Starting phenix.real_space_refine on Thu Nov 16 00:57:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uur_26801/11_2023/7uur_26801_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uur_26801/11_2023/7uur_26801.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uur_26801/11_2023/7uur_26801_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uur_26801/11_2023/7uur_26801_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uur_26801/11_2023/7uur_26801_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uur_26801/11_2023/7uur_26801.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uur_26801/11_2023/7uur_26801.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uur_26801/11_2023/7uur_26801_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uur_26801/11_2023/7uur_26801_updated.pdb" } resolution = 1.67 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= 0.005 sd= 0.219 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: 7 Type Number sf(0) Gaussians Fe 20 7.16 5 Ni 2 6.56 5 Mg 2 5.21 5 S 102 5.16 5 C 8310 2.51 5 N 2208 2.21 5 O 3039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 311": "OE1" <-> "OE2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C GLU 418": "OE1" <-> "OE2" Residue "C GLU 453": "OE1" <-> "OE2" Residue "F GLU 311": "OE1" <-> "OE2" Residue "F GLU 320": "OE1" <-> "OE2" Residue "F GLU 322": "OE1" <-> "OE2" Residue "F GLU 418": "OE1" <-> "OE2" Residue "F GLU 453": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 13683 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4037 Classifications: {'peptide': 513} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 480} Chain: "D" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2459 Classifications: {'peptide': 322} Link IDs: {'PCIS': 5, 'PTRANS': 18, 'TRANS': 298} Chain: "F" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4037 Classifications: {'peptide': 513} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 480} Chain: "G" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2459 Classifications: {'peptide': 322} Link IDs: {'PCIS': 5, 'PTRANS': 18, 'TRANS': 298} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 9 Ad-hoc single atom residues: {'3NI': 1} Unusual residues: {' MG': 1, ' OH': 1, 'FCO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {'F3S': 3, 'VK3': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 9 Ad-hoc single atom residues: {'3NI': 1} Unusual residues: {' MG': 1, ' OH': 1, 'FCO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {'F3S': 3, 'VK3': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 182 Classifications: {'water': 182} Link IDs: {None: 181} Chain: "D" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 119 Classifications: {'water': 119} Link IDs: {None: 118} Chain: "F" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 183 Classifications: {'water': 183} Link IDs: {None: 182} Chain: "G" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 119 Classifications: {'water': 119} Link IDs: {None: 118} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 450 SG CYS C 62 36.911 37.181 41.368 1.00 9.17 S ATOM 468 SG CYS C 65 33.685 38.830 41.653 1.00 9.12 S ATOM 3991 SG CYS C 510 36.036 35.180 39.068 1.00 12.50 S ATOM 4012 SG CYS C 513 33.284 35.896 41.530 1.00 10.59 S ATOM 468 SG CYS C 65 33.685 38.830 41.653 1.00 9.12 S ATOM 4012 SG CYS C 513 33.284 35.896 41.530 1.00 10.59 S ATOM 5229 SG CYS D 161 42.349 37.386 52.187 1.00 6.08 S ATOM 4880 SG CYS D 113 43.393 32.173 50.398 1.00 7.34 S ATOM 4116 SG CYS D 12 40.729 36.462 46.193 1.00 7.78 S ATOM 6015 SG CYS D 260 45.279 45.221 60.399 1.00 5.87 S ATOM 5869 SG CYS D 242 48.645 46.722 54.913 1.00 5.37 S ATOM 6033 SG CYS D 263 45.667 41.418 55.021 1.00 6.21 S ATOM 5742 SG CYS D 226 42.980 53.274 67.586 1.00 7.52 S ATOM 5803 SG CYS D 233 42.956 48.748 63.331 1.00 6.49 S ATOM 5557 SG CYS D 203 45.612 54.270 61.449 1.00 5.75 S ATOM 6946 SG CYS F 62 64.765 77.636 41.372 1.00 9.04 S ATOM 6964 SG CYS F 65 67.997 75.971 41.655 1.00 9.01 S ATOM 10487 SG CYS F 510 65.644 79.622 39.072 1.00 12.45 S ATOM 10508 SG CYS F 513 68.397 78.906 41.529 1.00 10.58 S ATOM 6964 SG CYS F 65 67.997 75.971 41.655 1.00 9.01 S ATOM 10508 SG CYS F 513 68.397 78.906 41.529 1.00 10.58 S ATOM 11725 SG CYS G 161 59.339 77.414 52.193 1.00 6.17 S ATOM 11376 SG CYS G 113 58.295 82.628 50.407 1.00 7.30 S ATOM 10612 SG CYS G 12 60.957 78.342 46.198 1.00 7.83 S ATOM 12511 SG CYS G 260 56.411 69.575 60.401 1.00 5.93 S ATOM 12365 SG CYS G 242 53.044 68.077 54.915 1.00 5.52 S ATOM 12529 SG CYS G 263 56.021 73.381 55.025 1.00 6.22 S ATOM 12238 SG CYS G 226 58.711 61.517 67.583 1.00 7.51 S ATOM 12299 SG CYS G 233 58.734 66.046 63.331 1.00 6.50 S ATOM 12053 SG CYS G 203 56.077 60.525 61.446 1.00 5.58 S Time building chain proxies: 7.73, per 1000 atoms: 0.56 Number of scatterers: 13683 At special positions: 0 Unit cell: (102.5, 115.62, 92.