing helix chain 'F' and resid 281 through 286 Processing helix chain 'F' and resid 291 through 307 Processing helix chain 'F' and resid 320 through 334 Processing helix chain 'F' and resid 345 through 347 No H-bonds generated for 'chain 'F' and resid 345 through 347' Processing helix chain 'F' and resid 357 through 375 Processing helix chain 'F' and resid 387 through 391 removed outlier: 3.535A pdb=" N GLU F 390 " --> pdb=" O ARG F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 401 No H-bonds generated for 'chain 'F' and resid 399 through 401' Processing helix chain 'F' and resid 408 through 411 No H-bonds generated for 'chain 'F' and resid 408 through 411' Processing helix chain 'F' and resid 421 through 424 No H-bonds generated for 'chain 'F' and resid 421 through 424' Processing helix chain 'G' and resid 450 through 460 removed outlier: 3.848A pdb=" N LEU G 454 " --> pdb=" O THR G 450 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 465 removed outlier: 3.550A pdb=" N ALA G 465 " --> pdb=" O PRO G 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 462 through 465' Processing helix chain 'G' and resid 483 through 494 removed outlier: 3.783A pdb=" N GLU G 487 " --> pdb=" O GLY G 483 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU G 488 " --> pdb=" O LEU G 484 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL G 489 " --> pdb=" O PHE G 485 " (cutoff:3.500A) Processing helix chain 'G' and resid 500 through 506 Processing helix chain 'G' and resid 512 through 521 removed outlier: 4.066A pdb=" N GLU G 517 " --> pdb=" O ALA G 514 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET G 521 " --> pdb=" O LYS G 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 561 Processing helix chain 'G' and resid 565 through 580 removed outlier: 4.162A pdb=" N LEU G 569 " --> pdb=" O ASN G 565 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU G 577 " --> pdb=" O THR G 573 " (cutoff:3.500A) Processing helix chain 'H' and resid 450 through 460 Processing helix chain 'H' and resid 464 through 467 Processing helix chain 'H' and resid 483 through 494 removed outlier: 3.648A pdb=" N LEU H 488 " --> pdb=" O LEU H 484 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL H 489 " --> pdb=" O PHE H 485 " (cutoff:3.500A) Processing helix chain 'H' and resid 500 through 506 removed outlier: 3.754A pdb=" N LEU H 504 " --> pdb=" O THR H 500 " (cutoff:3.500A) Processing helix chain 'H' and resid 513 through 521 Processing helix chain 'H' and resid 529 through 561 Processing helix chain 'H' and resid 565 through 574 removed outlier: 3.564A pdb=" N TRP H 572 " --> pdb=" O CYS H 568 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR H 573 " --> pdb=" O LEU H 569 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 379 through 383 removed outlier: 3.608A pdb=" N SER A 383 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU A 414 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ALA A 230 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET A 416 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N PHE A 417 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE A 438 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR A 419 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE A 436 " --> pdb=" O TYR A 419 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY A 447 " --> pdb=" O ILE A 438 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 310 through 312 removed outlier: 6.425A pdb=" N VAL A 256 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU A 339 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N PHE A 259 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N MET A 341 " --> pdb=" O PHE A 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 451 through 454 Processing sheet with id= D, first strand: chain 'B' and resid 379 through 383 removed outlier: 3.711A pdb=" N SER B 383 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B 414 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ALA B 230 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N MET B 416 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 440 " --> pdb=" O ILE B 415 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE B 417 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE B 438 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N TYR B 419 " --> pdb=" O ILE B 436 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ILE B 436 " --> pdb=" O TYR B 419 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 310 through 313 removed outlier: 6.411A pdb=" N VAL B 256 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ASP B 313 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE B 258 " --> pdb=" O ASP B 313 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU B 257 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE B 340 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE B 259 " --> pdb=" O ILE B 340 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE B 342 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 459 through 462 removed outlier: 6.423A pdb=" N ILE C 415 " --> pdb=" O GLY C 439 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 414 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL C 379 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL C 229 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA C 381 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA C 231 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 459 through 462 removed outlier: 6.144A pdb=" N ILE D 415 " --> pdb=" O GLY D 439 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU D 414 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL D 379 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL D 229 " --> pdb=" O VAL D 379 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ALA D 381 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA D 231 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER D 383 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE D 340 " --> pdb=" O PRO D 378 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE D 340 " --> pdb=" O PRO D 255 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU D 257 " --> pdb=" O ILE D 340 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE D 342 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE D 259 " --> pdb=" O ILE D 342 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 310 through 313 removed outlier: 6.421A pdb=" N VAL E 256 " --> pdb=" O TYR E 311 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ASP E 313 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE E 258 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU E 257 " --> pdb=" O GLY E 338 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE E 340 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N PHE E 259 " --> pdb=" O ILE E 340 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE