Starting phenix.real_space_refine on Tue Mar 19 15:09:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t22_25609/03_2024/7t22_25609_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t22_25609/03_2024/7t22_25609.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/7t22_25609/03_2024/7t22_25609.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t22_25609/03_2024/7t22_25609.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t22_25609/03_2024/7t22_25609_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t22_25609/03_2024/7t22_25609_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 99 5.16 5 C 15138 2.51 5 N 4323 2.21 5 O 4923 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 TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 460": "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: 24536 Number of models: 1 Model: "" Number of chains: 15 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: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "H" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "I" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} 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: 12.38, per 1000 atoms: 0.50 Number of scatterers: 24536 At special positions: 0 Unit cell: (161.68, 155.1, 152.28, 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 99 16.00 P 23 15.00 Al 5 13.00 Mg 5 11.99 F 20 9.00 O 4923 8.00 N 4323 7.00 C 15138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, 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 Simple disulfide: pdb=" SG CYS F 103 " - pdb=" SG CYS I 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 Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.87 Conformation dependent library (CDL) restraints added in 4.6 seconds 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5790 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 158 helices and 6 sheets defined 57.5% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.64 Creating SS restraints... Processing helix chain 'A' and resid 31 through 43 Processing helix chain 'A' and resid 46 through 52 removed outlier: 3.940A pdb=" N ASP A 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 50 " --> pdb=" O ARG A 47 " (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 78 Processing helix chain 'A' and resid 84 through 93 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 102 through 112 Processing helix chain 'A' and resid 117 through 147 removed outlier: 4.569A pdb=" N SER A 120 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 171 Processing helix chain 'A' and resid 182 through 198 Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 237 through 250 removed outlier: 3.725A pdb=" N ALA A 241 " --> pdb=" O LYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 291 through 307 Processing helix chain 'A' and resid 320 through 334 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 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'A' and resid 408 through 411 No H-bonds generated for 'chain 'A' and resid 408 through 411' 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 Processing helix chain 'B' and resid 46 through 54 removed outlier: 4.183A pdb=" N ASP B 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU B 53 " --> pdb=" O ASP B 50 " (cutoff:3.500A) 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 102 through 112 Processing helix chain 'B' and resid 119 through 147 Processing helix chain 'B' and resid 154 through 176 removed outlier: 3.585A pdb=" N ILE B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU B 170 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP B 176 " --> pdb=" O ARG B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 198 Processing helix chain 'B' and resid 212 through 218 Processing helix chain 'B' and resid 237 through 250 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 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' 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 406 through 411 removed outlier: 3.918A pdb=" N GLN B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) 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 54 removed outlier: 3.822A pdb=" N ASP C 49 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU C 53 " --> pdb=" O ASP C 50 " (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 Processing helix chain 'C' and resid 117 through 147 removed outlier: 4.550A pdb=" N SER C 120 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 172 Processing helix chain 'C' and resid 182 through 198 Processing helix chain 'C' and resid 212 through 218 Processing helix chain 'C' and resid 237 through 250 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 333 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 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 357 through 375 Processing helix chain 'C' and resid 387 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 405 through 411 removed outlier: 3.814A pdb=" N GLU C 409 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLN C 410 " --> pdb=" O GLY C 406 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 46 through 54 removed outlier: 4.168A pdb=" N ASP D 49 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP D 50 " --> pdb=" O ARG D 47 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU D 53 " --> pdb=" O ASP D 50 " (cutoff:3.500A) 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 102 through 112 Processing helix chain 'D' and resid 119 through 147 Processing helix chain 'D' and resid 154 through 174 removed outlier: 3.810A pdb=" N ARG D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 198 Processing helix chain 'D' and resid 212 through 218 Processing helix chain 'D' and resid 237 through 251 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 351 through 353 No H-bonds generated for 'chain 'D' and resid 351 through 353' Processing helix chain 'D' and resid 357 through 375 Processing helix chain 'D' and resid 387 through 391 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 405 through 411 removed outlier: 3.559A pdb=" N GLN D 410 " --> pdb=" O GLY D 406 " (cutoff:3.500A) 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: 3.714A pdb=" N ASP E 49 " --> pdb=" O GLU E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 59 No H-bonds generated for 'chain 'E' and resid 57 through 59' Processing helix chain 'E' and resid 63 through 77 Processing helix chain 'E' and resid 84 through 94 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 117 through 147 removed outlier: 4.573A pdb=" N SER E 120 " --> pdb=" O ALA E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 172 removed outlier: 3.646A pdb=" N ARG E 172 " --> pdb=" O ILE E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 Processing helix chain 'E' and resid 212 through 218 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 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 357 through 375 Processing helix chain 'E' and resid 387 through 391 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 405 through 411 removed outlier: 3.597A pdb=" N GLN E 410 " --> pdb=" O GLY E 406 " (cutoff:3.500A) 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 Processing helix chain 'F' and resid 46 through 54 removed outlier: 4.221A pdb=" N ASP F 49 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU F 53 " --> pdb=" O ASP F 50 " (cutoff:3.500A) 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 97 through 100 No H-bonds generated for 'chain 'F' and resid 97 through 100' Processing helix chain 'F' and resid 102 through 111 Processing helix chain 'F' and resid 116 through 147 removed outlier: 4.885A pdb=" N SER F 120 " --> pdb=" O ALA F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 171 removed outlier: 3.968A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU F 170 " --> pdb=" O PHE F 166 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N SER F 171 " --> pdb=" O LYS F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 197 removed