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ni 2 28.00 Fe 20 26.01 S 102 16.00 Mg 2 11.99 O 3039 8.00 N 2208 7.00 C 8310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.53 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S D 402 " pdb="FE4 F3S D 402 " - pdb=" SG CYS D 12 " pdb="FE3 F3S D 402 " - pdb=" SG CYS D 113 " pdb="FE1 F3S D 402 " - pdb=" SG CYS D 161 " pdb=" F3S D 403 " pdb="FE3 F3S D 403 " - pdb=" SG CYS D 242 " pdb="FE4 F3S D 403 " - pdb=" SG CYS D 263 " pdb="FE1 F3S D 403 " - pdb=" SG CYS D 260 " pdb=" F3S D 404 " pdb="FE1 F3S D 404 " - pdb=" SG CYS D 226 " pdb="FE4 F3S D 404 " - pdb=" SG CYS D 203 " pdb="FE3 F3S D 404 " - pdb=" SG CYS D 233 " pdb=" F3S G 402 " pdb="FE4 F3S G 402 " - pdb=" SG CYS G 12 " pdb="FE3 F3S G 402 " - pdb=" SG CYS G 113 " pdb="FE1 F3S G 402 " - pdb=" SG CYS G 161 " pdb=" F3S G 403 " pdb="FE3 F3S G 403 " - pdb=" SG CYS G 242 " pdb="FE4 F3S G 403 " - pdb=" SG CYS G 263 " pdb="FE1 F3S G 403 " - pdb=" SG CYS G 260 " pdb=" F3S G 404 " pdb="FE1 F3S G 404 " - pdb=" SG CYS G 226 " pdb="FE4 F3S G 404 " - pdb=" SG CYS G 203 " pdb="FE3 F3S G 404 " - pdb=" SG CYS G 233 " Number of angles added : 54 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DHI C 166 " pdb=" CB DHI F 166 " Number of C-beta restraints generated: 3020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 10 sheets defined 40.9% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'C' and resid 42 through 46 Processing helix chain 'C' and resid 53 through 61 Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 66 through 80 Processing helix chain 'C' and resid 87 through 111 Proline residue: C 106 - end of helix Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 120 through 122 No H-bonds generated for 'chain 'C' and resid 120 through 122' Processing helix chain 'C' and resid 128 through 135 Processing helix chain 'C' and resid 143 through 161 removed outlier: 3.979A pdb=" N ALA C 151 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYS C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Proline residue: C 153 - end of helix removed outlier: 3.535A pdb=" N VAL C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 197 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 217 through 226 Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 234 through 245 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 277 through 280 No H-bonds generated for 'chain 'C' and resid 277 through 280' Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.579A pdb=" N ARG C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 367 Processing helix chain 'C' and resid 380 through 388 Processing helix chain 'C' and resid 392 through 416 removed outlier: 3.888A pdb=" N GLY C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 465 through 470 Processing helix chain 'C' and resid 481 through 486 Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 498 through 507 removed outlier: 3.508A pdb=" N PHE C 507 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 27 through 33 Processing helix chain 'D' and resid 49 through 61 Processing helix chain 'D' and resid 93 through 103 Processing helix chain 'D' and resid 111 through 116 Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 165 through 176 removed outlier: 4.380A pdb=" N ILE D 171 " --> pdb=" O TRP D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 192 through 195 No H-bonds generated for 'chain 'D' and resid 192 through 195' Processing helix chain 'D' and resid 206 through 210 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 235 through 237 No H-bonds generated for 'chain 'D' and resid 235 through 237' Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 253 through 256 No H-bonds generated for 'chain 'D' and resid 253 through 256' Processing helix chain 'D' and resid 270 through 273 removed outlier: 3.525A pdb=" N LEU D 273 " --> pdb=" O HIS D 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 270 through 273' Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 314 through 317 Processing helix chain 'F' and resid 42 through 46 Processing helix chain 'F' and resid 53 