E 342 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ILE E 342 " --> pdb=" O PRO E 378 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL E 380 " --> pdb=" O ILE E 342 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 459 through 462 removed outlier: 6.408A pdb=" N ILE E 415 " --> pdb=" O GLY E 439 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 459 through 462 removed outlier: 6.456A pdb=" N ILE F 415 " --> pdb=" O GLY F 439 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU F 226 " --> pdb=" O LEU F 414 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N MET F 416 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE F 228 " --> pdb=" O MET F 416 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE F 418 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ALA F 230 " --> pdb=" O ILE F 418 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL F 379 " --> pdb=" O ILE F 227 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL F 229 " --> pdb=" O VAL F 379 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA F 381 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ALA F 231 " --> pdb=" O ALA F 381 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER F 383 " --> pdb=" O ALA F 231 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N VAL F 380 " --> pdb=" O GLY F 338 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE F 340 " --> pdb=" O VAL F 380 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU F 382 " --> pdb=" O ILE F 340 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ILE F 342 " --> pdb=" O LEU F 382 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE F 340 " --> pdb=" O PRO F 255 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU F 257 " --> pdb=" O ILE F 340 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE F 342 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE F 259 " --> pdb=" O ILE F 342 " (cutoff:3.500A) 1095 hydrogen bonds defined for protein. 3051 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: 7.12 Time building geometry restraints manager: 10.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8128 1.34 - 1.46: 4787 1.46 - 1.59: 10703 1.59 - 1.71: 40 1.71 - 1.84: 198 Bond restraints: 23856 Sorted by residual: bond pdb=" F4 ALF B1002 " pdb="AL ALF B1002 " ideal model delta sigma weight residual 1.686 1.805 -0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" F1 ALF D1002 " pdb="AL ALF D1002 " ideal model delta sigma weight residual 1.684 1.803 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" F4 ALF F1002 " pdb="AL ALF F1002 " ideal model delta sigma weight residual 1.686 1.804 -0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" F1 ALF E1002 " pdb="AL ALF E1002 " ideal model delta sigma weight residual 1.684 1.802 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" F4 ALF E1002 " pdb="AL ALF E1002 " ideal model delta sigma weight residual 1.686 1.804 -0.118 2.00e-02 2.50e+03 3.45e+01 ... (remaining 23851 not shown) Histogram of bond angle deviations from ideal: 88.74 - 106.84: 761 106.84 - 124.93: 31265 124.93 - 143.03: 321 143.03 - 161.12: 0 161.12 - 179.22: 10 Bond angle restraints: 32357 Sorted by residual: angle pdb=" F1 ALF E1002 " pdb="AL ALF E1002 " pdb=" F2 ALF E1002 " ideal model delta sigma weight residual 108.68 179.06 -70.38 3.00e+00 1.11e-01 5.50e+02 angle pdb=" F1 ALF C1002 " pdb="AL ALF C1002 " pdb=" F2 ALF C1002 " ideal model delta sigma weight residual 108.68 179.05 -70.37 3.00e+00 1.11e-01 5.50e+02 angle pdb=" F1 ALF D1002 " pdb="AL ALF D1002 " pdb=" F2 ALF D1002 " ideal model delta sigma weight residual 108.68 179.05 -70.37 3.00e+00 1.11e-01 5.50e+02 angle pdb=" F1 ALF F1002 " pdb="AL ALF F1002 " pdb=" F2 ALF F1002 " ideal model delta sigma weight residual 108.68 179.03 -70.35 3.00e+00 1.11e-01 5.50e+02 angle pdb=" F1 ALF B1002 " pdb="AL ALF B1002 " pdb=" F2 ALF B1002 " ideal model delta sigma weight residual 108.68 178.81 -70.13 3.00e+00 1.11e-01 5.46e+02 ... (remaining 32352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.78: 14509 27.78 - 55.56: 178 55.56 - 83.34: 14 83.34 - 111.12: 2 111.12 - 138.89: 1 Dihedral angle restraints: 14704 sinusoidal: 6152 harmonic: 8552 Sorted by residual: dihedral pdb=" C5' ADP D1001 " pdb=" O5' ADP D1001 " pdb=" PA ADP D1001 " pdb=" O2A ADP D1001 " ideal model delta sinusoidal sigma weight residual 300.00 161.11 138.89 1 2.00e+01 2.50e-03 4.21e+01 dihedral pdb=" C5' ADP E1001 " pdb=" O5' ADP E1001 " pdb=" PA ADP E1001 " pdb=" O2A ADP E1001 " ideal model delta sinusoidal sigma weight residual -60.00 -146.95 86.96 1 2.00e+01 2.50e-03 2.27e+01 dihedral pdb=" C5' ADP F1001 " pdb=" O5' ADP F1001 " pdb=" PA ADP F1001 " pdb=" O2A ADP F1001 " ideal model delta sinusoidal sigma weight residual -60.00 16.62 -76.61 1 2.00e+01 2.50e-03 1.84e+01 ... (remaining 14701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2497 0.028 - 0.057: 747 0.057 - 0.085: 251 0.085 - 0.114: 120 0.114 - 0.142: 67 Chirality restraints: 3682 Sorted by residual: chirality pdb=" CA VAL C 377 " pdb=" N VAL C 377 " pdb=" C VAL C 377 " pdb=" CB VAL C 377 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA VAL B 26 " pdb=" N VAL B 26 " pdb=" C VAL B 26 " pdb=" CB VAL B 26 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE C 436 " pdb=" N ILE C 436 " pdb=" C ILE C 436 " pdb=" CB ILE C 436 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 3679 not shown) Planarity restraints: 4236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 199 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO A 200 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 63 " 0.018 5.00e-02 4.00e+02 2.65e-02 1.12e+00 pdb=" N PRO C 64 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 113 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO D 114 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO D 114 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 114 " 0.015 5.00e-02 4.00e+02 ... (remaining 4233 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 342 2.57 - 3.15: 20539 3.15 - 3.74: 38310 3.74 - 4.32: 51687 4.32 - 4.90: 85147 Nonbonded interactions: 196025 Sorted by model distance: nonbonded pdb=" F4 ALF C1002 " pdb="MG MG C1003 " model vdw 1.991 2.120 nonbonded pdb=" F1 ALF D1002 " pdb="MG MG D1003 " model vdw 1.992 2.120 nonbonded pdb=" F4 ALF D1002 " pdb="MG MG D1003 " model vdw 1.993 2.120 nonbonded pdb=" F1 ALF E1002 " pdb="MG MG E1003 " model vdw 1.993 2.120 nonbonded pdb=" F1 ALF C1002 " pdb="MG MG C1003 " model vdw 1.993 2.120 ... (remaining 196020 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' and resid 24 through 471) selection = (chain 'C' and resid 24 through 471) selection = (chain 'D' and resid 24 through 471) selection = (chain 'E' and resid 24 through 471) selection = (chain 'F' and resid 24 through 471) } ncs_group { reference = 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=0.42 