Starting phenix.real_space_refine on Sat Nov 18 15:23:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t23_25610/11_2023/7t23_25610_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t23_25610/11_2023/7t23_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_25610/11_2023/7t23_25610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t23_25610/11_2023/7t23_25610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t23_25610/11_2023/7t23_25610_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t23_25610/11_2023/7t23_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 12.84, per 1000 atoms: 0.55 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: 10.38 Conformation dependent library (CDL) restraints added in 4.4 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: 5.19 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: 7.39 Time building geometry restraints manager: 11.00 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: 1.560 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: 5.520 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 64.720 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.530 ------------------------------------------------------------------------------- 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 *********************** 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 : 2.691 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 outliers start: 38 outliers final: 8 residues processed: 740 average time/residue: 0.4399 time to fit residues: 478.6287 Evaluate side-chains 407 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 399 time to evaluate : 2.913 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2153 time to fit residues: 7.2321 ------------------------------------------------------------------------------- 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: 20.0000 chunk 220 optimal weight: 40.0000 chunk 122 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 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: 50.0000 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 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 399 ASN ** F 201 HIS ** 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: 0.7536 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23856 Z= 0.250 Angle : 1.033 30.482 32357 Z= 0.414 Chirality : 0.041 0.269 3682 Planarity : 0.005 0.166 4236 Dihedral : 6.229 102.428 3418 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.69 % Favored : 97.11 % Rotamer: Outliers : 0.28 % Allowed : 2.74 % Favored : 96.98 % 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: 1.30 (0.16), residues: 2938 helix: 2.14 (0.13), residues: 1591 sheet: -1.04 (0.28), residues: 325 loop : -0.49 (0.20), residues: 1022 *********************** 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 500 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 493 time to evaluate : 2.704 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 outliers start: 7 outliers final: 2 residues processed: 499 average time/residue: 0.4264 time to fit residues: 320.0537 Evaluate side-chains 365 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 363 time to evaluate : 2.718 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2672 time to fit residues: 4.6096 ------------------------------------------------------------------------------- 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: 6.9990 chunk 82 optimal weight: 7.9990 chunk 219 optimal weight: 8.9990 chunk 179 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 264 optimal weight: 30.0000 chunk 285 optimal weight: 8.9990 chunk 235 optimal weight: 6.9990 chunk 262 optimal weight: 30.0000 chunk 90 optimal weight: 8.9990 chunk 212 optimal weight: 8.9990 overall best weight: 6.3588 ------------------------------------------------------------------------------- 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 150 GLN C 376 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN ** G 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 23856 Z= 0.369 Angle : 1.106 33.170 32357 Z= 0.461 Chirality : 0.043 0.262 3682 Planarity : 0.005 0.068 4236 Dihedral : 6.565 98.561 3418 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.54 % Favored : 96.26 % Rotamer: Outliers : 0.20 % Allowed : 3.26 % Favored : 96.54 % 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: 0.52 (0.15), residues: 2938 helix: 1.35 (0.13), residues: 1595 sheet: -1.10 (0.29), residues: 315 loop : -0.68 (0.19), residues: 1028 *********************** 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 442 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 437 time to evaluate : 2.799 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 outliers start: 5 outliers final: 0 residues processed: 441 average time/residue: 0.4051 time to fit residues: 268.0026 Evaluate side-chains 318 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 3.013 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1802 ------------------------------------------------------------------------------- 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: 20.0000 chunk 199 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 177 optimal weight: 30.0000 chunk 265 optimal weight: 2.9990 chunk 281 optimal weight: 0.4980 chunk 138 optimal weight: 6.9990 chunk 251 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- 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** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN C 376 ASN ** D 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 386 ASN F 198 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23856 Z= 0.259 Angle : 1.040 31.363 32357 Z= 0.421 Chirality : 0.041 0.216 3682 Planarity : 0.004 0.056 4236 Dihedral : 6.491 91.147 3418 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.30 % Favored : 96.49 % Rotamer: Outliers : 0.04 % Allowed : 2.54 % Favored : 97.42 % 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: 0.46 (0.15), residues: 2938 helix: 1.25 (0.13), residues: 1594 sheet: -1.10 (0.29), residues: 328 loop : -0.62 (0.20), residues: 1016 *********************** 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 420 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 419 time to evaluate : 2.732 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 outliers start: 1 outliers final: 0 residues processed: 420 average time/residue: 0.3831 time to fit residues: 244.5999 Evaluate side-chains 326 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 2.541 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4501 ------------------------------------------------------------------------------- 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: 0.7980 chunk 159 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 240 optimal weight: 10.0000 chunk 194 optimal weight: 0.0980 chunk 0 optimal weight: 20.0000 chunk 143 optimal weight: 6.9990 chunk 252 optimal weight: 3.9990 chunk 70 optimal weight: 0.2980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 67 HIS ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 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 384 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23856 Z= 0.177 Angle : 1.012 30.276 32357 Z= 0.401 Chirality : 0.040 0.203 3682 Planarity : 0.004 0.055 4236 Dihedral : 6.251 82.062 3418 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.00 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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: 0.66 (0.16), residues: 2938 helix: 1.44 (0.13), residues: 1586 sheet: -0.97 (0.29), residues: 324 loop : -0.58 (0.20), residues: 1028 *********************** 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 442 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 442 time to evaluate : 3.219 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 outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.3690 time to fit residues: 252.0396 Evaluate side-chains 340 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 2.902 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9599 ------------------------------------------------------------------------------- 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: 5.9990 chunk 253 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 281 optimal weight: 5.9990 chunk 233 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 150 GLN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23856 Z= 0.201 Angle : 1.029 31.102 32357 Z= 0.412 Chirality : 0.041 0.454 3682 Planarity : 0.004 0.074 4236 Dihedral : 6.175 80.520 3418 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.47 % Favored : 96.29 % Rotamer: Outliers : 0.12 % Allowed : 1.31 % Favored : 98.57 % 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: 0.57 (0.16), residues: 2938 helix: 1.32 (0.13), residues: 1583 sheet: -0.90 (0.29), residues: 325 loop : -0.57 (0.20), residues: 1030 *********************** 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 428 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 425 time to evaluate : 2.638 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 outliers start: 3 outliers final: 0 residues processed: 428 average time/residue: 0.3744 time to fit residues: 248.1317 Evaluate side-chains 334 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 time to evaluate : 2.658 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6667 ------------------------------------------------------------------------------- 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: 1.9990 chunk 31 optimal weight: 9.9990 chunk 160 optimal weight: 0.1980 chunk 205 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 237 optimal weight: 0.2980 chunk 157 optimal weight: 0.9980 chunk 280 optimal weight: 50.0000 chunk 175 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN D 65 HIS ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 461 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23856 Z= 0.179 Angle : 1.023 30.194 32357 Z= 0.406 Chirality : 0.041 0.294 3682 Planarity : 0.004 0.052 4236 Dihedral : 6.001 74.819 3418 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.52 % Favored : 97.28 % Rotamer: Outliers : 0.04 % Allowed : 0.95 % Favored : 99.01 % 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 (0.16), residues: 2938 helix: 1.33 (0.13), residues: 1578 sheet: -0.87 (0.30), residues: 312 loop : -0.53 (0.20), residues: 1048 *********************** 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 430 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 429 time to evaluate : 2.985 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 outliers start: 1 outliers final: 1 residues processed: 430 average time/residue: 0.3719 time to fit residues: 250.0848 Evaluate side-chains 324 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 323 time to evaluate : 2.762 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2182 time to fit residues: 4.3470 ------------------------------------------------------------------------------- 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: 8.9990 chunk 112 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 84 optimal weight: 0.2980 chunk 55 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 178 optimal weight: 0.2980 chunk 191 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN C 376 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23856 