through 61 Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 66 through 80 Processing helix chain 'F' and resid 87 through 111 Proline residue: F 106 - end of helix Processing helix chain 'F' and resid 114 through 118 Processing helix chain 'F' and resid 120 through 122 No H-bonds generated for 'chain 'F' and resid 120 through 122' Processing helix chain 'F' and resid 128 through 135 Processing helix chain 'F' and resid 143 through 161 removed outlier: 3.980A pdb=" N ALA F 151 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) Proline residue: F 153 - end of helix removed outlier: 3.535A pdb=" N VAL F 156 " --> pdb=" O LYS F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 197 Processing helix chain 'F' and resid 208 through 213 Processing helix chain 'F' and resid 217 through 226 Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 234 through 245 Processing helix chain 'F' and resid 266 through 268 No H-bonds generated for 'chain 'F' and resid 266 through 268' Processing helix chain 'F' and resid 277 through 280 No H-bonds generated for 'chain 'F' and resid 277 through 280' Processing helix chain 'F' and resid 298 through 300 No H-bonds generated for 'chain 'F' and resid 298 through 300' Processing helix chain 'F' and resid 318 through 320 No H-bonds generated for 'chain 'F' and resid 318 through 320' Processing helix chain 'F' and resid 328 through 334 removed outlier: 3.579A pdb=" N ARG F 333 " --> pdb=" O GLU F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 367 Processing helix chain 'F' and resid 380 through 388 Processing helix chain 'F' and resid 392 through 416 removed outlier: 3.886A pdb=" N GLY F 403 " --> pdb=" O ARG F 399 " (cutoff:3.500A) Proline residue: F 404 - end of helix Processing helix chain 'F' and resid 465 through 470 Processing helix chain 'F' and resid 481 through 486 Processing helix chain 'F' and resid 494 through 496 No H-bonds generated for 'chain 'F' and resid 494 through 496' Processing helix chain 'F' and resid 498 through 507 removed outlier: 3.509A pdb=" N PHE F 507 " --> pdb=" O VAL F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 515 Processing helix chain 'G' and resid 14 through 21 Processing helix chain 'G' and resid 27 through 33 Processing helix chain 'G' and resid 49 through 61 Processing helix chain 'G' and resid 93 through 103 Processing helix chain 'G' and resid 111 through 116 Processing helix chain 'G' and resid 119 through 121 No H-bonds generated for 'chain 'G' and resid 119 through 121' Processing helix chain 'G' and resid 165 through 176 removed outlier: 4.380A pdb=" N ILE G 171 " --> pdb=" O TRP G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 182 No H-bonds generated for 'chain 'G' and resid 180 through 182' Processing helix chain 'G' and resid 192 through 195 No H-bonds generated for 'chain 'G' and resid 192 through 195' Processing helix chain 'G' and resid 206 through 210 Processing helix chain 'G' and resid 219 through 223 Processing helix chain 'G' and resid 235 through 237 No H-bonds generated for 'chain 'G' and resid 235 through 237' Processing helix chain 'G' and resid 247 through 249 No H-bonds generated for 'chain 'G' and resid 247 through 249' Processing helix chain 'G' and resid 253 through 256 No H-bonds generated for 'chain 'G' and resid 253 through 256' Processing helix chain 'G' and resid 270 through 273 removed outlier: 3.524A pdb=" N LEU G 273 " --> pdb=" O HIS G 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 270 through 273' Processing helix chain 'G' and resid 298 through 311 Processing helix chain 'G' and resid 314 through 317 Processing sheet with id= A, first strand: chain 'C' and resid 5 through 8 removed outlier: 3.502A pdb=" N SER C 31 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASN C 25 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 257 through 259 Processing sheet with id= C, first strand: chain 'C' and resid 301 through 304 Processing sheet with id= D, first strand: chain 'C' and resid 433 through 441 removed outlier: 5.948A pdb=" N GLU C 453 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE C 457 " --> pdb=" O GLU C 453 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 156 through 158 removed outlier: 6.235A pdb=" N ASP D 37 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N TRP D 6 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LEU D 39 " --> pdb=" O TRP D 6 " (cutoff:3.500A) removed outlier: 12.225A pdb=" N GLN D 8 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 