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: 0.750 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: 5.290 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 61.160 Find NCS groups from input model: 1.810 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: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 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 0.119 23856 Z= 0.261 Angle : 1.428 70.375 32357 Z= 0.525 Chirality : 0.038 0.142 3682 Planarity : 0.003 0.036 4236 Dihedral : 9.478 138.895 9154 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.28 % Favored : 97.55 % Rotamer: Outliers : 1.51 % Allowed : 3.49 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 1.97 (0.16), residues: 2938 helix: 2.95 (0.13), residues: 1584 sheet: -1.22 (0.27), residues: 346 loop : -0.46 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 48 HIS 0.003 0.001 HIS B 334 PHE 0.009 0.001 PHE F 197 TYR 0.005 0.001 TYR F 344 ARG 0.003 0.000 ARG E 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 712 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8528 (m-80) cc_final: 0.7980 (m-80) REVERT: A 67 HIS cc_start: 0.9025 (m-70) cc_final: 0.8668 (m90) REVERT: A 132 VAL cc_start: 0.9252 (t) cc_final: 0.9006 (m) REVERT: A 156 ASP cc_start: 0.9263 (m-30) cc_final: 0.9033 (t0) REVERT: A 157 LEU cc_start: 0.8274 (mt) cc_final: 0.7935 (mp) REVERT: A 163 SER cc_start: 0.8494 (t) cc_final: 0.8272 (p) REVERT: A 196 LEU cc_start: 0.9510 (mt) cc_final: 0.9031 (mt) REVERT: A 201 HIS cc_start: 0.7499 (m-70) cc_final: 0.7224 (m170) REVERT: A 240 PHE cc_start: 0.9321 (t80) cc_final: 0.9075 (t80) REVERT: A 332 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7848 (ttt180) REVERT: A 385 LEU cc_start: 0.8839 (mt) cc_final: 0.8512 (mm) REVERT: A 426 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8276 (pm20) REVERT: B 49 ASP cc_start: 0.7813 (m-30) cc_final: 0.7008 (p0) REVERT: B 202 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7343 (m-30) REVERT: B 257 LEU cc_start: 0.8932 (tp) cc_final: 0.8574 (mm) REVERT: B 348 MET cc_start: 0.7878 (mtp) cc_final: 0.7480 (ttm) REVERT: B 364 ILE cc_start: 0.9128 (mt) cc_final: 0.8851 (mt) REVERT: C 85 ILE cc_start: 0.8867 (mt) cc_final: 0.7780 (mp) REVERT: C 150 GLN cc_start: 0.8349 (tt0) cc_final: 0.7994 (pp30) REVERT: C 337 ILE cc_start: 0.9501 (mt) cc_final: 0.9291 (mm) REVERT: C 339 LEU cc_start: 0.9646 (tp) cc_final: 0.9369 (tt) REVERT: C 363 GLU cc_start: 0.8371 (tp30) cc_final: 0.7979 (tp30) REVERT: C 373 LYS cc_start: 0.8696 (mtpt) cc_final: 0.8375 (mttm) REVERT: C 387 ARG cc_start: 0.6683 (mtt-85) cc_final: 0.6019 (ttm-80) REVERT: C 417 PHE cc_start: 0.8637 (m-80) cc_final: 0.8343 (m-10) REVERT: D 32 GLU cc_start: 0.9572 (mp0) cc_final: 0.9277 (pm20) REVERT: D 34 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7476 (pt0) REVERT: D 122 TYR cc_start: 0.7925 (m-10) cc_final: 0.7616 (m-80) REVERT: D 345 LEU cc_start: 0.9123 (mt) cc_final: 0.8819 (mt) REVERT: D 356 ASN cc_start: 0.8334 (t0) cc_final: 0.8134 (t0) REVERT: D 443 ASN cc_start: 0.7996 (m-40) cc_final: 0.7022 (m110) REVERT: D 453 PHE cc_start: 0.8066 (t80) cc_final: 0.7843 (t80) REVERT: E 72 MET cc_start: 0.4240 (mtt) cc_final: 0.3871 (mtt) REVERT: E 135 MET cc_start: 0.7566 (ttm) cc_final: 0.6718 (tmm) REVERT: E 234 SER cc_start: 0.9515 (m) cc_final: 0.9255 (p) REVERT: E 259 PHE cc_start: 0.7762 (m-80) cc_final: 0.7348 (m-10) REVERT: E 339 LEU cc_start: 0.9237 (tp) cc_final: 0.8834 (tt) REVERT: E 364 ILE cc_start: 0.8777 (mt) cc_final: 0.8467 (mt) REVERT: E 384 GLN cc_start: 0.7193 (mm-40) cc_final: 0.6894 (mm110) REVERT: E 443 ASN cc_start: 0.7933 (m-40) cc_final: 0.6750 (t0) REVERT: F 238 THR cc_start: 0.9214 (m) cc_final: 0.8991 (m) REVERT: F 263 MET cc_start: 0.8190 (mtp) cc_final: 0.7820 (mmm) REVERT: F 270 MET cc_start: 0.8777 (mtm) cc_final: 0.8547 (mmm) REVERT: F 321 THR cc_start: 0.8901 (m) cc_final: 0.8664 (t) REVERT: G 522 TRP cc_start: 0.7600 (t60) cc_final: 0.7236 (t-100) REVERT: G 553 GLU cc_start: 0.8685 (tt0) cc_final: 0.7847 (mp0) REVERT: G 572 TRP cc_start: 0.7682 (t60) cc_final: 0.6683 (t-100) REVERT: G 577 GLU cc_start: 0.9004 (mp0) cc_final: 0.8513 (pp20) REVERT: H 451 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6598 (mmt) REVERT: H 529 ASN cc_start: 0.8651 (p0) cc_final: 0.8190 (p0) REVERT: H 534 THR cc_start: 0.8440 (m) cc_final: 0.7736 (p) outliers start: 38 outliers final: 8 residues processed: 740 average time/residue: 0.3967 time to fit residues: 429.9103 Evaluate side-chains 431 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 420 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 9.9990 chunk 220 optimal weight: 40.0000 chunk 122 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 228 optimal weight: 20.0000 chunk 88 optimal weight: 0.0370 chunk 138 optimal weight: 8.9990 chunk 169 optimal weight: 0.5980 chunk 264 optimal weight: 6.9990 overall best weight: 3.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 HIS A 454 ASN B 67 HIS ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 HIS B 243 ASN C 376 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN ** E 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 399 ASN ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 533 GLN H 551 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23856 Z= 0.243 Angle : 1.029 30.710 32357 Z= 0.412 Chirality : 0.041 0.260 3682 Planarity : 0.005 0.154 4236 Dihedral : 6.224 103.754 3418 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.69 % Favored : 97.11 % Rotamer: Outliers : 0.24 % Allowed : 2.42 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 1.32 (0.16), residues: 2938 helix: 2.15 (0.13), residues: 1593 sheet: -1.05 (0.28), residues: 325 loop : -0.49 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 294 HIS 0.013 0.002 HIS H 541 PHE 0.029 0.002 PHE A 166 TYR 0.029 0.001 TYR F 122 ARG 0.012 0.001 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 514 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8695 (m-80) cc_final: 0.7929 (m-80) REVERT: A 67 HIS cc_start: 0.9057 (m-70) cc_final: 0.8727 (m90) REVERT: A 132 VAL cc_start: 0.8858 (t) cc_final: 0.8635 (t) REVERT: A 156 ASP cc_start: 0.9209 (m-30) cc_final: 0.8978 (t0) REVERT: A 157 LEU cc_start: 0.8221 (mt) cc_final: 0.7916 (mp) REVERT: A 163 SER cc_start: 0.8478 (t) cc_final: 0.8276 (p) REVERT: A 213 ASP cc_start: 0.8268 (m-30) cc_final: 0.8053 (t0) REVERT: A 242 MET cc_start: 0.8168 (tmm) cc_final: 0.7452 (tmm) REVERT: A 244 LEU cc_start: 0.9193 (mt) cc_final: 0.8946 (mt) REVERT: A 269 MET cc_start: 0.8557 (mmt) cc_final: 0.8309 (mmm) REVERT: A 318 LEU cc_start: 0.7632 (mt) cc_final: 0.7396 (mt) REVERT: A 324 ARG cc_start: 0.8562 (ppt170) cc_final: 0.8031 (ttp80) REVERT: A 426 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8303 (pm20) REVERT: A 427 ASN cc_start: 0.8208 (p0) cc_final: 0.7162 (p0) REVERT: A 451 LEU cc_start: 