outlier: 4.310A pdb=" N PHE F 197 " --> pdb=" O ILE F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 218 Processing helix chain 'F' and resid 237 through 250 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 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 357 through 375 Processing helix chain 'F' and resid 387 through 391 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 405 through 411 removed outlier: 4.180A pdb=" N GLN F 410 " --> pdb=" O GLY F 406 " (cutoff:3.500A) 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 Processing helix chain 'G' and resid 462 through 467 removed outlier: 3.603A pdb=" N THR G 466 " --> pdb=" O GLU G 463 " (cutoff:3.500A) Processing helix chain 'G' and resid 483 through 494 Processing helix chain 'G' and resid 500 through 509 removed outlier: 3.706A pdb=" N HIS G 506 " --> pdb=" O GLN G 502 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR G 507 " --> pdb=" O LEU G 503 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG G 508 " --> pdb=" O LEU G 504 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLY G 509 " --> pdb=" O GLU G 505 " (cutoff:3.500A) Processing helix chain 'G' and resid 511 through 521 removed outlier: 3.773A pdb=" N ALA G 514 " --> pdb=" O ASN G 511 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET G 521 " --> pdb=" O LYS G 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 559 removed outlier: 4.225A pdb=" N GLN G 533 " --> pdb=" O ASN G 529 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR G 534 " --> pdb=" O ILE G 530 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU G 553 " --> pdb=" O LEU G 549 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU G 558 " --> pdb=" O LEU G 554 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG G 559 " --> pdb=" O ILE G 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 565 through 579 removed outlier: 3.587A pdb=" N LEU G 574 " --> pdb=" O GLU G 570 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN G 575 " --> pdb=" O LEU G 571 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN G 576 " --> pdb=" O TRP G 572 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU G 577 " --> pdb=" O THR G 573 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU G 578 " --> pdb=" O LEU G 574 " (cutoff:3.500A) Processing helix chain 'H' and resid 450 through 460 Processing helix chain 'H' and resid 462 through 467 removed outlier: 3.821A pdb=" N THR H 466 " --> pdb=" O GLU H 463 " (cutoff:3.500A) Processing helix chain 'H' and resid 482 through 494 removed outlier: 3.738A pdb=" N SER H 494 " --> pdb=" O ASN H 490 " (cutoff:3.500A) Processing helix chain 'H' and resid 500 through 507 removed outlier: 3.622A pdb=" N HIS H 506 " --> pdb=" O GLN H 502 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR H 507 " --> pdb=" O LEU H 503 " (cutoff:3.500A) Processing helix chain 'H' and resid 511 through 521 removed outlier: 3.857A pdb=" N ALA H 514 " --> pdb=" O ASN H 511 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET H 521 " --> pdb=" O LYS H 518 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 561 removed outlier: 4.523A pdb=" N GLN H 533 " --> pdb=" O ASN H 529 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR H 534 " --> pdb=" O ILE H 530 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU H 546 " --> pdb=" O MET H 542 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU H 547 " --> pdb=" O PHE H 543 " (cutoff:3.500A) Processing helix chain 'H' and resid 565 through 579 removed outlier: 3.589A pdb=" N LEU H 578 " --> pdb=" O LEU H 574 " (cutoff:3.500A) Processing helix chain 'I' and resid 450 through 460 Processing helix chain 'I' and resid 462 through 467 Processing helix chain 'I' and resid 482 through 494 Processing helix chain 'I' and resid 500 through 509 removed outlier: 3.758A pdb=" N HIS I 506 " --> pdb=" O GLN I 502 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR I 507 " --> pdb=" O LEU I 503 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ARG I 508 " --> pdb=" O LEU I 504 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLY I 509 " --> pdb=" O GLU I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 511 through 521 removed outlier: 4.066A pdb=" N ALA I 514 " --> pdb=" O ASN I 511 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET I 521 " --> pdb=" O LYS I 518 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 561 removed outlier: 4.318A pdb=" N GLN I 533 " --> pdb=" O ASN I 529 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR I 534 " --> pdb=" O ILE I 530 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER I 545 " --> pdb=" O HIS I 541 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU I 546 " --> pdb=" O MET I 542 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU I 547 " --> pdb=" O PHE I 543 " (cutoff:3.500A) Processing helix chain 'I' and resid 565 through 579 removed outlier: 3.642A pdb=" N GLU I 577 " --> pdb=" O THR I 573 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU I 578 " --> pdb=" O LEU I 574 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA I 579 " --> pdb=" O ASN I 575 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 459 through 462 removed outlier: 6.059A pdb=" N ILE A 415 " --> pdb=" O GLY A 439 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU A 226 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N MET A 416 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A 228 " --> pdb=" O MET A 416 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE A 418 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA A 230 " --> pdb=" O ILE A 418 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL A 379 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL A 229 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA A 381 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N ALA A 231 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER A 383 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE A 340 " --> pdb=" O PRO A 255 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU A 257 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ILE A 342 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE A 259 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 459 through 462 removed outlier: 6.399A pdb=" N ILE B 415 " --> pdb=" O GLY B 439 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL B 379 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL B 229 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA B 381 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N ALA B 231 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER B 383 " --> pdb=" O ALA B 231 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 459 through 462 removed outlier: 6.407A pdb=" N ILE C 415 " --> pdb=" O GLY C 439 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL C 379 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL C 229 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA C 381 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ALA C 231 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER C 383 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE C 340 " --> pdb=" O PRO C 255 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU C 257 " --> pdb=" O ILE C 340 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ILE C 342 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE C 259 " --> pdb=" O ILE C 342 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 459 through 462 removed outlier: 6.358A pdb=" N ILE D 415 " --> pdb=" O GLY D 439 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL D 379 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL D 229 " --> pdb=" O VAL D 379 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA D 381 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE D 340 " --> pdb=" O PRO D 255 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU D 257 " --> pdb=" O ILE D 340 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE D 342 