10.204A pdb=" N HIS D 41 " --> pdb=" O GLN D 8 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 5 through 8 removed outlier: 3.502A pdb=" N SER F 31 " --> pdb=" O THR F 23 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASN F 25 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL F 29 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 257 through 259 Processing sheet with id= H, first strand: chain 'F' and resid 301 through 304 Processing sheet with id= I, first strand: chain 'F' and resid 433 through 441 removed outlier: 5.947A pdb=" N GLU F 453 " --> pdb=" O ILE F 457 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE F 457 " --> pdb=" O GLU F 453 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 156 through 158 removed outlier: 6.236A pdb=" N ASP G 37 " --> pdb=" O VAL G 4 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N TRP G 6 " --> pdb=" O ASP G 37 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU G 39 " --> pdb=" O TRP G 6 " (cutoff:3.500A) removed outlier: 12.224A pdb=" N GLN G 8 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 10.204A pdb=" N HIS G 41 " --> pdb=" O GLN G 8 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1206 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: 4.41 Time building geometry restraints manager: 7.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.68: 13278 1.68 - 2.25: 126 2.25 - 2.83: 30 2.83 - 3.41: 0 3.41 - 3.99: 18 Bond restraints: 13452 Sorted by residual: bond pdb=" S4 F3S G 402 " pdb="FE1 F3S G 402 " ideal model delta sigma weight residual 2.233 3.988 -1.755 2.00e-02 2.50e+03 7.70e+03 bond pdb=" S4 F3S D 402 " pdb="FE1 F3S D 402 " ideal model delta sigma weight residual 2.233 3.988 -1.755 2.00e-02 2.50e+03 7.70e+03 bond pdb=" S4 F3S D 403 " pdb="FE1 F3S D 403 " ideal model delta sigma weight residual 2.233 3.963 -1.730 2.00e-02 2.50e+03 7.48e+03 bond pdb=" S4 F3S G 403 " pdb="FE1 F3S G 403 " ideal model delta sigma weight residual 2.233 3.962 -1.729 2.00e-02 2.50e+03 7.47e+03 bond pdb=" S2 F3S D 403 " pdb="FE3 F3S D 403 " ideal model delta sigma weight residual 2.300 3.955 -1.655 2.00e-02 2.50e+03 6.85e+03 ... (remaining 13447 not shown) Histogram of bond angle deviations from ideal: 39.78 - 66.59: 32 66.59 - 93.39: 46 93.39 - 120.20: 12618 120.20 - 147.01: 5630 147.01 - 173.81: 6 Bond angle restraints: 18332 Sorted by residual: angle pdb=" C1 FCO F 602 " pdb="FE FCO F 602 " pdb=" C3 FCO F 602 " ideal model delta sigma weight residual 180.00 86.02 93.98 3.00e+00 1.11e-01 9.81e+02 angle pdb=" C1 FCO C 602 " pdb="FE FCO C 602 " pdb=" C3 FCO C 602 " ideal model delta sigma weight residual 180.00 86.07 93.93 3.00e+00 1.11e-01 9.80e+02 angle pdb=" S1 F3S D 404 " pdb="FE4 F3S D 404 " pdb=" S3 F3S D 404 " ideal model delta sigma weight residual 114.75 65.26 49.49 3.00e+00 1.11e-01 2.72e+02 angle pdb=" S1 F3S G 404 " pdb="FE4 F3S G 404 " pdb=" S3 F3S G 404 " ideal model delta sigma weight residual 114.75 65.27 49.48 3.00e+00 1.11e-01 2.72e+02 angle pdb=" S1 F3S G 403 " pdb="FE4 F3S G 403 " pdb=" S3 F3S G 403 " ideal model delta sigma weight residual 114.75 66.48 48.27 3.00e+00 1.11e-01 2.59e+02 ... (remaining 18327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 7083 17.01 - 34.01: 537 34.01 - 51.02: 128 51.02 - 68.02: 44 68.02 - 85.03: 24 Dihedral angle restraints: 7816 sinusoidal: 3074 harmonic: 4742 Sorted by residual: dihedral pdb=" CA PHE D 134 " pdb=" C PHE D 134 " pdb=" N HIS D 135 " pdb=" CA HIS D 135 " ideal model delta harmonic sigma weight residual 180.00 157.94 22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA PHE G 134 " pdb=" C PHE G 134 " pdb=" N HIS G 135 " pdb=" CA HIS G 135 " ideal model delta harmonic sigma weight residual 180.00 157.97 22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA SER D 214 " pdb=" C SER D 214 " pdb=" N THR D 215 " pdb=" CA THR D 215 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 7813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.530: 1932 3.530 - 7.059: 0 7.059 - 10.589: 0 10.589 - 14.118: 0 14.118 - 17.648: 6 Chirality restraints: 1938 Sorted by residual: chirality pdb=" S2 F3S G 403 " pdb="FE1 F3S G 403 " pdb="FE3 F3S G 403 " pdb="FE4 F3S G 403 " both_signs ideal model delta sigma weight residual False 10.77 -6.88 17.65 2.00e-01 2.50e+01 7.79e+03 chirality pdb=" S2 F3S D 403 " pdb="FE1 F3S D 403 " pdb="FE3 F3S D 403 " pdb="FE4 F3S D 403 " both_signs ideal model delta sigma weight residual False 10.77 -6.88 17.65 2.00e-01 2.50e+01 