0.8743 (mt) cc_final: 0.8463 (mt) REVERT: B 49 ASP cc_start: 0.7795 (m-30) cc_final: 0.7067 (p0) REVERT: B 257 LEU cc_start: 0.9169 (tp) cc_final: 0.8702 (mt) REVERT: B 270 MET cc_start: 0.8431 (tmm) cc_final: 0.8186 (tmm) REVERT: B 348 MET cc_start: 0.8085 (mtp) cc_final: 0.7575 (ttm) REVERT: B 364 ILE cc_start: 0.9184 (mt) cc_final: 0.8977 (mt) REVERT: C 85 ILE cc_start: 0.8811 (mt) cc_final: 0.8143 (mp) REVERT: C 150 GLN cc_start: 0.8507 (tt0) cc_final: 0.8093 (pp30) REVERT: C 235 MET cc_start: 0.8626 (mmp) cc_final: 0.8285 (mmp) REVERT: C 363 GLU cc_start: 0.8495 (tp30) cc_final: 0.7952 (tp30) REVERT: C 366 ARG cc_start: 0.8643 (tmm-80) cc_final: 0.7341 (ttp80) REVERT: C 417 PHE cc_start: 0.8581 (m-80) cc_final: 0.8299 (m-10) REVERT: D 32 GLU cc_start: 0.9568 (mp0) cc_final: 0.9338 (pm20) REVERT: D 34 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7448 (pt0) REVERT: D 344 TYR cc_start: 0.7757 (p90) cc_final: 0.7503 (p90) REVERT: D 345 LEU cc_start: 0.9218 (mt) cc_final: 0.8870 (mt) REVERT: E 135 MET cc_start: 0.7207 (ttm) cc_final: 0.6351 (tmm) REVERT: E 202 ASP cc_start: 0.7293 (m-30) cc_final: 0.7068 (m-30) REVERT: E 234 SER cc_start: 0.9587 (m) cc_final: 0.9318 (p) REVERT: E 373 LYS cc_start: 0.9025 (mmtm) cc_final: 0.8781 (mmmm) REVERT: E 419 TYR cc_start: 0.7836 (t80) cc_final: 0.7344 (t80) REVERT: F 152 ARG cc_start: 0.8832 (mtt180) cc_final: 0.8568 (mpp80) REVERT: F 250 MET cc_start: 0.8649 (ptm) cc_final: 0.8275 (ptm) REVERT: F 263 MET cc_start: 0.8232 (mtp) cc_final: 0.7963 (mtm) REVERT: F 321 THR cc_start: 0.8887 (m) cc_final: 0.8618 (t) REVERT: F 414 LEU cc_start: 0.9165 (tp) cc_final: 0.8807 (tp) REVERT: G 472 GLU cc_start: 0.6608 (mm-30) cc_final: 0.6386 (mm-30) REVERT: G 522 TRP cc_start: 0.7542 (t60) cc_final: 0.7085 (t-100) REVERT: G 528 LYS cc_start: 0.7708 (mmpt) cc_final: 0.7500 (mmmt) REVERT: G 553 GLU cc_start: 0.8536 (tt0) cc_final: 0.7934 (mp0) REVERT: G 572 TRP cc_start: 0.7601 (t60) cc_final: 0.6597 (t-100) REVERT: G 577 GLU cc_start: 0.8997 (mp0) cc_final: 0.8531 (pp20) REVERT: H 451 MET cc_start: 0.7449 (tpt) cc_final: 0.7232 (mmt) REVERT: H 548 GLU cc_start: 0.8780 (tp30) cc_final: 0.8506 (tp30) outliers start: 6 outliers final: 2 residues processed: 519 average time/residue: 0.3783 time to fit residues: 292.3954 Evaluate side-chains 385 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 383 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 219 optimal weight: 6.9990 chunk 179 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 264 optimal weight: 40.0000 chunk 285 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 262 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 212 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN C 222 GLN C 376 ASN D 118 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN ** G 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 551 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 23856 Z= 0.354 Angle : 1.089 32.871 32357 Z= 0.450 Chirality : 0.042 0.227 3682 Planarity : 0.005 0.063 4236 Dihedral : 6.490 96.674 3418 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.51 % Favored : 96.29 % Rotamer: Outliers : 0.20 % Allowed : 3.38 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 0.60 (0.15), residues: 2938 helix: 1.45 (0.13), residues: 1591 sheet: -1.19 (0.28), residues: 328 loop : -0.65 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 522 HIS 0.007 0.001 HIS H 541 PHE 0.029 0.003 PHE C 166 TYR 0.020 0.002 TYR F 122 ARG 0.010 0.001 ARG H 452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 459 time to evaluate : 3.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8755 (m-80) cc_final: 0.7899 (m-80) REVERT: A 67 HIS cc_start: 0.9093 (m-70) cc_final: 0.8753 (m90) REVERT: A 69 PHE cc_start: 0.9143 (t80) cc_final: 0.8938 (t80) REVERT: A 163 SER cc_start: 0.8364 (t) cc_final: 0.8096 (p) REVERT: A 213 ASP cc_start: 0.8543 (m-30) cc_final: 0.8043 (t0) REVERT: A 270 MET cc_start: 0.7589 (mmt) cc_final: 0.7386 (mmt) REVERT: A 324 ARG cc_start: 0.8633 (ppt170) cc_final: 0.8169 (ttp80) REVERT: A 341 MET cc_start: 0.7589 (ttp) cc_final: 0.7377 (ttp) REVERT: A 348 MET cc_start: 0.9022 (ttm) cc_final: 0.8652 (tpp) REVERT: A 426 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8365 (pm20) REVERT: A 427 ASN cc_start: 0.8192 (p0) cc_final: 0.7274 (p0) REVERT: A 463 TYR cc_start: 0.8123 (t80) cc_final: 0.7915 (t80) REVERT: B 49 ASP cc_start: 0.7900 (m-30) cc_final: 0.7118 (p0) REVERT: B 112 ASN cc_start: 0.7592 (m110) cc_final: 0.7044 (p0) REVERT: B 257 LEU cc_start: 0.9227 (tp) cc_final: 0.8748 (mp) REVERT: B 270 MET cc_start: 0.8646 (tmm) cc_final: 0.8239 (tmm) REVERT: B 348 MET cc_start: 0.8411 (mtp) cc_final: 0.8107 (ttm) REVERT: B 440 LYS cc_start: 0.8466 (tmtt) cc_final: 0.8253 (tmtt) REVERT: C 85 ILE cc_start: 0.8972 (mt) cc_final: 0.8297 (mp) REVERT: C 150 GLN cc_start: 0.8625 (tt0) cc_final: 0.8230 (tp40) REVERT: C 235 MET cc_start: 0.8804 (mmp) cc_final: 0.8347 (mmp) REVERT: C 263 MET cc_start: 0.8933 (mtp) cc_final: 0.7921 (ttm) REVERT: C 268 ILE cc_start: 0.9394 (mm) cc_final: 0.9167 (mm) REVERT: C 363 GLU cc_start: 0.8470 (tp30) cc_final: 0.8051 (tp30) REVERT: C 366 ARG cc_start: 0.8741 (tmm-80) cc_final: 0.7494 (ttp80) REVERT: C 417 PHE cc_start: 0.8701 (m-80) cc_final: 0.8319 (m-10) REVERT: C 440 LYS cc_start: 0.6344 (mmmt) cc_final: 0.5328 (mmtp) REVERT: D 32 GLU cc_start: 0.9595 (mp0) cc_final: 0.9365 (pm20) REVERT: D 235 MET cc_start: 0.7509 (mmp) cc_final: 0.6458 (mmm) REVERT: D 318 LEU cc_start: 0.8496 (mm) cc_final: 0.8236 (mm) REVERT: D 356 ASN cc_start: 0.8698 (t0) cc_final: 0.8461 (t0) REVERT: E 135 MET cc_start: 0.7369 (ttm) cc_final: 0.6804 (tmm) REVERT: E 153 THR cc_start: 0.8502 (p) cc_final: 0.7778 (p) REVERT: E 234 SER cc_start: 0.9671 (m) cc_final: 0.9242 (p) REVERT: E 235 MET cc_start: 0.8484 (mmt) cc_final: 0.7198 (mmt) REVERT: E 270 MET cc_start: 0.8768 (ttt) cc_final: 0.8483 (ttm) REVERT: E 337 ILE cc_start: 0.8113 (tp) cc_final: 0.7782 (tp) REVERT: E 364 ILE cc_start: 0.8858 (mt) cc_final: 0.8556 (mt) REVERT: E 366 ARG cc_start: 0.9193 (ttp-110) cc_final: 0.8904 (ttp80) REVERT: E 373 LYS cc_start: 0.9112 (mmtm) cc_final: 0.8880 (mmmm) REVERT: E 419 TYR cc_start: 0.8011 (t80) cc_final: 0.7639 (t80) REVERT: F 42 MET cc_start: -0.1294 (mtp) cc_final: -0.1497 (mtp) REVERT: F 152 ARG cc_start: 0.8860 (mtt180) cc_final: 0.8592 (mpp80) REVERT: F 263 MET cc_start: 0.8437 (mtp) cc_final: 0.7998 (mtm) REVERT: F 321 THR cc_start: 0.8895 (m) cc_final: 0.8630 (t) REVERT: F 341 MET cc_start: 0.8392 (tpp) cc_final: 0.8094 (tpp) REVERT: F 414 LEU cc_start: 0.9199 (tp) cc_final: 0.8802 (tp) REVERT: G 472 GLU cc_start: 0.6656 (mm-30) cc_final: 0.6445 (mm-30) REVERT: G 522 TRP cc_start: 0.7395 (t60) cc_final: 0.7037 (t-100) REVERT: G 528 LYS cc_start: 0.7701 (mmpt) cc_final: 0.7435 (mmmt) REVERT: G 553 GLU cc_start: 0.8565 (tt0) cc_final: 