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N PHE D 259 " --> pdb=" O ILE D 342 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 459 through 462 removed outlier: 6.399A pdb=" N ILE E 415 " --> pdb=" O GLY E 439 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL E 379 " --> pdb=" O ILE E 227 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL E 229 " --> pdb=" O VAL E 379 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA E 381 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N ALA E 231 " --> pdb=" O ALA E 381 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER E 383 " --> pdb=" O ALA E 231 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE E 340 " --> pdb=" O PRO E 255 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU E 257 " --> pdb=" O ILE E 340 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ILE E 342 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE E 259 " --> pdb=" O ILE E 342 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 459 through 462 removed outlier: 6.492A pdb=" N ILE F 415 " --> pdb=" O GLY F 439 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL F 379 " --> pdb=" O ILE F 227 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL F 229 " --> pdb=" O VAL F 379 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA F 381 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N ALA F 231 " --> pdb=" O ALA F 381 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER F 383 " --> pdb=" O ALA F 231 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE F 340 " --> pdb=" O PRO F 255 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU F 257 " --> pdb=" O ILE F 340 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE F 342 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE F 259 " --> pdb=" O ILE F 342 " (cutoff:3.500A) 1275 hydrogen bonds defined for protein. 3279 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: 8.22 Time building geometry restraints manager: 12.53 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: 8476 1.34 - 1.46: 4408 1.46 - 1.58: 11770 1.58 - 1.70: 40 1.70 - 1.82: 206 Bond restraints: 24900 Sorted by residual: bond pdb=" F1 ALF F1002 " pdb="AL ALF F1002 " ideal model delta sigma weight residual 1.684 1.805 -0.121 2.00e-02 2.50e+03 3.63e+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 3.56e+01 bond pdb=" F1 ALF B1002 " pdb="AL ALF B1002 " ideal model delta sigma weight residual 1.684 1.803 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" F1 ALF E1002 " pdb="AL ALF E1002 " ideal model delta sigma weight residual 1.684 1.803 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" F4 ALF C1002 " pdb="AL ALF C1002 " ideal model delta sigma weight residual 1.686 1.804 -0.118 2.00e-02 2.50e+03 3.50e+01 ... (remaining 24895 not shown) Histogram of bond angle deviations from ideal: 88.49 - 106.66: 772 106.66 - 124.84: 32624 124.84 - 143.02: 371 143.02 - 161.19: 0 161.19 - 179.37: 10 Bond angle restraints: 33777 Sorted by residual: angle pdb=" F1 ALF E1002 " pdb="AL ALF E1002 " pdb=" F2 ALF E1002 " ideal model delta sigma weight residual 108.68 179.14 -70.46 3.00e+00 1.11e-01 5.52e+02 angle pdb=" F1 ALF C1002 " pdb="AL ALF C1002 " pdb=" F2 ALF C1002 " ideal model delta sigma weight residual 108.68 179.11 -70.43 3.00e+00 1.11e-01 5.51e+02 angle pdb=" F1 ALF D1002 " pdb="AL ALF D1002 " pdb=" F2 ALF D1002 " ideal model delta sigma weight residual 108.68 179.08 -70.40 3.00e+00 1.11e-01 5.51e+02 angle pdb=" F1 ALF B1002 " pdb="AL ALF B1002 " pdb=" F2 ALF B1002 " 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 F1002 " pdb="AL ALF F1002 " pdb=" F2 ALF F1002 " ideal model delta sigma weight residual 108.68 178.95 -70.27 3.00e+00 1.11e-01 5.49e+02 ... (remaining 33772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.03: 15164 30.03 - 60.06: 166 60.06 - 90.09: 6 90.09 - 120.12: 7 120.12 - 150.15: 1 Dihedral angle restraints: 15344 sinusoidal: 6416 harmonic: 8928 Sorted by residual: dihedral pdb=" CA GLU D 404 " pdb=" C GLU D 404 " pdb=" N SER D 405 " pdb=" CA SER D 405 " ideal model delta harmonic sigma weight residual 180.00 -142.98 -37.02 0 5.00e+00 4.00e-02 5.48e+01 dihedral pdb=" O1B ADP F1001 " pdb=" O3A ADP F1001 " pdb=" PB ADP F1001 " pdb=" PA ADP F1001 " ideal model delta sinusoidal sigma weight residual -60.00 90.15 -150.15 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" CA GLU E 404 " pdb=" C GLU E 404 " pdb=" N SER E 405 " pdb=" CA SER E 405 " ideal model delta harmonic sigma weight residual -180.00 -147.90 -32.10 0 5.00e+00 4.00e-02 4.12e+01 ... (remaining 15341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2718 0.029 - 0.058: 718 0.058 - 0.088: 219 0.088 - 0.117: 147 0.117 - 0.146: 50 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA VAL C 449 " pdb=" N VAL C 449 " pdb=" C VAL C 449 " pdb=" CB VAL C 449 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA VAL E 449 " pdb=" N VAL E 449 " pdb=" C VAL E 449 " pdb=" CB VAL E 449 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA VAL D 449 " pdb=" N VAL D 449 " pdb=" C VAL D 449 " pdb=" CB VAL D 449 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 3849 not shown) Planarity restraints: 4422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 199 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO F 200 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO F 200 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 200 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 199 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO B 200 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 200 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 200 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 468 " 0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO G 469 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO G 469 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO G 469 " 0.015 5.00e-02 4.00e+02 ... (remaining 4419 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 350 2.57 - 3.15: 21711 3.15 - 3.74: 40134 3.74 - 4.32: 54124 4.32 - 4.90: 90529 Nonbonded interactions: 206848 Sorted by model distance: nonbonded pdb=" F4 ALF F1002 " pdb="MG MG F1003 " model vdw 1.992 2.120 nonbonded pdb=" F4 ALF B1002 " pdb="MG MG B1003 " model vdw 1.993 2.120 nonbonded pdb=" F1 ALF B1002 " pdb="MG MG B1003 " model vdw 1.993 2.120 nonbonded pdb=" F4 ALF D1002 " pdb="MG MG D1003 " model vdw 1.993 2.120 nonbonded pdb=" F1 ALF F1002 " pdb="MG MG F1003 " model vdw 1.994 2.120 ... (remaining 206843 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' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.430 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: 5.340 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 72.450 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 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 0.121 24900 Z= 0.299 Angle : 1.412 70.464 33777 Z= 0.532 Chirality : 0.037 0.146 3852 Planarity : 0.003 0.038 4422 Dihedral : 10.318 150.151 9545 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.18 % Allowed : 3.45 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.16), residues: 3066 helix: 2.89 (0.13), residues: 1717 sheet: -0.92 (0.26), residues: 319 loop : 0.48 (0.21), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 48 HIS 0.003 0.001 HIS E 334 PHE 0.006 0.001 PHE D 166 TYR 0.008 0.001 TYR B 344 ARG 0.006 0.000 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 659 time to evaluate : 2.678 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: A 53 GLU cc_start: 0.8368 (tt0) cc_final: 0.8072 (pp20) REVERT: A 58 ASP cc_start: 0.9083 (m-30) cc_final: 0.8654 (p0) REVERT: A 135 MET cc_start: 0.9057 (ttm) cc_final: 0.8515 (ppp) REVERT: A 291 ASP cc_start: 0.8674 (m-30) cc_final: 0.8095 (p0) REVERT: A 345 LEU cc_start: 0.8307 (mt) cc_final: 0.7830 (mt) REVERT: B 72 MET cc_start: 0.8897 (mtt) cc_final: 0.8637 (mtt) REVERT: B 226 LEU cc_start: 0.8288 (tp) cc_final: 0.7775 (mm) REVERT: B 240 PHE