7.78e+03 chirality pdb=" S2 F3S G 402 " pdb="FE1 F3S G 402 " pdb="FE3 F3S G 402 " pdb="FE4 F3S G 402 " both_signs ideal model delta sigma weight residual False 10.77 -6.75 17.52 2.00e-01 2.50e+01 7.68e+03 ... (remaining 1935 not shown) Planarity restraints: 2396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB DHI C 166 " 0.016 2.00e-02 2.50e+03 6.22e-02 5.81e+01 pdb=" CG DHI C 166 " -0.004 2.00e-02 2.50e+03 pdb=" ND1 DHI C 166 " -0.076 2.00e-02 2.50e+03 pdb=" CD2 DHI C 166 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 DHI C 166 " 0.103 2.00e-02 2.50e+03 pdb=" NE2 DHI C 166 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB DHI F 166 " -0.017 2.00e-02 2.50e+03 6.07e-02 5.53e+01 pdb=" CG DHI F 166 " 0.003 2.00e-02 2.50e+03 pdb=" ND1 DHI F 166 " 0.075 2.00e-02 2.50e+03 pdb=" CD2 DHI F 166 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 DHI F 166 " -0.101 2.00e-02 2.50e+03 pdb=" NE2 DHI F 166 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 513 " -0.011 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C CYS C 513 " 0.042 2.00e-02 2.50e+03 pdb=" O CYS C 513 " -0.016 2.00e-02 2.50e+03 pdb=" N THR C 514 " -0.014 2.00e-02 2.50e+03 ... (remaining 2393 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 48 2.32 - 2.96: 8671 2.96 - 3.61: 25687 3.61 - 4.25: 43775 4.25 - 4.90: 68286 Nonbonded interactions: 146467 Sorted by model distance: nonbonded pdb="NI 3NI F 601 " pdb=" O OH F 603 " model vdw 1.674 2.920 nonbonded pdb="NI 3NI C 601 " pdb=" O OH C 603 " model vdw 1.692 2.920 nonbonded pdb=" OE2 GLU C 43 " pdb="MG MG C 604 " model vdw 1.947 2.170 nonbonded pdb=" OE2 GLU F 43 " pdb="MG MG F 604 " model vdw 1.957 2.170 nonbonded pdb=" O VAL F 462 " pdb="MG MG F 604 " model vdw 1.973 2.170 ... (remaining 146462 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 'C' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.010 Extract box with map and model: 6.580 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 45.700 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 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 : 0.061 1.755 13452 Z= 4.124 Angle : 2.451 93.977 18332 Z= 0.909 Chirality : 0.979 17.648 1938 Planarity : 0.007 0.062 2396 Dihedral : 14.570 85.031 4796 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.54 % Favored : 97.22 % Rotamer: Outliers : 0.44 % Allowed : 6.56 % Favored : 93.00 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 12.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.19), residues: 1656 helix: -0.74 (0.17), residues: 644 sheet: -0.39 (0.39), residues: 136 loop : -0.36 (0.22), residues: 876 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 1.424 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 160 average time/residue: 1.8947 time to fit residues: 324.1759 Evaluate side-chains 143 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 141 time to evaluate : 1.567 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.0794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 150 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 484 GLN D 53 GLN D 84 GLN D 282 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 ASN F 484 GLN G 53 GLN G 84 GLN G 282 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.195 13452 Z= 0.493 Angle : 2.462 86.075 18332 Z= 0.863 Chirality : 0.124 2.512 1938 Planarity : 0.005 0.052 2396 Dihedral : 6.167 71.632 1812 Min Nonbonded Distance : 1.527 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.24 % Allowed : 6.05 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.21), residues: 1656 helix: 0.29 (0.19), residues: 652 sheet: -0.73 (0.38), residues: 136 loop : 0.04 (0.23), residues: 868 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 1.620 Fit side-chains outliers start: 17 outliers final: 2 residues processed: 166 average time/residue: 1.7705 time to fit residues: 315.6389 Evaluate side-chains 149 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 1.613 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.1416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 484 GLN D 84 GLN D 282 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN F 484 GLN G 84 GLN ** G 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.168 13452 Z= 0.578 Angle : 2.731 91.505 18332 Z= 0.975 Chirality : 0.079 1.472 1938 Planarity : 0.007 0.078 2396 Dihedral : 6.517 73.106 1812 Min Nonbonded Distance : 1.609 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.02 % Allowed : 6.56 