0.7995 (mp0) REVERT: G 577 GLU cc_start: 0.8994 (mp0) cc_final: 0.8451 (pp20) outliers start: 5 outliers final: 0 residues processed: 462 average time/residue: 0.4042 time to fit residues: 281.5570 Evaluate side-chains 341 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 126 optimal weight: 0.6980 chunk 177 optimal weight: 20.0000 chunk 265 optimal weight: 5.9990 chunk 281 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 GLN ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 GLN ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 23856 Z= 0.310 Angle : 1.064 31.693 32357 Z= 0.438 Chirality : 0.042 0.191 3682 Planarity : 0.005 0.061 4236 Dihedral : 6.630 97.346 3418 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.68 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 2938 helix: 1.13 (0.13), residues: 1592 sheet: -1.16 (0.29), residues: 328 loop : -0.67 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 294 HIS 0.010 0.002 HIS B 67 PHE 0.020 0.002 PHE G 543 TYR 0.014 0.002 TYR B 122 ARG 0.011 0.001 ARG F 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 426 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8702 (m-80) cc_final: 0.7875 (m-80) REVERT: A 67 HIS cc_start: 0.9112 (m-70) cc_final: 0.8772 (m90) REVERT: A 132 VAL cc_start: 0.8938 (t) cc_final: 0.8632 (t) REVERT: A 211 TYR cc_start: 0.8153 (m-80) cc_final: 0.7892 (m-80) REVERT: A 213 ASP cc_start: 0.8500 (m-30) cc_final: 0.8025 (t0) REVERT: A 263 MET cc_start: 0.7126 (mtp) cc_final: 0.6899 (mtp) REVERT: A 348 MET cc_start: 0.9098 (ttm) cc_final: 0.8740 (tpp) REVERT: A 426 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8409 (pm20) REVERT: A 427 ASN cc_start: 0.8182 (p0) cc_final: 0.7569 (p0) REVERT: A 463 TYR cc_start: 0.8221 (t80) cc_final: 0.7995 (t80) REVERT: B 49 ASP cc_start: 0.7992 (m-30) cc_final: 0.7221 (p0) REVERT: B 74 ARG cc_start: 0.8233 (tmm160) cc_final: 0.7304 (ptt90) REVERT: B 112 ASN cc_start: 0.7528 (m110) cc_final: 0.7005 (p0) REVERT: B 225 ASP cc_start: 0.6789 (m-30) cc_final: 0.6530 (m-30) REVERT: B 257 LEU cc_start: 0.9230 (tp) cc_final: 0.8797 (mp) REVERT: B 270 MET cc_start: 0.8716 (tmm) cc_final: 0.8249 (tmm) REVERT: B 348 MET cc_start: 0.8427 (mtp) cc_final: 0.8179 (ttm) REVERT: B 415 ILE cc_start: 0.9124 (mt) cc_final: 0.8902 (mt) REVERT: C 85 ILE cc_start: 0.9040 (mt) cc_final: 0.8403 (mp) REVERT: C 150 GLN cc_start: 0.8650 (tt0) cc_final: 0.8336 (tp40) REVERT: C 235 MET cc_start: 0.8827 (mmp) cc_final: 0.8338 (mmp) REVERT: C 263 MET cc_start: 0.8703 (mtp) cc_final: 0.7704 (ttm) REVERT: C 268 ILE cc_start: 0.9426 (mm) cc_final: 0.9202 (mm) REVERT: C 363 GLU cc_start: 0.8480 (tp30) cc_final: 0.8008 (tp30) REVERT: C 366 ARG cc_start: 0.8711 (tmm-80) cc_final: 0.7469 (ttp80) REVERT: C 387 ARG cc_start: 0.7363 (mtt-85) cc_final: 0.6650 (mtm-85) REVERT: C 417 PHE cc_start: 0.8748 (m-80) cc_final: 0.8380 (m-10) REVERT: D 32 GLU cc_start: 0.9588 (mp0) cc_final: 0.9356 (pm20) REVERT: D 237 LYS cc_start: 0.8658 (mtmt) cc_final: 0.8197 (mttt) REVERT: D 356 ASN cc_start: 0.8762 (t0) cc_final: 0.8521 (t0) REVERT: E 135 MET cc_start: 0.7482 (ttm) cc_final: 0.6880 (tmm) REVERT: E 234 SER cc_start: 0.9664 (m) cc_final: 0.9339 (p) REVERT: E 235 MET cc_start: 0.8562 (mmt) cc_final: 0.7289 (mmt) REVERT: E 366 ARG cc_start: 0.9268 (ttp-110) cc_final: 0.8870 (ttp80) REVERT: E 373 LYS cc_start: 0.9169 (mmtm) cc_final: 0.8918 (mmmm) REVERT: E 419 TYR cc_start: 0.8047 (t80) cc_final: 0.7702 (t80) REVERT: F 235 MET cc_start: 0.7258 (mmt) cc_final: 0.6304 (mtp) REVERT: F 263 MET cc_start: 0.8352 (mtp) cc_final: 0.8059 (mtm) REVERT: F 270 MET cc_start: 0.8253 (ttt) cc_final: 0.7994 (mmm) REVERT: F 321 THR cc_start: 0.8808 (m) cc_final: 0.8544 (t) REVERT: F 341 MET cc_start: 0.8373 (tpp) cc_final: 0.8095 (tpp) REVERT: F 414 LEU cc_start: 0.9133 (tp) cc_final: 0.8740 (tp) REVERT: G 522 TRP cc_start: 0.7439 (t60) cc_final: 0.7042 (t-100) REVERT: G 577 GLU cc_start: 0.8972 (mp0) cc_final: 0.8475 (pp20) REVERT: H 552 GLU cc_start: 0.9414 (tp30) cc_final: 0.9042 (pp20) outliers start: 0 outliers final: 0 residues processed: 426 average time/residue: 0.3728 time to fit residues: 239.5011 Evaluate side-chains 334 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 20.0000 chunk 159 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 240 optimal weight: 6.9990 chunk 194 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 143 optimal weight: 8.9990 chunk 252 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 HIS ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN B 252 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN C 456 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 GLN ** E 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 GLN ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 461 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 23856 Z= 0.322 Angle : 1.078 32.550 32357 Z= 0.445 Chirality : 0.042 0.175 3682 Planarity : 0.005 0.051 4236 Dihedral : 6.830 93.998 3418 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 22.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.49 % Favored : 95.30 % Rotamer: Outliers : 0.04 % Allowed : 3.34 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 0.12 (0.15), residues: 2938 helix: 0.95 (0.12), residues: 1591 sheet: -1.25 (0.30), residues: 307 loop : -0.72 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 457 HIS 0.007 0.001 HIS E 334 PHE 0.021 0.002 PHE G 543 TYR 0.017 0.002 TYR F 122 ARG 0.010 0.001 ARG D 164 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 427 time to evaluate : 2.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8725 (m-80) cc_final: 0.7888 (m-80) REVERT: A 67 HIS cc_start: 0.9136 (m-70) cc_final: 0.8804 (m90) REVERT: A 132 VAL cc_start: 0.8902 (t) cc_final: 0.8570 (t) REVERT: A 211 TYR cc_start: 0.8263 (m-80) cc_final: 0.7992 (m-80) REVERT: A 263 MET cc_start: 0.7079 (mtp) cc_final: 0.6794 (mtp) REVERT: A 324 ARG cc_start: 0.8562 (ppt170) cc_final: 0.8210 (ttp80) REVERT: A 348 MET cc_start: 0.9162 (ttm) cc_final: 0.8805 (tpp) REVERT: A 426 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8499 (pm20) REVERT: A 427 ASN cc_start: 0.8237 (p0) cc_final: 0.7605 (p0) REVERT: A 463 TYR cc_start: 0.8080 (t80) cc_final: 0.7836 (t80) REVERT: B 49 ASP cc_start: 0.7998 (m-30) cc_final: 0.7192 (p0) REVERT: B 54 ARG cc_start: 0.7479 (mtt180) cc_final: 0.7190 (mtt-85) REVERT: B 224 SER cc_start: 0.8873 (m) cc_final: 0.8472 (m) REVERT: B 225 ASP cc_start: 0.6733 (m-30) cc_final: 0.6517 (m-30) REVERT: B 235 MET cc_start: 0.8773 (mmp) cc_final: 0.7921 (mmm) REVERT: B 257 LEU cc_start: 0.9221 (tp) cc_final: 0.8790 (mp) REVERT: B 269 MET cc_start: 0.8892 (tpp) cc_final: 0.8634 (tpp) REVERT: B 270 MET cc_start: 0.8890 (tmm) cc_final: 0.8325 (tmm) REVERT: B 364 ILE cc_start: 0.9172 (mt) cc_final: 0.8897 (mt) REVERT: C 150 GLN cc_start: 0.8661 (tt0) cc_final: 0.8452 (tp40) REVERT: C 235 MET cc_start: 0.8906 (mmp) cc_final: 0.8418 (mmp) REVERT: C 263 MET cc_start: 0.8779 (mtp) cc_final: 0.7813 (ttm) REVERT: C 268 ILE cc_start: 0.9441 (mm) cc_final: 0.9068 (mm) REVERT: C 363 GLU cc_start: 0.8540 (tp30) cc_final: 0.8188 (tp30) REVERT: C 416 MET cc_start: 0.8332 (mtp) cc_final: 0.8116 (mtp) REVERT: C 417 PHE cc_start: 0.8793 (m-80) cc_final: 0.8537 (m-10) REVERT: D 34 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7797 (mt-10) REVERT: D 237 LYS cc_start: 0.8841 (mtmt) cc_final: 0.8324 (mttt) REVERT: D 318 LEU cc_start: 0.8600 (mm) cc_final: 0.8296 (mm) REVERT: E 135 MET cc_start: 0.7700 (ttm) cc_final: 0.7100 (tmm) REVERT: E 337 ILE cc_start: 0.8089 (tp) cc_final: 0.7810 (tp) REVERT: E 339 LEU cc_start: 0.9409 (tp) cc_final: 0.9085 (tt) REVERT: E 364 ILE cc_start: 0.8626 (mt) cc_final: 0.8380 (mt) REVERT: E 373 LYS cc_start: 0.9142 (mmtm) cc_final: 0.8872 (mmmm) REVERT: E 419 TYR cc_start: 0.8122 (t80) cc_final: 0.7858 (t80) REVERT: F 42 MET cc_start: -0.1099 (mtp) cc_final: -0.1303 (mtp) REVERT: F 235 MET cc_start: 0.7218 (mmt) cc_final: 0.6177 (mtp) REVERT: F 263 MET cc_start: 0.8357 (mtp) cc_final: 0.8075 (mtm) REVERT: F 270 MET cc_start: 0.8396 (ttt) cc_final: 0.8053 (mmm) REVERT: F 321 THR cc_start: 0.8855 (m) cc_final: 0.8581 (t) REVERT: F 341 MET cc_start: 0.8309 (tpp) cc_final: 0.7890 (tpp) REVERT: F 414 LEU cc_start: 0.9090 (tp) cc_final: 0.8772 (tp) REVERT: G 577 GLU cc_start: 0.8973 (mp0) cc_final: 0.8432 (pp20) outliers start: 1 outliers final: 0 residues processed: 428 average time/residue: 0.3768 time to fit residues: 247.0138 Evaluate side-chains 332 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 6.9990 chunk 253 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 281 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 HIS ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 HIS ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23856 Z= 0.259 Angle : 1.048 31.766 32357 Z= 0.426 Chirality : 0.042 0.173 3682 Planarity : 0.004 0.072 4236 Dihedral : 6.719 85.863 3418 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.02 % Favored : 95.78 % Rotamer: Outliers : 0.04 % Allowed : 1.91 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 0.16 (0.16), residues: 2938 helix: 1.01 (0.13), residues: 1589 sheet: -1.28 (0.29), residues: 318 loop : -0.73 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 457 HIS 0.007 0.001 HIS D 65 PHE 0.020 0.002 PHE G 543 TYR 0.017 0.002 TYR B 122 ARG 0.007 0.001 ARG H 550 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 414 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.8651 (m-80) cc_final: 0.7813 (m-80) REVERT: A 67 HIS cc_start: 0.9080 (m-70) cc_final: 0.8716 (m-70) REVERT: A 69 PHE cc_start: 0.9200 (t80) cc_final: 0.8965 (t80) REVERT: A 132 VAL cc_start: 0.8911 (t) cc_final: 0.8608 (t) REVERT: A 211 TYR cc_start: 0.8265 (m-80) cc_final: 0.8032 (m-80) REVERT: A 324 ARG cc_start: 0.8579 (ppt170) cc_final: 0.8208 (ttp80) REVERT: A 348 MET cc_start: 0.9140 (ttm) cc_final: 0.8803 (tpp) REVERT: A 426 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8509 (pm20) REVERT: A 427 ASN cc_start: 0.8259 (p0) cc_final: 0.7659 (p0) REVERT: A 463 TYR cc_start: 0.8069 (t80) cc_final: 0.7814 (t80) REVERT: B 49 ASP cc_start: 0.8068 (m-30) cc_final: 0.7287 (p0) REVERT: B 54 ARG cc_start: 0.7637 (mtt180) cc_final: 0.7381 (mtp85) REVERT: B 235 MET cc_start: 0.8802 (mmp) cc_final: 0.7978 (mmm) REVERT: B 250 MET cc_start: 0.8797 (ppp) cc_final: 0.8362 (ppp) REVERT: B 257 LEU cc_start: 0.9200 (tp) cc_final: 0.8786 (mp) REVERT: B 270 MET cc_start: 0.8784 (tmm) cc_final: 0.8245 (tmm) REVERT: C 235 MET cc_start: 0.8811 (mmp) cc_final: 0.8250 (mmp) REVERT: C 263 MET cc_start: 0.8794 (mtp) cc_final: 0.7856 (ttm) REVERT: C 268 ILE cc_start: 0.9444 (mm) cc_final: 0.9174 (mm) REVERT: C 345 LEU cc_start: 0.9222 (mt) cc_final: 0.8981 (mt) REVERT: C 363 GLU cc_start: 0.8444 (tp30) cc_final: 0.8112 (tp30) REVERT: C 387 ARG cc_start: 0.7374 (mtt-85) cc_final: 0.6836 (mtt90) REVERT: C 417 PHE cc_start: 0.8864 (m-80) cc_final: 0.8521 (m-10) REVERT: D 237 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8316 (mttt) REVERT: D 318 LEU cc_start: 0.8417 (mm) cc_final: 0.8208 (mm) REVERT: D 361 ILE cc_start: 0.9470 (mm) cc_final: 0.9183 (tt) REVERT: E 135 MET cc_start: 0.7694 (ttm) cc_final: 0.7120 (tmm) REVERT: E 337 ILE cc_start: 0.7988 (tp) cc_final: 0.7724 (tp) REVERT: E 339 LEU cc_start: 0.9397 (tp) cc_final: 0.9093 (tt) REVERT: E 373 LYS cc_start: 0.9122 (mmtm) cc_final: 0.8844 (mmmm) REVERT: F 106 LEU cc_start: 0.6267 (mt) cc_final: 0.6062 (mt) REVERT: F 235 MET cc_start: 0.7089 (mmt) cc_final: 0.6045 (mtp) REVERT: F 263 MET cc_start: 0.8298 (mtp) cc_final: 0.8067 (mtm) REVERT: F 270 MET cc_start: 0.8360 (ttt) cc_final: 0.8031 (mmm) REVERT: F 321 THR cc_start: 0.8827 (m) cc_final: 0.8553 (t) REVERT: F 414 LEU cc_start: 0.9030 (tp) cc_final: 0.8698 (tp) REVERT: G 577 GLU cc_start: 0.8993 (mp0) cc_final: 0.8476 (pp20) outliers start: 1 outliers final: 0 residues processed: 415 average time/residue: 0.3788 time to fit residues: 238.5725 Evaluate side-chains 335 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 237 optimal weight: 0.5980 chunk 157 optimal weight: 8.9990 chunk 280 optimal weight: 20.0000 chunk 175 optimal weight: 0.8980 chunk 170 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 ASN F 267 GLN ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23856 Z= 0.238 Angle : 1.044 31.194 32357 Z= 0.423 Chirality : 0.042 0.359 3682 Planarity : 0.004 0.093 4236 Dihedral : 6.604 82.190 3418 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.02 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 0.13 (0.16), residues: 2938 helix: 0.99 (0.13), residues: 1588 sheet: -1.30 (0.28), residues: 328 loop : -0.75 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 48 HIS 0.007 0.001 HIS H 541 PHE 0.022 0.002 PHE G 543 TYR 0.020 0.001 TYR E 105 ARG 0.012 0.001 ARG E 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.9072 (m-70) cc_final: 0.8691 (m-70) REVERT: A 132 VAL cc_start: 0.8900 (t) cc_final: 0.8600 (t) REVERT: A 324 ARG cc_start: 0.8536 (ppt170) cc_final: 0.8094 (ttp80) REVERT: A 348 MET cc_start: 0.9089 (ttm) cc_final: 0.8865 (tpp) REVERT: A 426 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8477 (pm20) REVERT: A 427 ASN cc_start: 0.8287 (p0) cc_final: 0.7477 (p0) REVERT: B 49 ASP cc_start: 0.8051 (m-30) cc_final: 0.7275 (p0) REVERT: B 54 ARG cc_start: 0.7626 (mtt180) cc_final: 0.7116 (mtp85) REVERT: B 235 MET cc_start: 0.8829 (mmp) cc_final: 0.8043 (mmm) REVERT: B 269 MET cc_start: 0.8708 (tpp) cc_final: 0.8412 (tpp) REVERT: B 270 MET cc_start: 0.8832 (tmm) cc_final: 0.8258 (tmm) REVERT: B 415 ILE cc_start: 0.9242 (mt) cc_final: 0.8958 (mt) REVERT: C 235 MET cc_start: 0.8782 (mmp) cc_final: 0.8203 (mmp) REVERT: C 263 MET cc_start: 0.8852 (mtp) cc_final: 0.8012 (ttm) REVERT: C 301 MET cc_start: 0.9116 (ptp) cc_final: 0.8859 (ptp) REVERT: C 345 LEU cc_start: 0.9184 (mt) cc_final: 0.8979 (mt) REVERT: C 363 GLU cc_start: 0.8432 (tp30) cc_final: 0.8112 (tp30) REVERT: C 387 ARG cc_start: 0.7319 (mtt-85) cc_final: 0.7021 (mtt90) REVERT: C 417 PHE cc_start: 0.8861 (m-80) cc_final: 0.8523 (m-10) REVERT: D 63 ARG cc_start: 0.9405 (mmp80) cc_final: 0.9201 (mmm160) REVERT: D 318 LEU cc_start: 0.8366 (mm) cc_final: 0.8124 (mm) REVERT: E 135 MET cc_start: 0.7713 (ttm) cc_final: 0.7142 (tmm) REVERT: E 235 MET cc_start: 0.8403 (mmt) cc_final: 0.7099 (mmt) REVERT: E 366 ARG cc_start: 0.9314 (ttp-110) cc_final: 0.8887 (ttp80) REVERT: E 373 LYS cc_start: 0.9036 (mmtm) cc_final: 0.8777 (mmmm) REVERT: E 417 PHE cc_start: 0.7790 (m-10) cc_final: 0.7451 (m-10) REVERT: F 42 MET cc_start: -0.1612 (mtp) cc_final: -0.1959 (mtp) REVERT: F 106 LEU cc_start: 0.6151 (mt) cc_final: 0.5893 (mt) REVERT: F 235 MET cc_start: 0.6983 (mmt) cc_final: 0.5964 (mtp) REVERT: F 263 MET cc_start: 0.8286 (mtp) cc_final: 0.7975 (mtm) REVERT: F 270 MET cc_start: 0.8396 (ttt) cc_final: 0.8012 (mmm) REVERT: F 310 ILE cc_start: 0.8455 (mt) cc_final: 0.8251 (mt) REVERT: F 321 THR cc_start: 0.8793 (m) cc_final: 0.8545 (t) REVERT: F 341 MET cc_start: 0.7810 (tpp) cc_final: 0.7477 (tpp) REVERT: F 414 LEU cc_start: 0.8976 (tp) cc_final: 0.8652 (tp) REVERT: G 577 GLU cc_start: 0.9014 (mp0) cc_final: 0.8517 (pp20) outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.3874 time to fit residues: 244.4559 Evaluate side-chains 332 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 9.9990 chunk 112 optimal weight: 0.0050 chunk 167 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 220 optimal weight: 10.0000 overall best weight: 4.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN A 462 ASN ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** G 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23856 Z= 0.283 Angle : 1.067 32.062 32357 Z= 0.439 Chirality : 0.042 0.199 3682 Planarity : 0.004 0.054 4236 Dihedral : 6.689 83.025 3418 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.49 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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 (0.15), residues: 2938 helix: 0.93 (0.13), residues: 1581 sheet: -1.34 (0.29), residues: 321 loop : -0.75 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 457 HIS 0.006 0.001 HIS H 541 PHE 0.022 0.002 PHE C 166 TYR 0.022 0.002 TYR E 105 ARG 0.015 0.001 ARG C 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.9092 (m-70) cc_final: 0.8708 (m-70) REVERT: A 132 VAL cc_start: 0.8908 (t) cc_final: 0.8569 (t) REVERT: A 324 ARG cc_start: 0.8624 (ppt170) cc_final: 0.8265 (ttp80) REVERT: A 348 MET cc_start: 0.9147 (ttm) cc_final: 0.8859 (tpp) REVERT: A 426 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8471 (pm20) REVERT: A 427 ASN cc_start: 0.8313 (p0) cc_final: 0.7498 (p0) REVERT: B 49 ASP cc_start: 0.8067 (m-30) cc_final: 0.7237 (p0) REVERT: B 54 ARG cc_start: 0.7660 (mtt180) cc_final: 0.7144 (mtp85) REVERT: B 235 MET cc_start: 0.8922 (mmp) cc_final: 0.8133 (mmm) REVERT: B 257 LEU cc_start: 0.9153 (tp) cc_final: 0.8876 (tp) REVERT: B 270 MET cc_start: 0.8843 (tmm) cc_final: 0.8216 (tmm) REVERT: B 415 ILE cc_start: 0.9289 (mt) cc_final: 0.9088 (mt) REVERT: C 235 MET cc_start: 0.8869 (mmp) cc_final: 0.8303 (mmp) REVERT: C 263 MET cc_start: 0.8866 (mtp) cc_final: 0.7800 (ttm) REVERT: C 268 ILE cc_start: 0.9448 (mm) cc_final: 0.8862 (mm) REVERT: C 301 MET cc_start: 0.9192 (ptp) cc_final: 0.8952 (ptp) REVERT: C 363 GLU cc_start: 0.8467 (tp30) cc_final: 0.8167 (tp30) REVERT: C 366 ARG cc_start: 0.8783 (tmm160) cc_final: 0.8335 (ttp80) REVERT: C 387 ARG cc_start: 0.7455 (mtt-85) cc_final: 0.6862 (mtt90) REVERT: C 401 ASP cc_start: 0.7820 (t0) cc_final: 0.7526 (t0) REVERT: C 417 PHE cc_start: 0.8902 (m-80) cc_final: 0.8554 (m-10) REVERT: C 440 LYS cc_start: 0.7650 (mmtm) cc_final: 0.7374 (mmtt) REVERT: D 291 ASP cc_start: 0.8647 (m-30) cc_final: 0.8165 (p0) REVERT: D 361 ILE cc_start: 0.9497 (mm) cc_final: 0.9229 (tt) REVERT: E 135 MET cc_start: 0.7792 (ttm) cc_final: 0.7191 (tmm) REVERT: E 318 LEU cc_start: 0.8202 (tp) cc_final: 0.7679 (tp) REVERT: E 337 ILE cc_start: 0.7878 (tp) cc_final: 0.7643 (tp) REVERT: E 366 ARG cc_start: 0.9326 (ttp-110) cc_final: 0.8899 (ttp80) REVERT: E 373 LYS cc_start: 0.9081 (mmtm) cc_final: 0.8816 (mmmm) REVERT: F 42 MET cc_start: -0.1343 (mtp) cc_final: -0.1659 (mtp) REVERT: F 106 LEU cc_start: 0.6197 (mt) cc_final: 0.5944 (mt) REVERT: F 235 MET cc_start: 0.7108 (mmt) cc_final: 0.6039 (mtp) REVERT: F 263 MET cc_start: 0.8304 (mtp) cc_final: 0.7916 (mtm) REVERT: F 270 MET cc_start: 0.8434 (ttt) cc_final: 0.8052 (mmm) REVERT: F 321 THR cc_start: 0.8817 (m) cc_final: 0.8578 (t) REVERT: F 414 LEU cc_start: 0.8991 (tp) cc_final: 0.8624 (tp) REVERT: G 577 GLU cc_start: 0.8976 (mp0) cc_final: 0.8478 (pp20) REVERT: H 522 TRP cc_start: 0.3776 (t60) cc_final: 0.3426 (t60) outliers start: 0 outliers final: 0 residues processed: 400 average time/residue: 0.3842 time to fit residues: 231.5421 Evaluate side-chains 320 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 2.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 6.9990 chunk 268 optimal weight: 8.9990 chunk 245 optimal weight: 9.9990 chunk 261 optimal weight: 20.0000 chunk 157 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 205 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 236 optimal weight: 20.0000 chunk 247 optimal weight: 10.0000 chunk 260 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 GLN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23856 Z= 0.294 Angle : 1.077 32.265 32357 Z= 0.446 Chirality : 0.042 0.234 3682 Planarity : 0.004 0.064 4236 Dihedral : 6.768 81.920 3418 Min Nonbonded Distance : 1.613 Molprobity Statistics. All-atom Clashscore : 23.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.46 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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 (0.16), residues: 2938 helix: 0.80 (0.13), residues: 1585 sheet: -1.40 (0.29), residues: 316 loop : -0.78 (0.20), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 457 HIS 0.011 0.002 HIS D 67 PHE 0.023 0.002 PHE C 166 TYR 0.016 0.002 TYR F 311 ARG 0.009 0.001 ARG H 550 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 2.