cc_start: 0.9322 (t80) cc_final: 0.9079 (t80) REVERT: B 263 MET cc_start: 0.6032 (mtp) cc_final: 0.5786 (mtt) REVERT: B 269 MET cc_start: 0.8878 (tpp) cc_final: 0.8591 (tpp) REVERT: B 291 ASP cc_start: 0.8979 (m-30) cc_final: 0.8735 (p0) REVERT: B 324 ARG cc_start: 0.9166 (ttm170) cc_final: 0.8898 (ttm-80) REVERT: B 348 MET cc_start: 0.7184 (mtp) cc_final: 0.6966 (ttm) REVERT: B 414 LEU cc_start: 0.9277 (tp) cc_final: 0.8938 (tp) REVERT: C 60 PHE cc_start: 0.9225 (m-80) cc_final: 0.8922 (m-10) REVERT: C 61 TYR cc_start: 0.8669 (t80) cc_final: 0.8430 (t80) REVERT: C 240 PHE cc_start: 0.8919 (t80) cc_final: 0.8480 (t80) REVERT: C 259 PHE cc_start: 0.9023 (m-80) cc_final: 0.8749 (m-80) REVERT: C 263 MET cc_start: 0.7866 (mtp) cc_final: 0.7514 (ttm) REVERT: C 269 MET cc_start: 0.8870 (tpp) cc_final: 0.8559 (ttt) REVERT: C 270 MET cc_start: 0.9052 (mtm) cc_final: 0.8236 (mtp) REVERT: C 382 LEU cc_start: 0.8828 (mt) cc_final: 0.8326 (mt) REVERT: D 50 ASP cc_start: 0.8181 (m-30) cc_final: 0.7810 (p0) REVERT: D 58 ASP cc_start: 0.9006 (m-30) cc_final: 0.8762 (p0) REVERT: D 87 LEU cc_start: 0.8533 (tp) cc_final: 0.7932 (pp) REVERT: D 118 ASN cc_start: 0.9391 (m-40) cc_final: 0.9089 (m-40) REVERT: D 160 LEU cc_start: 0.9159 (tp) cc_final: 0.8873 (tt) REVERT: D 228 ILE cc_start: 0.8273 (mm) cc_final: 0.8045 (mm) REVERT: D 237 LYS cc_start: 0.8552 (ttpt) cc_final: 0.8189 (ptpt) REVERT: D 263 MET cc_start: 0.8062 (mtp) cc_final: 0.7790 (mtt) REVERT: D 337 ILE cc_start: 0.8701 (mt) cc_final: 0.8411 (mm) REVERT: D 341 MET cc_start: 0.7657 (tmt) cc_final: 0.7042 (tmm) REVERT: D 363 GLU cc_start: 0.7849 (tp30) cc_final: 0.7256 (tm-30) REVERT: D 426 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7601 (tp30) REVERT: E 60 PHE cc_start: 0.8983 (m-80) cc_final: 0.8285 (m-80) REVERT: E 92 GLU cc_start: 0.8879 (tt0) cc_final: 0.8484 (tm-30) REVERT: E 135 MET cc_start: 0.9300 (ttm) cc_final: 0.8934 (tmm) REVERT: E 235 MET cc_start: 0.8937 (mmt) cc_final: 0.8143 (mmm) REVERT: E 270 MET cc_start: 0.8963 (mtm) cc_final: 0.8354 (ppp) REVERT: E 301 MET cc_start: 0.9056 (mtp) cc_final: 0.8105 (tpp) REVERT: E 310 ILE cc_start: 0.9285 (mt) cc_final: 0.8954 (mm) REVERT: E 320 PRO cc_start: 0.8637 (Cg_exo) cc_final: 0.7891 (Cg_endo) REVERT: E 363 GLU cc_start: 0.9103 (tp30) cc_final: 0.8898 (tp30) REVERT: E 443 ASN cc_start: 0.8521 (m-40) cc_final: 0.7423 (t0) REVERT: F 282 THR cc_start: 0.9096 (m) cc_final: 0.8803 (p) REVERT: F 361 ILE cc_start: 0.9135 (mm) cc_final: 0.8910 (mm) REVERT: F 414 LEU cc_start: 0.9094 (tp) cc_final: 0.8892 (tp) REVERT: G 471 LEU cc_start: 0.7256 (pp) cc_final: 0.6464 (mp) REVERT: G 521 MET cc_start: 0.9210 (ppp) cc_final: 0.9009 (ppp) REVERT: G 553 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8743 (pm20) REVERT: G 568 CYS cc_start: 0.8504 (m) cc_final: 0.8111 (t) REVERT: H 498 LEU cc_start: 0.0378 (pt) cc_final: -0.0328 (pt) REVERT: H 550 ARG cc_start: 0.8960 (mmp80) cc_final: 0.8648 (mmm160) REVERT: I 530 ILE cc_start: 0.8998 (tt) cc_final: 0.8670 (pt) outliers start: 31 outliers final: 4 residues processed: 683 average time/residue: 0.4193 time to fit residues: 421.0914 Evaluate side-chains 377 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 372 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 7.9990 chunk 230 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 238 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 177 optimal weight: 10.0000 chunk 276 optimal weight: 0.7980 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 76 GLN ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 ASN G 495 GLN G 541 HIS I 502 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24900 Z= 0.249 Angle : 1.032 30.703 33777 Z= 0.418 Chirality : 0.042 0.236 3852 Planarity : 0.005 0.087 4422 Dihedral : 7.575 129.674 3554 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.27 % Allowed : 2.16 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.78 (0.16), residues: 3066 helix: 2.06 (0.12), residues: 1745 sheet: -0.82 (0.26), residues: 340 loop : 0.46 (0.22), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 294 HIS 0.008 0.001 HIS G 541 PHE 0.022 0.002 PHE B 197 TYR 0.022 0.002 TYR B 122 ARG 0.012 0.001 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 453 time to evaluate : 2.960 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: A 58 ASP cc_start: 0.9109 (m-30) cc_final: 0.8639 (p0) REVERT: A 194 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8956 (tp30) REVERT: A 291 ASP cc_start: 0.8695 (m-30) cc_final: 0.8077 (p0) REVERT: A 345 LEU cc_start: 0.8061 (mt) cc_final: 0.7771 (mt) REVERT: B 72 MET cc_start: 0.8666 (mtt) cc_final: 0.8421 (mtt) REVERT: B 226 LEU cc_start: 0.8441 (tp) cc_final: 0.7697 (mm) REVERT: B 235 MET cc_start: 0.8897 (mmt) cc_final: 0.8434 (mmt) REVERT: B 269 MET cc_start: 0.9008 (tpp) cc_final: 0.8711 (tpp) REVERT: B 291 ASP cc_start: 0.8965 (m-30) cc_final: 0.8725 (p0) REVERT: B 297 ILE cc_start: 0.9544 (mm) cc_final: 0.9293 (pt) REVERT: B 301 MET cc_start: 0.9055 (tmm) cc_final: 0.8831 (tmm) REVERT: B 414 LEU cc_start: 0.9180 (tp) cc_final: 0.8771 (tp) REVERT: C 60 PHE cc_start: 0.9323 (m-80) cc_final: 0.8946 (m-10) REVERT: C 61 TYR cc_start: 0.8752 (t80) cc_final: 0.8457 (t80) REVERT: C 235 MET cc_start: 0.9115 (mmp) cc_final: 0.8859 (mmm) REVERT: C 259 PHE cc_start: 0.9091 (m-80) cc_final: 0.8668 (m-80) REVERT: C 269 MET cc_start: 0.8895 (tpp) cc_final: 0.8604 (ttt) REVERT: C 270 MET cc_start: 0.9253 (mtm) cc_final: 0.8539 (mtp) REVERT: C 322 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8477 (mt-10) REVERT: C 382 LEU cc_start: 0.8914 (mt) cc_final: 0.8667 (mt) REVERT: C 427 ASN cc_start: 0.8049 (p0) cc_final: 0.7726 (p0) REVERT: D 50 ASP cc_start: 0.8138 (m-30) cc_final: 0.7777 (p0) REVERT: D 58 ASP cc_start: 0.9041 (m-30) cc_final: 0.8777 (p0) REVERT: D 118 ASN cc_start: 0.9479 (m-40) cc_final: 0.9261 (m-40) REVERT: D 160 LEU cc_start: 0.9202 (tp) cc_final: 0.8913 (tt) REVERT: D 237 LYS cc_start: 0.8657 (ttpt) cc_final: 0.8354 (ptpt) REVERT: D 269 MET cc_start: 0.8422 (ttm) cc_final: 0.8163 (ttm) REVERT: D 301 MET cc_start: 0.8845 (mtm) cc_final: 0.8559 (mtt) REVERT: D 337 ILE cc_start: 0.8548 (mt) cc_final: 0.8310 (mm) REVERT: D 390 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7670 (mp0) REVERT: E 60 PHE cc_start: 0.9257 (m-80) cc_final: 0.8446 (m-80) REVERT: E 85 ILE cc_start: 0.9575 (pt) cc_final: 0.9276 (mp) REVERT: E 92 GLU cc_start: 0.8812 (tt0) cc_final: 0.8534 (tm-30) REVERT: E 235 MET cc_start: 0.8934 (mmt) cc_final: 0.8337 (mmm) REVERT: E 310 ILE cc_start: 0.9329 (mt) cc_final: 0.9066 (mm) REVERT: E 363 GLU cc_start: 0.9142 (tp30) cc_final: 0.8803 (tp30) REVERT: F 235 MET cc_start: 0.7366 (mtt) cc_final: 0.6513 (mtp) REVERT: F 263 MET cc_start: 0.7191 (mpp) cc_final: 0.6922 (mpp) REVERT: F 270 MET cc_start: 0.8504 (ttt) cc_final: 0.8275 (ttt) REVERT: F 282 THR cc_start: 0.9197 (m) cc_final: 0.8845 (p) REVERT: F 318 LEU cc_start: 0.8412 (mp) cc_final: 0.8105 (mp) REVERT: G 468 VAL cc_start: 0.7452 (t) cc_final: 0.7187 (t) REVERT: H 541 HIS cc_start: 0.8619 (m90) cc_final: 0.8400 (m90) REVERT: H 550 ARG cc_start: 0.8967 (mmp80) cc_final: 0.8661 (mmm160) REVERT: I 530 ILE cc_start: 0.8891 (tt) cc_final: 0.8617 (pt) outliers start: 7 outliers final: 2 residues processed: 457 average time/residue: 0.3913 time to fit residues: 270.2798 Evaluate side-chains 319 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 317 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 229 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 276 optimal weight: 6.9990 chunk 298 optimal weight: 8.9990 chunk 246 optimal weight: 2.9990 chunk 274 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 221 optimal weight: 30.