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1656 helix: 0.14 (0.19), residues: 648 sheet: -0.62 (0.37), residues: 136 loop : 0.10 (0.22), residues: 872 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 1.791 Fit side-chains outliers start: 14 outliers final: 2 residues processed: 149 average time/residue: 1.9375 time to fit residues: 309.4877 Evaluate side-chains 146 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 1.661 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.1332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 484 GLN D 53 GLN D 84 GLN D 282 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN F 484 GLN G 53 GLN G 84 GLN G 282 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.185 13452 Z= 0.421 Angle : 2.493 84.837 18332 Z= 0.868 Chirality : 0.117 2.507 1938 Planarity : 0.005 0.041 2396 Dihedral : 6.048 71.837 1812 Min Nonbonded Distance : 1.571 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.51 % Allowed : 7.00 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1656 helix: 0.55 (0.20), residues: 640 sheet: -0.87 (0.37), residues: 136 loop : 0.14 (0.22), residues: 880 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 165 time to evaluate : 1.595 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 168 average time/residue: 1.8142 time to fit residues: 326.9037 Evaluate side-chains 157 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 1.768 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.2255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 484 GLN D 53 GLN D 84 GLN D 282 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN F 484 GLN G 84 GLN G 282 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.174 13452 Z= 0.516 Angle : 2.502 90.997 18332 Z= 0.893 Chirality : 0.069 1.333 1938 Planarity : 0.006 0.074 2396 Dihedral : 6.427 73.455 1812 Min Nonbonded Distance : 1.610 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.66 % Allowed : 7.14 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.21), residues: 1656 helix: 0.35 (0.20), residues: 636 sheet: -0.78 (0.37), residues: 136 loop : 0.11 (0.22), residues: 884 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 1.717 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 155 average time/residue: 1.8140 time to fit residues: 302.2882 Evaluate side-chains 153 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 149 time to evaluate : 1.567 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 1.6686 time to fit residues: 5.6463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 484 GLN D 53 GLN D 84 GLN D 282 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN F 484 GLN G 53 GLN G 84 GLN G 282 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.181 13452 Z= 0.401 Angle : 2.417 86.388 18332 Z= 0.847 Chirality : 0.079 1.934 1938 Planarity : 0.005 0.049 2396 Dihedral : 6.167 72.544 1812 Min Nonbonded Distance : 1.581 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.66 % Allowed : 6.92 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1656 helix: 0.51 (0.20), residues: 642 sheet: -0.95 (0.37), residues: 136 loop : 0.18 (0.23), residues: 878 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 154 time to evaluate : 1.623 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 156 average time/residue: 1.8221 time to fit residues: 305.3267 Evaluate side-chains 155 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 151 time to evaluate : 1.826 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 1.9844 time to fit residues: 6.3901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 484 GLN D 84 GLN D 282 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN F 484 GLN G 53 GLN G 84 GLN G 282 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.182 13452 Z= 0.402 Angle : 2.422 86.266 18332 Z= 0.849 Chirality : 0.078 1.913 1938 Planarity : 0.005 0.050 2396 Dihedral : 6.111 71.888 1812 Min Nonbonded Distance : 1.583 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.51 % Allowed : 7.07 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1656 helix: 0.54 (0.20), residues: 642 sheet: -0.98 (0.37), residues: 136 loop : 0.17 (0.23), residues: 878 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 1.533 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 157 average time/residue: 1.9033 time to fit residues: 319.5355 Evaluate side-chains 151 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 147 time to evaluate : 1.435 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 1.7241 time to fit residues: 5.7695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 31 optimal weight: 0.0020 chunk 30 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 125 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 overall best weight: 2.