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 HIS cc_start: 0.9089 (m-70) cc_final: 0.8701 (m-70) REVERT: A 132 VAL cc_start: 0.8963 (t) cc_final: 0.8647 (t) REVERT: A 263 MET cc_start: 0.7852 (mtm) cc_final: 0.7401 (mtm) REVERT: A 324 ARG cc_start: 0.8569 (ppt170) cc_final: 0.8225 (ttp80) REVERT: A 348 MET cc_start: 0.9175 (ttm) cc_final: 0.8967 (tpp) REVERT: A 426 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8467 (pm20) REVERT: A 427 ASN cc_start: 0.8379 (p0) cc_final: 0.7315 (p0) REVERT: B 49 ASP cc_start: 0.8051 (m-30) cc_final: 0.7175 (p0) REVERT: B 235 MET cc_start: 0.8904 (mmp) cc_final: 0.8076 (mmm) REVERT: B 250 MET cc_start: 0.8608 (ppp) cc_final: 0.8346 (ppp) REVERT: B 257 LEU cc_start: 0.9144 (tp) cc_final: 0.8863 (tp) REVERT: B 269 MET cc_start: 0.8693 (tpp) cc_final: 0.8409 (tpp) REVERT: B 270 MET cc_start: 0.8894 (tmm) cc_final: 0.8238 (tmm) REVERT: B 348 MET cc_start: 0.8823 (mmm) cc_final: 0.8556 (tpt) REVERT: C 135 MET cc_start: 0.9061 (ptt) cc_final: 0.8581 (ppp) REVERT: C 235 MET cc_start: 0.8846 (mmp) cc_final: 0.8243 (mmp) REVERT: C 263 MET cc_start: 0.8871 (mtp) cc_final: 0.7845 (ttm) REVERT: C 268 ILE cc_start: 0.9449 (mm) cc_final: 0.8866 (mm) REVERT: C 363 GLU cc_start: 0.8493 (tp30) cc_final: 0.8183 (tp30) REVERT: C 366 ARG cc_start: 0.8755 (tmm160) cc_final: 0.8334 (ttp80) REVERT: C 387 ARG cc_start: 0.7470 (mtt-85) cc_final: 0.6836 (mtt90) REVERT: C 401 ASP cc_start: 0.8008 (t0) cc_final: 0.7746 (t0) REVERT: C 417 PHE cc_start: 0.8902 (m-80) cc_final: 0.8555 (m-10) REVERT: D 291 ASP cc_start: 0.8642 (m-30) cc_final: 0.8151 (p0) REVERT: D 361 ILE cc_start: 0.9501 (mm) cc_final: 0.9211 (tt) REVERT: E 135 MET cc_start: 0.7810 (ttm) cc_final: 0.7225 (tmm) REVERT: E 337 ILE cc_start: 0.7934 (tp) cc_final: 0.7640 (tp) REVERT: E 366 ARG cc_start: 0.9313 (ttp-110) cc_final: 0.8847 (ttp80) REVERT: E 373 LYS cc_start: 0.9074 (mmtm) cc_final: 0.8845 (mmmm) REVERT: F 235 MET cc_start: 0.7110 (mmt) cc_final: 0.6055 (mtp) REVERT: F 263 MET cc_start: 0.8341 (mtp) cc_final: 0.7952 (mtm) REVERT: F 321 THR cc_start: 0.8838 (m) cc_final: 0.8587 (t) REVERT: F 341 MET cc_start: 0.7526 (tpp) cc_final: 0.7297 (tpp) REVERT: F 414 LEU cc_start: 0.8959 (tp) cc_final: 0.8595 (tp) REVERT: G 521 MET cc_start: 0.7062 (ttt) cc_final: 0.6758 (ppp) REVERT: G 572 TRP cc_start: 0.7216 (t60) cc_final: 0.6752 (t-100) REVERT: G 577 GLU cc_start: 0.8941 (mp0) cc_final: 0.8471 (pp20) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.3663 time to fit residues: 221.1900 Evaluate side-chains 315 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 0.9990 chunk 276 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 192 optimal weight: 6.9990 chunk 289 optimal weight: 0.8980 chunk 266 optimal weight: 0.7980 chunk 230 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 178 optimal weight: 20.0000 chunk 141 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23856 Z= 0.185 Angle : 1.053 30.337 32357 Z= 0.429 Chirality : 0.042 0.218 3682 Planarity : 0.004 0.059 4236 Dihedral : 6.436 73.856 3418 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.13 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 0.15 (0.16), residues: 2938 helix: 0.94 (0.13), residues: 1588 sheet: -1.22 (0.29), residues: 314 loop : -0.65 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 457 HIS 0.006 0.001 HIS H 541 PHE 0.023 0.002 PHE C 166 TYR 0.024 0.001 TYR B 419 ARG 0.011 0.000 ARG E 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8760 (mm) cc_final: 0.8460 (pp) REVERT: A 67 HIS cc_start: 0.9055 (m-70) cc_final: 0.8664 (m-70) REVERT: A 132 VAL cc_start: 0.8893 (t) cc_final: 0.8614 (t) REVERT: A 263 MET cc_start: 0.7761 (mtm) cc_final: 0.7262 (mtm) REVERT: A 324 ARG cc_start: 0.8575 (ppt170) cc_final: 0.8104 (ttp80) REVERT: A 348 MET cc_start: 0.9041 (ttm) cc_final: 0.8681 (tpp) REVERT: A 426 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8343 (pm20) REVERT: B 49 ASP cc_start: 0.8080 (m-30) cc_final: 0.7289 (p0) REVERT: B 156 ASP cc_start: 0.9099 (m-30) cc_final: 0.8854 (t70) REVERT: B 235 MET cc_start: 0.8751 (mmp) cc_final: 0.7885 (mmm) REVERT: B 250 MET cc_start: 0.8676 (ppp) cc_final: 0.8396 (ppp) REVERT: B 270 MET cc_start: 0.8809 (tmm) cc_final: 0.8166 (tmm) REVERT: B 348 MET cc_start: 0.8694 (mmm) cc_final: 0.8372 (tpt) REVERT: C 135 MET cc_start: 0.9004 (ptm) cc_final: 0.8594 (ppp) REVERT: C 235 MET cc_start: 0.8701 (mmp) cc_final: 0.8148 (mmp) REVERT: C 263 MET cc_start: 0.8704 (mtp) cc_final: 0.8424 (mtm) REVERT: C 363 GLU cc_start: 0.8440 (tp30) cc_final: 0.8115 (tp30) REVERT: C 366 ARG cc_start: 0.8720 (tmm160) cc_final: 0.8356 (ttp80) REVERT: C 401 ASP cc_start: 0.7969 (t0) cc_final: 0.7673 (t0) REVERT: C 417 PHE cc_start: 0.8819 (m-80) cc_final: 0.8458 (m-10) REVERT: C 440 LYS cc_start: 0.7501 (mmtm) cc_final: 0.7179 (mmtp) REVERT: D 226 LEU cc_start: 0.7552 (tp) cc_final: 0.7338 (tp) REVERT: D 235 MET cc_start: 0.7214 (mmp) cc_final: 0.6964 (mmp) REVERT: D 237 LYS cc_start: 0.8501 (mtmt) cc_final: 0.8198 (mtmt) REVERT: D 291 ASP cc_start: 0.8596 (m-30) cc_final: 0.8095 (p0) REVERT: D 361 ILE cc_start: 0.9464 (mm) cc_final: 0.9208 (tt) REVERT: E 135 MET cc_start: 0.7767 (ttm) cc_final: 0.7174 (tmm) REVERT: E 366 ARG cc_start: 0.9276 (ttp-110) cc_final: 0.8929 (ttp80) REVERT: F 42 MET cc_start: -0.1705 (mtp) cc_final: -0.1959 (mtp) REVERT: F 235 MET cc_start: 0.6695 (mmt) cc_final: 0.5819 (mtp) REVERT: F 263 MET cc_start: 0.8056 (mtp) cc_final: 0.7712 (mtt) REVERT: F 270 MET cc_start: 0.8502 (ttt) cc_final: 0.7709 (mmm) REVERT: F 321 THR cc_start: 0.8776 (m) cc_final: 0.8553 (t) REVERT: F 387 ARG cc_start: 0.7129 (mtt-85) cc_final: 0.6363 (ttm-80) REVERT: F 414 LEU cc_start: 0.8970 (tp) cc_final: 0.8707 (tp) REVERT: G 521 MET cc_start: 0.7041 (ttt) cc_final: 0.6710 (ppp) REVERT: G 577 GLU cc_start: 0.8915 (mp0) cc_final: 0.8472 (pp20) REVERT: H 522 TRP cc_start: 0.3865 (t60) cc_final: 0.3659 (t60) outliers start: 0 outliers final: 0 residues processed: 406 average time/residue: 0.3645 time to fit residues: 224.4442 Evaluate side-chains 324 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 7.9990 chunk 245 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 212 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 231 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 237 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.108285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.079784 restraints weight = 113604.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.081868 restraints weight = 76605.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.083292 restraints weight = 56733.735| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23856 Z= 0.260 Angle : 1.072 31.572 32357 Z= 0.443 Chirality : 0.042 0.186 3682 Planarity : 0.005 0.099 4236 Dihedral : 6.530 74.888 3418 Min Nonbonded Distance : 1.575 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.25 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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 (0.16), residues: 2938 helix: 0.89 (0.13), residues: 1582 sheet: -1.30 (0.29), residues: 322 loop : -0.72 (0.20), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 457 HIS 0.005 0.001 HIS E 334 PHE 0.022 0.002 PHE G 543 TYR 0.013 0.001 TYR E 344 ARG 0.017 0.001 ARG F 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5489.54 seconds wall clock time: 99 minutes 35.15 seconds (5975.15 seconds total)