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN G 541 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24900 Z= 0.210 Angle : 1.005 29.963 33777 Z= 0.400 Chirality : 0.040 0.226 3852 Planarity : 0.005 0.075 4422 Dihedral : 7.364 132.056 3554 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.53 (0.16), residues: 3066 helix: 1.75 (0.12), residues: 1746 sheet: -0.64 (0.26), residues: 334 loop : 0.46 (0.22), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 48 HIS 0.007 0.001 HIS G 541 PHE 0.020 0.002 PHE F 240 TYR 0.023 0.001 TYR B 122 ARG 0.011 0.001 ARG G 557 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 2.849 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: A 58 ASP cc_start: 0.9101 (m-30) cc_final: 0.8601 (p0) REVERT: A 194 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8974 (tp30) REVERT: A 242 MET cc_start: 0.9014 (ppp) cc_final: 0.8766 (ppp) REVERT: A 291 ASP cc_start: 0.8661 (m-30) cc_final: 0.8065 (p0) REVERT: A 345 LEU cc_start: 0.8030 (mt) cc_final: 0.7709 (mt) REVERT: A 348 MET cc_start: 0.9014 (ttm) cc_final: 0.8458 (ttm) REVERT: B 72 MET cc_start: 0.8757 (mtt) cc_final: 0.8522 (mtt) REVERT: B 269 MET cc_start: 0.9057 (tpp) cc_final: 0.8746 (tpp) REVERT: B 291 ASP cc_start: 0.9005 (m-30) cc_final: 0.8730 (p0) REVERT: B 297 ILE cc_start: 0.9524 (mm) cc_final: 0.9282 (pt) REVERT: B 301 MET cc_start: 0.9120 (tmm) cc_final: 0.8908 (tmm) REVERT: C 60 PHE cc_start: 0.9298 (m-80) cc_final: 0.8898 (m-10) REVERT: C 61 TYR cc_start: 0.8773 (t80) cc_final: 0.8468 (t80) REVERT: C 235 MET cc_start: 0.9150 (mmp) cc_final: 0.8850 (mmm) REVERT: C 259 PHE cc_start: 0.9031 (m-80) cc_final: 0.8675 (m-80) REVERT: C 269 MET cc_start: 0.8877 (tpp) cc_final: 0.8504 (ttt) REVERT: C 270 MET cc_start: 0.9250 (mtm) cc_final: 0.8541 (mtp) REVERT: C 314 ASP cc_start: 0.6300 (t0) cc_final: 0.6093 (t0) REVERT: C 322 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8477 (mt-10) REVERT: C 382 LEU cc_start: 0.8878 (mt) cc_final: 0.8435 (mt) REVERT: C 419 TYR cc_start: 0.7885 (t80) cc_final: 0.7628 (t80) REVERT: C 427 ASN cc_start: 0.8066 (p0) cc_final: 0.7821 (p0) REVERT: D 50 ASP cc_start: 0.8205 (m-30) cc_final: 0.7833 (p0) REVERT: D 58 ASP cc_start: 0.9026 (m-30) cc_final: 0.8758 (p0) REVERT: D 160 LEU cc_start: 0.9228 (tp) cc_final: 0.8939 (tt) REVERT: D 284 ILE cc_start: 0.9175 (mt) cc_final: 0.8960 (mt) REVERT: D 301 MET cc_start: 0.8845 (mtm) cc_final: 0.8533 (mtt) REVERT: D 337 ILE cc_start: 0.8627 (mt) cc_final: 0.8389 (mm) REVERT: D 390 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7678 (mp0) REVERT: E 42 MET cc_start: 0.8349 (mtm) cc_final: 0.7985 (ptp) REVERT: E 60 PHE cc_start: 0.9196 (m-80) cc_final: 0.8312 (m-80) REVERT: E 85 ILE cc_start: 0.9563 (pt) cc_final: 0.9248 (mp) REVERT: E 92 GLU cc_start: 0.8828 (tt0) cc_final: 0.8539 (tm-30) REVERT: E 235 MET cc_start: 0.8951 (mmt) cc_final: 0.8451 (mmm) REVERT: E 310 ILE cc_start: 0.9337 (mt) cc_final: 0.9050 (mm) REVERT: E 344 TYR cc_start: 0.7723 (p90) cc_final: 0.6932 (p90) REVERT: E 363 GLU cc_start: 0.9100 (tp30) cc_final: 0.8784 (tp30) REVERT: F 98 ASP cc_start: 0.7754 (t0) cc_final: 0.7492 (p0) REVERT: F 235 MET cc_start: 0.7558 (mtt) cc_final: 0.6763 (mtp) REVERT: F 282 THR cc_start: 0.9190 (m) cc_final: 0.8869 (p) REVERT: G 537 ASP cc_start: 0.8812 (t0) cc_final: 0.8463 (t0) REVERT: H 541 HIS cc_start: 0.8703 (m90) cc_final: 0.8496 (m90) REVERT: H 550 ARG cc_start: 0.8974 (mmp80) cc_final: 0.8660 (mmm160) REVERT: I 530 ILE cc_start: 0.8950 (tt) cc_final: 0.8672 (pt) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.3816 time to fit residues: 241.5186 Evaluate side-chains 319 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 131 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 277 optimal weight: 50.0000 chunk 293 optimal weight: 40.0000 chunk 145 optimal weight: 9.9990 chunk 263 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 ASN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 140 ASN ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS ** H 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 24900 Z= 0.275 Angle : 1.027 30.829 33777 Z= 0.417 Chirality : 0.040 0.168 3852 Planarity : 0.005 0.063 4422 Dihedral : 7.364 137.897 3554 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.04 % Allowed : 2.58 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.17 (0.15), residues: 3066 helix: 1.47 (0.12), residues: 1756 sheet: -0.78 (0.26), residues: 328 loop : 0.25 (0.21), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 294 HIS 0.007 0.001 HIS G 541 PHE 0.016 0.002 PHE F 240 TYR 0.022 0.002 TYR D 122 ARG 0.014 0.001 ARG C 459 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 399 time to evaluate : 2.878 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: A 58 ASP cc_start: 0.9130 (m-30) cc_final: 0.8616 (p0) REVERT: A 194 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8967 (tp30) REVERT: A 242 MET cc_start: 0.8982 (ppp) cc_final: 0.8738 (ppp) REVERT: A 291 ASP cc_start: 0.8681 (m-30) cc_final: 0.8047 (p0) REVERT: A 345 LEU cc_start: 0.7976 (mt) cc_final: 0.7583 (mt) REVERT: A 416 MET cc_start: 0.8663 (mmm) cc_final: 0.8387 (mmm) REVERT: A 438 ILE cc_start: 0.8055 (mp) cc_final: 0.7817 (mp) REVERT: B 72 MET cc_start: 0.8831 (mtt) cc_final: 0.8624 (mtt) REVERT: B 235 MET cc_start: 0.8993 (mmt) cc_final: 0.8636 (mmm) REVERT: B 269 MET cc_start: 0.9036 (tpp) cc_final: 0.8714 (tpp) REVERT: B 291 ASP cc_start: 0.9049 (m-30) cc_final: 0.8768 (p0) REVERT: B 297 ILE cc_start: 0.9532 (mm) cc_final: 0.9295 (pt) REVERT: B 301 MET cc_start: 0.9157 (tmm) cc_final: 0.8883 (tmm) REVERT: C 60 PHE cc_start: 0.9299 (m-80) cc_final: 0.8966 (m-10) REVERT: C 235 MET cc_start: 0.9172 (mmp) cc_final: 0.8859 (mmm) REVERT: C 259 PHE cc_start: 0.9097 (m-80) cc_final: 0.8758 (m-80) REVERT: C 269 MET cc_start: 0.8941 (tpp) cc_final: 0.8492 (ttt) REVERT: C 322 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8430 (mt-10) REVERT: C 382 LEU cc_start: 0.8885 (mt) cc_final: 0.8458 (mt) REVERT: C 419 TYR cc_start: 0.7904 (t80) cc_final: 0.7561 (t80) REVERT: C 427 ASN cc_start: 0.8151 (p0) cc_final: 0.7922 (p0) REVERT: D 42 MET cc_start: 0.7191 (mtp) cc_final: 0.6806 (mtp) REVERT: D 50 ASP cc_start: 0.8228 (m-30) cc_final: 0.7803 (p0) REVERT: D 160 LEU cc_start: 0.9239 (tp) cc_final: 0.8947 (tt) REVERT: D 269 MET cc_start: 0.8499 (ttm) cc_final: 0.8225 (ttm) REVERT: D 301 MET cc_start: 0.8890 (mtm) cc_final: 0.8560 (mtt) REVERT: D 337 ILE cc_start: 0.8629 (mt) cc_final: 0.8414 (mm) REVERT: E 42 MET cc_start: 0.8373 (mtm) cc_final: 0.8152 (ptm) REVERT: E 60 PHE cc_start: 0.9248 (m-80) cc_final: 0.8979 (m-10) REVERT: E 85 ILE cc_start: 0.9476 (pt) cc_final: 0.9267 (mp) REVERT: E 92 GLU cc_start: 0.8848 (tt0) cc_final: 0.8502 (tp30) REVERT: E 235 MET cc_start: 0.9006 (mmt) cc_final: 0.8371 (mmm) REVERT: E 301 MET cc_start: 0.9094 (mtm) cc_final: 0.8783 (mtt) REVERT: E 348 MET cc_start: 0.8538 (mmp) cc_final: 0.8174 (mmp) REVERT: E 363 GLU cc_start: 0.9104 (tp30) cc_final: 0.8774 (tp30) REVERT: F 235 MET cc_start: 0.7645 (mtt) cc_final: 0.6708 (mtp) REVERT: F 391 GLN cc_start: 0.9314 (mt0) cc_final: 0.9025 (mt0) REVERT: G 537 ASP cc_start: 0.8817 (t0) cc_final: 0.8469 (t0) REVERT: H 498 LEU cc_start: 0.1827 (pt) cc_final: 0.1475 (pt) REVERT: H 541 HIS cc_start: 0.8737 (m90) cc_final: 0.8470 (m-70) REVERT: H 550 ARG cc_start: 0.8993 (mmp80) cc_final: 0.8669 (mmm160) REVERT: I 530 ILE cc_start: 0.8967 (tt) cc_final: 0.8684 (pt) outliers start: 1 outliers final: 0 residues processed: 400 average time/residue: 0.3879 time to fit residues: 238.8815 Evaluate side-chains 301 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 218 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 250 optimal weight: 8.9990 chunk 203 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 150 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 ASN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS ** H 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24900 Z= 0.205 Angle : 1.007 30.926 33777 Z= 0.402 Chirality : 0.040 0.176 3852 Planarity : 0.004 0.063 4422 Dihedral : 7.163 139.000 3554 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.13 (0.15), residues: 3066 helix: 1.43 (0.12), residues: 