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 484 GLN D 53 GLN D 84 GLN D 282 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN F 484 GLN G 84 GLN G 282 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.172 13452 Z= 0.495 Angle : 2.513 90.750 18332 Z= 0.896 Chirality : 0.067 1.335 1938 Planarity : 0.006 0.073 2396 Dihedral : 6.429 73.638 1812 Min Nonbonded Distance : 1.621 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.66 % Allowed : 7.29 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1656 helix: 0.41 (0.20), residues: 630 sheet: -0.81 (0.37), residues: 136 loop : 0.16 (0.22), residues: 890 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 151 time to evaluate : 1.641 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 156 average time/residue: 1.8330 time to fit residues: 307.3523 Evaluate side-chains 152 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 1.539 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.1297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 134 optimal weight: 0.5980 chunk 141 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 484 GLN D 84 GLN D 282 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN F 484 GLN G 84 GLN G 282 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.180 13452 Z= 0.405 Angle : 2.427 86.774 18332 Z= 0.852 Chirality : 0.077 1.857 1938 Planarity : 0.005 0.049 2396 Dihedral : 6.180 72.538 1812 Min Nonbonded Distance : 1.587 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.22 % Allowed : 7.80 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1656 helix: 0.52 (0.20), residues: 642 sheet: -0.89 (0.37), residues: 136 loop : 0.16 (0.23), residues: 878 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 1.620 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 155 average time/residue: 1.9052 time to fit residues: 316.2861 Evaluate side-chains 151 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 1.370 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.2265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 484 GLN D 53 GLN D 84 GLN D 282 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN F 484 GLN G 53 GLN G 84 GLN G 282 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.182 13452 Z= 0.397 Angle : 2.408 85.675 18332 Z= 0.844 Chirality : 0.082 2.033 1938 Planarity : 0.005 0.044 2396 Dihedral : 6.078 71.828 1812 Min Nonbonded Distance : 1.582 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.36 % Allowed : 7.80 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1656 helix: 0.57 (0.20), residues: 642 sheet: -0.97 (0.37), residues: 136 loop : 0.16 (0.23), residues: 878 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 155 time to evaluate : 1.879 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 157 average time/residue: 1.8085 time to fit residues: 305.3551 Evaluate side-chains 157 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 153 time to evaluate : 1.702 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 1.9908 time to fit residues: 6.4263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 135 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 484 GLN D 84 GLN D 282 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN F 484 GLN G 84 GLN ** G 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.136479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.115920 restraints weight = 6361.461| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 0.47 r_work: 0.3174 rms_B_bonded: 0.75 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 1.23 restraints_weight: 0.2500 r_work: 0.2895 rms_B_bonded: 3.05 restraints_weight: 0.1250 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.176 13452 Z= 0.458 Angle : 2.486 89.205 18332 Z= 0.881 Chirality : 0.069 1.468 1938 Planarity : 0.006 0.067 2396 Dihedral : 6.305 72.989 1812 Min Nonbonded Distance : 1.611 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.36 % Allowed : 7.94 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1656 helix: 0.45 (0.20), residues: 638 sheet: -0.84 (0.37), residues: 136 loop : 0.20 (0.23), residues: 882 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5997.75 seconds wall clock time: 109 minutes 53.57 seconds (6593.57 seconds total)