Z= 0.189 Angle : 1.035 30.696 32357 Z= 0.412 Chirality : 0.041 0.251 3682 Planarity : 0.005 0.152 4236 Dihedral : 5.922 71.585 3418 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.86 % Favored : 96.94 % Rotamer: Outliers : 0.04 % Allowed : 0.68 % Favored : 99.29 % 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: 0.54 (0.16), residues: 2938 helix: 1.28 (0.13), residues: 1582 sheet: -0.95 (0.29), residues: 320 loop : -0.54 (0.20), residues: 1036 *********************** 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 420 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 419 time to evaluate : 2.478 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 outliers start: 1 outliers final: 0 residues processed: 420 average time/residue: 0.3681 time to fit residues: 242.7929 Evaluate side-chains 322 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 2.759 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8320 ------------------------------------------------------------------------------- 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: 5.9990 chunk 268 optimal weight: 0.3980 chunk 245 optimal weight: 6.9990 chunk 261 optimal weight: 0.3980 chunk 157 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 205 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 236 optimal weight: 9.9990 chunk 247 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 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 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 ASN G 461 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23856 Z= 0.186 Angle : 1.040 30.789 32357 Z= 0.417 Chirality : 0.041 0.253 3682 Planarity : 0.005 0.136 4236 Dihedral : 5.949 67.986 3418 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.17 % Favored : 96.63 % Rotamer: Outliers : 0.04 % Allowed : 0.36 % 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: 0.48 (0.16), residues: 2938 helix: 1.19 (0.13), residues: 1590 sheet: -0.90 (0.29), residues: 318 loop : -0.53 (0.20), residues: 1030 *********************** 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 411 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 410 time to evaluate : 2.800 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 outliers start: 1 outliers final: 0 residues processed: 411 average time/residue: 0.3641 time to fit residues: 235.6673 Evaluate side-chains 311 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 2.750 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7599 ------------------------------------------------------------------------------- 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: 5.9990 chunk 276 optimal weight: 6.9990 chunk 168 optimal weight: 0.4980 chunk 131 optimal weight: 7.9990 chunk 192 optimal weight: 6.9990 chunk 289 optimal weight: 4.9990 chunk 266 optimal weight: 40.0000 chunk 230 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 178 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN D 65 HIS ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 461 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23856 Z= 0.215 Angle : 1.044 31.203 32357 Z= 0.420 Chirality : 0.041 0.232 3682 Planarity : 0.004 0.111 4236 Dihedral : 5.986 71.350 3418 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.23 % Favored : 96.60 % Rotamer: Outliers : 0.04 % Allowed : 0.32 % Favored : 99.64 % 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: 0.48 (0.16), residues: 2938 helix: 1.21 (0.13), residues: 1584 sheet: -0.91 (0.29), residues: 323 loop : -0.56 (0.20), residues: 1031 ********************** 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 399 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 398 time to evaluate : 3.234 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 outliers start: 1 outliers final: 0 residues processed: 399 average time/residue: 0.3595 time to fit residues: 225.3410 Evaluate side-chains 315 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 2.915 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8870 ------------------------------------------------------------------------------- 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: 1.9990 chunk 245 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 96 optimal weight: 0.0970 chunk 237 optimal weight: 0.0470 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 overall best weight: 1.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 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 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 461 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.111531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.083520 restraints weight = 112304.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.086426 restraints weight = 75541.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.088571 restraints weight = 48488.645| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3946 r_free = 0.3946 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3946 r_free = 0.3946 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23856 Z= 0.187 Angle : 1.041 30.572 32357 Z= 0.417 Chirality : 0.041 0.213 3682 Planarity : 0.004 0.097 4236 Dihedral : 5.901 69.544 3418 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.03 % Favored : 96.80 % Rotamer: Outliers : 0.04 % Allowed : 0.20 % Favored : 99.76 % 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: 0.47 (0.16), residues: 2938 helix: 1.21 (0.13), residues: 1586 sheet: -0.88 (0.29), residues: 315 loop : -0.60 (0.20), residues: 1037 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5543.37 seconds wall clock time: 101 minutes 31.62 seconds (6091.62 seconds total)