1753 sheet: -0.87 (0.25), residues: 332 loop : 0.29 (0.21), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 48 HIS 0.006 0.001 HIS G 541 PHE 0.014 0.002 PHE F 240 TYR 0.020 0.001 TYR D 122 ARG 0.014 0.001 ARG D 459 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 2.634 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: A 58 ASP cc_start: 0.9150 (m-30) cc_final: 0.8595 (p0) REVERT: A 194 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8966 (tp30) REVERT: A 242 MET cc_start: 0.8945 (ppp) cc_final: 0.8670 (ppp) REVERT: A 291 ASP cc_start: 0.8692 (m-30) cc_final: 0.8053 (p0) REVERT: A 345 LEU cc_start: 0.7989 (mt) cc_final: 0.7629 (mt) REVERT: B 235 MET cc_start: 0.8968 (mmt) cc_final: 0.8560 (mmm) REVERT: B 291 ASP cc_start: 0.9039 (m-30) cc_final: 0.8758 (p0) REVERT: B 297 ILE cc_start: 0.9536 (mm) cc_final: 0.9306 (pt) REVERT: B 301 MET cc_start: 0.9158 (tmm) cc_final: 0.8867 (tmm) REVERT: C 60 PHE cc_start: 0.9259 (m-80) cc_final: 0.8885 (m-10) REVERT: C 235 MET cc_start: 0.9072 (mmp) cc_final: 0.8719 (mmm) REVERT: C 259 PHE cc_start: 0.9054 (m-80) cc_final: 0.8794 (m-80) REVERT: C 269 MET cc_start: 0.8917 (tpp) cc_final: 0.8567 (ttt) REVERT: C 322 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8433 (mt-10) REVERT: C 382 LEU cc_start: 0.8961 (mt) cc_final: 0.8545 (mt) REVERT: C 419 TYR cc_start: 0.7838 (t80) cc_final: 0.7372 (t80) REVERT: D 42 MET cc_start: 0.7309 (mtp) cc_final: 0.6972 (mtp) REVERT: D 50 ASP cc_start: 0.8283 (m-30) cc_final: 0.7818 (p0) REVERT: D 160 LEU cc_start: 0.9263 (tp) cc_final: 0.8979 (tt) REVERT: D 269 MET cc_start: 0.8476 (ttm) cc_final: 0.8203 (ttm) REVERT: D 301 MET cc_start: 0.8893 (mtm) cc_final: 0.8566 (mtt) REVERT: E 42 MET cc_start: 0.8388 (mtm) cc_final: 0.8080 (ptm) REVERT: E 60 PHE cc_start: 0.9160 (m-80) cc_final: 0.8878 (m-10) REVERT: E 92 GLU cc_start: 0.8945 (tt0) cc_final: 0.8493 (tp30) REVERT: E 235 MET cc_start: 0.8944 (mmt) cc_final: 0.8472 (mmm) REVERT: E 301 MET cc_start: 0.8970 (mtm) cc_final: 0.8674 (mtp) REVERT: E 344 TYR cc_start: 0.8096 (p90) cc_final: 0.7731 (p90) REVERT: E 348 MET cc_start: 0.8530 (mmp) cc_final: 0.8119 (mmp) REVERT: E 363 GLU cc_start: 0.9092 (tp30) cc_final: 0.8773 (tp30) REVERT: F 391 GLN cc_start: 0.9324 (mt0) cc_final: 0.8999 (mt0) REVERT: G 537 ASP cc_start: 0.8755 (t0) cc_final: 0.8377 (t0) REVERT: H 541 HIS cc_start: 0.8708 (m90) cc_final: 0.8372 (m-70) REVERT: H 550 ARG cc_start: 0.9024 (mmp80) cc_final: 0.8699 (mmm160) REVERT: I 530 ILE cc_start: 0.8948 (tt) cc_final: 0.8668 (pt) outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.3750 time to fit residues: 222.8772 Evaluate side-chains 300 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 0.9990 chunk 264 optimal weight: 30.0000 chunk 58 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 294 optimal weight: 20.0000 chunk 244 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS ** H 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24900 Z= 0.189 Angle : 1.001 30.804 33777 Z= 0.398 Chirality : 0.040 0.197 3852 Planarity : 0.004 0.063 4422 Dihedral : 7.001 138.272 3554 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.04 % Allowed : 1.56 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.16 (0.15), residues: 3066 helix: 1.42 (0.12), residues: 1749 sheet: -0.77 (0.27), residues: 312 loop : 0.33 (0.21), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 48 HIS 0.006 0.001 HIS G 541 PHE 0.043 0.002 PHE C 166 TYR 0.019 0.001 TYR D 122 ARG 0.012 0.000 ARG E 329 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 386 time to evaluate : 2.703 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: A 58 ASP cc_start: 0.9146 (m-30) cc_final: 0.8604 (p0) REVERT: A 194 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8954 (tp30) REVERT: A 242 MET cc_start: 0.8956 (ppp) cc_final: 0.8724 (ppp) REVERT: A 269 MET cc_start: 0.7163 (tpt) cc_final: 0.6620 (tpt) REVERT: A 291 ASP cc_start: 0.8695 (m-30) cc_final: 0.8058 (p0) REVERT: A 345 LEU cc_start: 0.7962 (mt) cc_final: 0.7585 (mt) REVERT: B 235 MET cc_start: 0.8964 (mmt) cc_final: 0.8607 (mmm) REVERT: B 291 ASP cc_start: 0.9036 (m-30) cc_final: 0.8742 (p0) REVERT: B 297 ILE cc_start: 0.9528 (mm) cc_final: 0.9294 (pt) REVERT: B 301 MET cc_start: 0.9212 (tmm) cc_final: 0.8912 (tmm) REVERT: B 348 MET cc_start: 0.7466 (ttm) cc_final: 0.7259 (tpp) REVERT: B 364 ILE cc_start: 0.8844 (mt) cc_final: 0.8552 (mt) REVERT: B 382 LEU cc_start: 0.8429 (tt) cc_final: 0.8205 (tt) REVERT: B 414 LEU cc_start: 0.9181 (tp) cc_final: 0.8954 (mm) REVERT: C 60 PHE cc_start: 0.9236 (m-80) cc_final: 0.8832 (m-10) REVERT: C 235 MET cc_start: 0.9080 (mmp) cc_final: 0.8708 (mmm) REVERT: C 269 MET cc_start: 0.8915 (tpp) cc_final: 0.8699 (ttt) REVERT: C 322 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8350 (mt-10) REVERT: C 382 LEU cc_start: 0.8927 (mt) cc_final: 0.8572 (mt) REVERT: C 419 TYR cc_start: 0.7841 (t80) cc_final: 0.7377 (t80) REVERT: C 427 ASN cc_start: 0.8309 (p0) cc_final: 0.8026 (p0) REVERT: D 34 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8580 (tt0) REVERT: D 42 MET cc_start: 0.7282 (mtp) cc_final: 0.7066 (mtp) REVERT: D 50 ASP cc_start: 0.8328 (m-30) cc_final: 0.7830 (p0) REVERT: D 160 LEU cc_start: 0.9251 (tp) cc_final: 0.8960 (tt) REVERT: D 269 MET cc_start: 0.8494 (ttm) cc_final: 0.8190 (ttm) REVERT: D 301 MET cc_start: 0.8873 (mtm) cc_final: 0.8532 (mtt) REVERT: E 42 MET cc_start: 0.8316 (mtm) cc_final: 0.8011 (ptm) REVERT: E 60 PHE cc_start: 0.9129 (m-80) cc_final: 0.8829 (m-10) REVERT: E 92 GLU cc_start: 0.8949 (tt0) cc_final: 0.8511 (tp30) REVERT: E 167 LYS cc_start: 0.9260 (pttp) cc_final: 0.8984 (pttt) REVERT: E 235 MET cc_start: 0.8935 (mmt) cc_final: 0.8545 (mmm) REVERT: E 301 MET cc_start: 0.8892 (mtm) cc_final: 0.8650 (mtp) REVERT: E 344 TYR cc_start: 0.8078 (p90) cc_final: 0.7714 (p90) REVERT: E 348 MET cc_start: 0.8547 (mmp) cc_final: 0.8109 (mmp) REVERT: E 363 GLU cc_start: 0.9067 (tp30) cc_final: 0.8762 (tp30) REVERT: F 235 MET cc_start: 0.7622 (mtt) cc_final: 0.6765 (mtt) REVERT: F 263 MET cc_start: 0.7104 (mpp) cc_final: 0.6855 (mpp) REVERT: F 391 GLN cc_start: 0.9323 (mt0) cc_final: 0.9005 (mt0) REVERT: F 418 ILE cc_start: 0.8185 (mp) cc_final: 0.7865 (mp) REVERT: H 539 LEU cc_start: 0.9224 (mm) cc_final: 0.9013 (pp) REVERT: H 541 HIS cc_start: 0.8744 (m90) cc_final: 0.8501 (m-70) REVERT: H 550 ARG cc_start: 0.9032 (mmp80) cc_final: 0.8704 (mmm160) REVERT: I 521 MET cc_start: 0.7022 (ppp) cc_final: 0.6813 (pmm) REVERT: I 530 ILE cc_start: 0.8936 (tt) cc_final: 0.8665 (pt) outliers start: 1 outliers final: 0 residues processed: 387 average time/residue: 0.3725 time to fit residues: 221.2929 Evaluate side-chains 290 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 8.9990 chunk 33 optimal weight: 0.4980 chunk 167 optimal weight: 7.9990 chunk 214 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 293 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 178 optimal weight: 0.4980 chunk 135 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 ASN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24900 Z= 0.167 Angle : 0.997 30.574 33777 Z= 0.393 Chirality : 0.040 0.170 3852 Planarity : 0.004 0.067 4422 Dihedral : 6.831 136.835 3554 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.23 (0.16), residues: 3066 helix: 1.47 (0.13), residues: 1743 sheet: -0.60 (0.26), residues: 315 loop : 0.31 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 457 HIS 0.009 0.001 HIS H 506 PHE 0.035 0.001 PHE C 166 TYR 0.022 0.001 TYR B 122 ARG 0.018 0.000 ARG C 392 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 2.931 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: A 58 ASP cc_start: 0.9128 (m-30) cc_final: 0.8580 (p0) REVERT: A 84 LEU cc_start: 0.9385 (pp) cc_final: 0.9033 (mt) REVERT: A 167 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8584 (mttt) REVERT: A 194 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8959 (tp30) REVERT: A 242 MET cc_start: 0.8887 (ppp) cc_final: 0.8602 (ppp) REVERT: A 291 ASP cc_start: 0.8747 (m-30) cc_final: 0.8125 (p0) REVERT: A 341 MET cc_start: 0.3974 (ttm) cc_final: 0.3226 (tmm) REVERT: A 345 LEU cc_start: 0.7966 (mt) cc_final: 0.7615 (mt) REVERT: B 235 MET cc_start: 0.8927 (mmt) cc_final: 0.8574 (mmm) REVERT: B 291 ASP cc_start: 0.9008 (m-30) cc_final: 0.8735 (p0) REVERT: B 301 MET cc_start: 0.9212 (tmm) cc_final: 0.8740 (ppp) REVERT: B 364 ILE cc_start: 0.8838 (mt) cc_final: 0.8554 (mt) REVERT: B 382 LEU cc_start: 0.8407 (tt) cc_final: 0.8163 (tt) REVERT: C 60 PHE cc_start: 0.9194 (m-80) cc_final: 0.8853 (m-10) REVERT: C 235 MET cc_start: 0.9086 (mmp) cc_final: 0.8683 (mmm) REVERT: C 269 MET cc_start: 0.8888 (tpp) cc_final: 0.8624 (ttt) REVERT: C 322 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8331 (mt-10) REVERT: C 337 ILE cc_start: 0.8893 (tt) cc_final: 0.8292 (mt) REVERT: C 339 LEU cc_start: 0.9398 (tt) cc_final: 0.9143 (tt) REVERT: C 382 LEU cc_start: 0.8908 (mt) cc_final: 0.8559 (mt) REVERT: C 419 TYR cc_start: 0.7783 (t80) cc_final: 0.7400 (t80) REVERT: C 427 ASN cc_start: 0.8298 (p0) cc_final: 0.8038 (p0) REVERT: D 50 ASP cc_start: 0.8327 (m-30) cc_final: 0.7814 (p0) REVERT: D 160 LEU cc_start: 0.9257 (tp) cc_final: 0.8972 (tt) REVERT: D 269 MET cc_start: 0.8500 (ttm) cc_final: 0.8177 (ttm) REVERT: D 301 MET cc_start: 0.8865 (mtm) cc_final: 0.8530 (mtt) REVERT: E 60 PHE cc_start: 0.9070 (m-80) cc_final: 0.8161 (m-80) REVERT: E 89 GLU cc_start: 0.9426 (mp0) cc_final: 0.9144 (mp0) REVERT: E 92 GLU cc_start: 0.8939 (tt0) cc_final: 0.8529 (tp30) REVERT: E 235 MET cc_start: 0.8886 (mmt) cc_final: 0.8535 (mmm) REVERT: E 348 MET cc_start: 0.8542 (mmp) cc_final: 0.8076 (mmp) REVERT: E 363 GLU cc_start: 0.9083 (tp30) cc_final: 0.8827 (tp30) REVERT: F 72 MET cc_start: 0.8796 (ptt) cc_final: 0.8529 (ptt) REVERT: F 235 MET cc_start: 0.7541 (mtt) cc_final: 0.6690 (mtt) REVERT: F 263 MET cc_start: 0.7025 (mpp) cc_final: 0.6783 (mpp) REVERT: F 391 GLN cc_start: 0.9327 (mt0) cc_final: 0.9012 (mt0) REVERT: F 418 ILE cc_start: 0.8227 (mp) cc_final: 0.7932 (mp) REVERT: H 541 HIS cc_start: 0.8748 (m90) cc_final: 0.8498 (m-70) REVERT: H 550 ARG cc_start: 0.9055 (mmp80) cc_final: 0.8715 (mmm160) REVERT: I 530 ILE cc_start: 0.8930 (tt) cc_final: 0.8666 (pt) outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.3665 time to fit residues: 217.4307 Evaluate side-chains 290 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 174 optimal weight: 20.0000 chunk 88 optimal weight: 0.0170 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 186 optimal weight: 7.9990 chunk 199 optimal weight: 3.9990 chunk 144 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 230 optimal weight: 6.9990 overall best weight: 3.8026 ------------------------------------------------------------------------------- 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 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 490 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 24900 Z= 0.216 Angle : 1.016 31.338 33777 Z= 0.405 Chirality : 0.041 0.331 3852 Planarity : 0.005 0.084 4422 Dihedral : 6.857 136.258 3554 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 1.13 (0.16), residues: 3066 helix: 1.41 (0.13), residues: 1744 sheet: -0.72 (0.26), residues: 316 loop : 0.28 (0.21), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 457 HIS 0.007 0.001 HIS G 541 PHE 0.023 0.001 PHE F 240 TYR 0.017 0.001 TYR D 122 ARG 0.012 0.001 ARG F 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 2.967 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: A 58 ASP cc_start: 0.9161 (m-30) cc_final: 0.8607 (p0) REVERT: A 167 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8613 (mttt) REVERT: A 194 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8932 (tp30) REVERT: A 242 MET cc_start: 0.8943 (ppp) cc_final: 0.8655 (ppp) REVERT: A 291 ASP cc_start: 0.8714 (m-30) cc_final: 0.8071 (p0) REVERT: A 341 MET cc_start: 0.4353 (ttm) cc_final: 0.3551 (tmm) REVERT: A 345 LEU cc_start: 0.7900 (mt) cc_final: 0.7544 (mt) REVERT: A 451 LEU cc_start: 0.8691 (mt) cc_final: 0.8464 (mt) REVERT: B 235 MET cc_start: 0.8980 (mmt) cc_final: 0.8600 (mmm) REVERT: B 291 ASP cc_start: 0.9054 (m-30) cc_final: 0.8782 (p0) REVERT: B 301 MET cc_start: 0.9227 (tmm) cc_final: 0.8946 (tmm) REVERT: B 382 LEU cc_start: 0.8483 (tt) cc_final: 0.8223 (tt) REVERT: C 60 PHE cc_start: 0.9248 (m-80) cc_final: 0.8889 (m-10) REVERT: C 235 MET cc_start: 0.9086 (mmp) cc_final: 0.8681 (mmm) REVERT: C 269 MET cc_start: 0.8935 (tpp) cc_final: 0.8589 (ttt) REVERT: C 322 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8373 (mt-10) REVERT: C 382 LEU cc_start: 0.8954 (mt) cc_final: 0.8579 (mt) REVERT: C 419 TYR cc_start: 0.7858 (t80) cc_final: 0.7387 (t80) REVERT: C 427 ASN cc_start: 0.8292 (p0) cc_final: 0.8042 (p0) REVERT: D 34 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8570 (tt0) REVERT: D 50 ASP cc_start: 0.8389 (m-30) cc_final: 0.7899 (p0) REVERT: D 160 LEU cc_start: 0.9269 (tp) cc_final: 0.8994 (tt) REVERT: D 269 MET cc_start: 0.8532 (ttm) cc_final: 0.8297 (ttm) REVERT: D 301 MET cc_start: 0.8866 (mtm) cc_final: 0.8521 (mtt) REVERT: E 60 PHE cc_start: 0.9127 (m-80) cc_final: 0.8878 (m-10) REVERT: E 92 GLU cc_start: 0.8999 (tt0) cc_final: 0.8558 (tp30) REVERT: E 235 MET cc_start: 0.8941 (mmt) cc_final: 0.8639 (mmm) REVERT: E 344 TYR cc_start: 0.8313 (p90) cc_final: 0.7872 (p90) REVERT: E 348 MET cc_start: 0.8575 (mmp) cc_final: 0.8134 (mmp) REVERT: E 363 GLU cc_start: 0.9075 (tp30) cc_final: 0.8839 (tp30) REVERT: F 72 MET cc_start: 0.8812 (ptt) cc_final: 0.8509 (ptt) REVERT: F 235 MET cc_start: 0.7625 (mtt) cc_final: 0.6774 (mtt) REVERT: F 391 GLN cc_start: 0.9338 (mt0) cc_final: 0.9020 (mt0) REVERT: F 418 ILE cc_start: 0.8224 (mp) cc_final: 0.7911 (mp) REVERT: H 541 HIS cc_start: 0.8736 (m90) cc_final: 0.8400 (m-70) REVERT: H 550 ARG cc_start: 0.9053 (mmp80) cc_final: 0.8715 (mmm160) REVERT: I 530 ILE cc_start: 0.8925 (tt) cc_final: 0.8667 (pt) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.3720 time to fit residues: 209.1369 Evaluate side-chains 278 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 2.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 0.0170 chunk 280 optimal weight: 40.0000 chunk 256 optimal weight: 5.9990 chunk 273 optimal weight: 5.9990 chunk 164 optimal weight: 0.4980 chunk 118 optimal weight: 5.9990 chunk 214 optimal weight: 0.6980 chunk 83 optimal weight: 8.9990 chunk 246 optimal weight: 6.9990 chunk 258 optimal weight: 6.9990 chunk 272 optimal weight: 10.0000 overall best weight: 2.6422 ------------------------------------------------------------------------------- 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 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24900 Z= 0.182 Angle : 1.009 31.291 33777 Z= 0.400 Chirality : 0.041 0.260 3852 Planarity : 0.004 0.054 4422 Dihedral : 6.768 134.561 3554 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.15), residues: 3066 helix: 1.41 (0.13), residues: 1744 sheet: -0.64 (0.26), residues: 308 loop : 0.25 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 457 HIS 0.006 0.001 HIS G 541 PHE 0.025 0.001 PHE F 240 TYR 0.016 0.001 TYR B 122 ARG 0.013 0.000 ARG F 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 3.019 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 58 ASP cc_start: 0.9160 (m-30) cc_final: 0.8601 (p0) REVERT: A 84 LEU cc_start: 0.9409 (pp) cc_final: 0.9060 (mt) REVERT: A 167 LYS cc_start: 0.8941 (mmtt) cc_final: 0.8633 (mttt) REVERT: A 194 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8930 (tp30) REVERT: A 214 LEU cc_start: 0.9019 (tt) cc_final: 0.8804 (tt) REVERT: A 218 THR cc_start: 0.8042 (m) cc_final: 0.7765 (p) REVERT: A 242 MET cc_start: 0.8976 (ppp) cc_final: 0.8690 (ppp) REVERT: A 291 ASP cc_start: 0.8756 (m-30) cc_final: 0.8115 (p0) REVERT: A 341 MET cc_start: 0.4283 (ttm) cc_final: 0.3516 (tmm) REVERT: A 345 LEU cc_start: 0.7843 (mt) cc_final: 0.7501 (mt) REVERT: A 451 LEU cc_start: 0.8669 (mt) cc_final: 0.8451 (mt) REVERT: B 72 MET cc_start: 0.8848 (mtt) cc_final: 0.8258 (mtp) REVERT: B 235 MET cc_start: 0.8955 (mmt) cc_final: 0.8580 (mmm) REVERT: B 291 ASP cc_start: 0.9050 (m-30) cc_final: 0.8759 (p0) REVERT: B 301 MET cc_start: 0.9215 (tmm) cc_final: 0.8750 (ppp) REVERT: B 382 LEU cc_start: 0.8489 (tt) cc_final: 0.8233 (tt) REVERT: C 60 PHE cc_start: 0.9189 (m-80) cc_final: 0.8866 (m-10) REVERT: C 235 MET cc_start: 0.9069 (mmp) cc_final: 0.8646 (mmm) REVERT: C 269 MET cc_start: 0.8918 (tpp) cc_final: 0.8590 (ttt) REVERT: C 322 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8350 (mt-10) REVERT: C 382 LEU cc_start: 0.8881 (mt) cc_final: 0.8551 (mt) REVERT: C 419 TYR cc_start: 0.7865 (t80) cc_final: 0.7510 (t80) REVERT: C 427 ASN cc_start: 0.8322 (p0) cc_final: 0.8082 (p0) REVERT: D 34 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8556 (tt0) REVERT: D 50 ASP cc_start: 0.8401 (m-30) cc_final: 0.7896 (p0) REVERT: D 160 LEU cc_start: 0.9273 (tp) cc_final: 0.8999 (tt) REVERT: D 269 MET cc_start: 0.8510 (ttm) cc_final: 0.8260 (ttm) REVERT: D 301 MET cc_start: 0.8819 (mtm) cc_final: 0.8464 (mtt) REVERT: E 60 PHE cc_start: 0.9033 (m-80) cc_final: 0.8739 (m-10) REVERT: E 92 GLU cc_start: 0.8995 (tt0) cc_final: 0.8550 (tp30) REVERT: E 235 MET cc_start: 0.8923 (mmt) cc_final: 0.8648 (mmm) REVERT: E 344 TYR cc_start: 0.8335 (p90) cc_final: 0.7893 (p90) REVERT: E 348 MET cc_start: 0.8586 (mmp) cc_final: 0.8075 (mmp) REVERT: E 363 GLU cc_start: 0.9096 (tp30) cc_final: 0.8876 (tp30) REVERT: F 72 MET cc_start: 0.8804 (ptt) cc_final: 0.8506 (ptt) REVERT: F 235 MET cc_start: 0.7566 (mtt) cc_final: 0.6664 (mtt) REVERT: F 284 ILE cc_start: 0.9078 (mt) cc_final: 0.8847 (mt) REVERT: F 301 MET cc_start: 0.8841 (mtm) cc_final: 0.8518 (tpt) REVERT: F 391 GLN cc_start: 0.9308 (mt0) cc_final: 0.8975 (mt0) REVERT: F 418 ILE cc_start: 0.8189 (mp) cc_final: 0.7806 (mp) REVERT: G 537 ASP cc_start: 0.8770 (t0) cc_final: 0.8418 (t0) REVERT: H 541 HIS cc_start: 0.8743 (m90) cc_final: 0.8470 (m-70) REVERT: H 550 ARG cc_start: 0.9060 (mmp80) cc_final: 0.8714 (mmm160) REVERT: I 530 ILE cc_start: 0.8922 (tt) cc_final: 0.8654 (pt) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.3566 time to fit residues: 200.8643 Evaluate side-chains 281 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 6.9990 chunk 288 optimal weight: 6.9990 chunk 176 optimal weight: 0.0070 chunk 136 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 chunk 302 optimal weight: 10.0000 chunk 278 optimal weight: 40.0000 chunk 241 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 chunk 147 optimal weight: 20.0000 overall best weight: 4.0004 ------------------------------------------------------------------------------- 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 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24900 Z= 0.221 Angle : 1.029 31.744 33777 Z= 0.412 Chirality : 0.041 0.237 3852 Planarity : 0.004 0.060 4422 Dihedral : 6.834 134.120 3554 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 1.08 (0.15), residues: 3066 helix: 1.38 (0.13), residues: 1736 sheet: -0.75 (0.26), residues: 313 loop : 0.23 (0.21), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 457 HIS 0.006 0.001 HIS G 541 PHE 0.015 0.001 PHE A 240 TYR 0.018 0.001 TYR D 122 ARG 0.008 0.001 ARG G 557 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 2.454 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: A 58 ASP cc_start: 0.9178 (m-30) cc_final: 0.8621 (p0) REVERT: A 214 LEU cc_start: 0.8998 (tt) cc_final: 0.8789 (tt) REVERT: A 218 THR cc_start: 0.8021 (m) cc_final: 0.7766 (p) REVERT: A 291 ASP cc_start: 0.8677 (m-30) cc_final: 0.8010 (p0) REVERT: A 345 LEU cc_start: 0.7808 (mt) cc_final: 0.7450 (mt) REVERT: A 416 MET cc_start: 0.8599 (mmp) cc_final: 0.7986 (mmm) REVERT: A 438 ILE cc_start: 0.8271 (mp) cc_final: 0.7697 (mp) REVERT: A 451 LEU cc_start: 0.8697 (mt) cc_final: 0.8495 (mt) REVERT: B 72 MET cc_start: 0.8864 (mtt) cc_final: 0.8306 (mtp) REVERT: B 82 ILE cc_start: 0.8577 (mt) cc_final: 0.8367 (mt) REVERT: B 235 MET cc_start: 0.8980 (mmt) cc_final: 0.8671 (mmm) REVERT: B 269 MET cc_start: 0.8889 (tpt) cc_final: 0.8044 (tpp) REVERT: B 291 ASP cc_start: 0.9065 (m-30) cc_final: 0.8773 (p0) REVERT: B 301 MET cc_start: 0.9230 (tmm) cc_final: 0.8786 (ppp) REVERT: B 382 LEU cc_start: 0.8512 (tt) cc_final: 0.8229 (tt) REVERT: C 60 PHE cc_start: 0.9221 (m-80) cc_final: 0.8884 (m-10) REVERT: C 235 MET cc_start: 0.9080 (mmp) cc_final: 0.8674 (mmm) REVERT: C 269 MET cc_start: 0.8946 (tpp) cc_final: 0.8565 (ttt) REVERT: C 322 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8358 (mt-10) REVERT: C 382 LEU cc_start: 0.8929 (mt) cc_final: 0.8603 (mt) REVERT: C 417 PHE cc_start: 0.7835 (m-80) cc_final: 0.7580 (m-80) REVERT: C 419 TYR cc_start: 0.7956 (t80) cc_final: 0.7397 (t80) REVERT: C 427 ASN cc_start: 0.8425 (p0) cc_final: 0.8209 (p0) REVERT: D 34 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8559 (tt0) REVERT: D 42 MET cc_start: 0.7262 (mtp) cc_final: 0.6932 (mtp) REVERT: D 50 ASP cc_start: 0.8355 (m-30) cc_final: 0.7829 (p0) REVERT: D 160 LEU cc_start: 0.9288 (tp) cc_final: 0.9022 (tt) REVERT: D 269 MET cc_start: 0.8552 (ttm) cc_final: 0.8285 (ttm) REVERT: D 301 MET cc_start: 0.8834 (mtm) cc_final: 0.8425 (mtt) REVERT: E 60 PHE cc_start: 0.9129 (m-80) cc_final: 0.8848 (m-10) REVERT: E 92 GLU cc_start: 0.9069 (tt0) cc_final: 0.8623 (tp30) REVERT: E 235 MET cc_start: 0.8919 (mmt) cc_final: 0.8679 (mmm) REVERT: E 344 TYR cc_start: 0.8471 (p90) cc_final: 0.7987 (p90) REVERT: E 348 MET cc_start: 0.8688 (mmp) cc_final: 0.8215 (mmp) REVERT: E 363 GLU cc_start: 0.9091 (tp30) cc_final: 0.8885 (tp30) REVERT: F 72 MET cc_start: 0.8812 (ptt) cc_final: 0.8518 (ptt) REVERT: F 235 MET cc_start: 0.7609 (mtt) cc_final: 0.6690 (mtt) REVERT: F 263 MET cc_start: 0.7011 (mpp) cc_final: 0.6503 (mmt) REVERT: F 270 MET cc_start: 0.8842 (ttt) cc_final: 0.8473 (ttt) REVERT: F 391 GLN cc_start: 0.9317 (mt0) cc_final: 0.8984 (mt0) REVERT: F 418 ILE cc_start: 0.8154 (mp) cc_final: 0.7784 (mp) REVERT: G 537 ASP cc_start: 0.8800 (t0) cc_final: 0.8434 (t0) REVERT: H 541 HIS cc_start: 0.8753 (m90) cc_final: 0.8421 (m-70) REVERT: H 550 ARG cc_start: 0.9062 (mmp80) cc_final: 0.8714 (mmm160) REVERT: I 530 ILE cc_start: 0.8918 (tt) cc_final: 0.8651 (pt) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.3720 time to fit residues: 208.5468 Evaluate side-chains 280 residues out of total 2634 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 20.0000 chunk 256 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 222 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 241 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 248 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- 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 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 GLN ** A 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 541 HIS ** H 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.072512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.056416 restraints weight = 179332.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.057735 restraints weight = 126776.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.058722 restraints weight = 97361.149| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24900 Z= 0.268 Angle : 1.049 32.424 33777 Z= 0.428 Chirality : 0.041 0.205 3852 Planarity : 0.005 0.069 4422 Dihedral : 7.015 135.202 3554 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 22.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.84 (0.15), residues: 3066 helix: 1.19 (0.12), residues: 1742 sheet: -0.88 (0.26), residues: 319 loop : 0.13 (0.21), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 457 HIS 0.009 0.002 HIS D 65 PHE 0.031 0.002 PHE C 166 TYR 0.035 0.002 TYR D 105 ARG 0.014 0.001 ARG D 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5212.88 seconds wall clock time: 94 minutes 55.83 seconds (5695.83 seconds total)