Starting phenix.real_space_refine on Fri Nov 17 01:07:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsj_34999/11_2023/8hsj_34999_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsj_34999/11_2023/8hsj_34999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsj_34999/11_2023/8hsj_34999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsj_34999/11_2023/8hsj_34999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsj_34999/11_2023/8hsj_34999_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsj_34999/11_2023/8hsj_34999_updated.pdb" } resolution = 3.6 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= 0.001 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 P 12 5.49 5 Mg 6 5.21 5 S 42 5.16 5 Be 6 3.05 5 C 10800 2.51 5 N 3132 2.21 5 O 3228 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B ARG 315": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 17244 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "B" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "C" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "D" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "E" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "F" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.66, per 1000 atoms: 0.56 Number of scatterers: 17244 At special positions: 0 Unit cell: (136.74, 130.38, 90.1, 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 42 16.00 P 12 15.00 Mg 6 11.99 F 18 9.00 O 3228 8.00 N 3132 7.00 C 10800 6.00 Be 6 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.44 Conformation dependent library (CDL) restraints added in 3.4 seconds 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4032 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 26 sheets defined 40.0% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.46 Creating SS restraints... Processing helix chain 'A' and resid 92 through 98 Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 191 through 204 removed outlier: 3.565A pdb=" N LYS A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 243 through 263 removed outlier: 3.775A pdb=" N GLU A 263 " --> pdb=" O ARG A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 300 through 309 removed outlier: 4.019A pdb=" N PHE A 303 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 333 through 343 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 375 through 378 No H-bonds generated for 'chain 'A' and resid 375 through 378' Processing helix chain 'A' and resid 381 through 394 Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.872A pdb=" N ARG A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'B' and resid 92 through 98 Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.677A pdb=" N LYS B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 133 through 137' Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 191 through 204 removed outlier: 3.512A pdb=" N LYS B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 228 Processing helix chain 'B' and resid 243 through 263 removed outlier: 3.944A pdb=" N GLU B 263 " --> pdb=" O ARG B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 301 through 309 Processing helix chain 'B' and resid 333 through 343 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 375 through 378 No H-bonds generated for 'chain 'B' and resid 375 through 378' Processing helix chain 'B' and resid 381 through 394 Processing helix chain 'B' and resid 399 through 412 removed outlier: 4.303A pdb=" N ARG B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.518A pdb=" N LYS C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 133 through 137' Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 191 through 204 removed outlier: 3.579A pdb=" N LYS C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 228 Processing helix chain 'C' and resid 243 through 263 removed outlier: 4.865A pdb=" N GLU C 263 " --> pdb=" O ARG C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 299 through 309 removed outlier: 4.134A pdb=" N PHE C 303 " --> pdb=" O ALA C 300 " (cutoff:3.500A) Proline residue: C 304 - end of helix Processing helix chain 'C' and resid 333 through 343 Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 375 through 378 No H-bonds generated for 'chain 'C' and resid 375 through 378' Processing helix chain 'C' and resid 381 through 394 Processing helix chain 'C' and resid 399 through 412 removed outlier: 3.696A pdb=" N ALA C 411 " --> pdb=" O LEU C 407 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'D' and resid 92 through 98 Processing helix chain 'D' and resid 133 through 137 removed outlier: 3.543A pdb=" N LYS D 137 " --> pdb=" O PRO D 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 133 through 137' Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 162 through 171 Processing helix chain 'D' and resid 191 through 204 removed outlier: 3.529A pdb=" N LYS D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 228 Processing helix chain 'D' and resid 243 through 263 removed outlier: 3.718A pdb=" N GLU D 263 " --> pdb=" O ARG D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 299 through 309 removed outlier: 3.528A pdb=" N PHE D 303 " --> pdb=" O ALA D 300 " (cutoff:3.500A) Proline residue: D 304 - end of helix Processing helix chain 'D' and resid 333 through 343 Processing helix chain 'D' and resid 354 through 358 Processing helix chain 'D' and resid 375 through 378 No H-bonds generated for 'chain 'D' and resid 375 through 378' Processing helix chain 'D' and resid 381 through 394 Processing helix chain 'D' and resid 399 through 410 Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'E' and resid 92 through 98 Processing helix chain 'E' and resid 133 through 137 Processing helix chain 'E' and resid 142 through 144 No H-bonds generated for 'chain 'E' and resid 142 through 144' Processing helix chain 'E' and resid 162 through 171 Processing helix chain 'E' and resid 191 through 204 removed outlier: 3.554A pdb=" N LYS E 203 " --> pdb=" O ASN E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 228 Processing helix chain 'E' and resid 243 through 263 removed outlier: 5.450A pdb=" N GLU E 263 " --> pdb=" O ARG E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 300 through 309 Proline residue: E 304 - end of helix Processing helix chain 'E' and resid 333 through 343 Processing helix chain 'E' and resid 354 through 358 Processing helix chain 'E' and resid 375 through 378 No H-bonds generated for 'chain 'E' and resid 375 through 378' Processing helix chain 'E' and resid 381 through 394 Processing helix chain 'E' and resid 399 through 412 removed outlier: 4.516A pdb=" N ARG E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 419 Processing helix chain 'F' and resid 92 through 98 Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 142 through 144 No H-bonds generated for 'chain 'F' and resid 142 through 144' Processing helix chain 'F' and resid 162 through 171 Processing helix chain 'F' and resid 191 through 204 removed outlier: 3.573A pdb=" N LYS F 203 " --> pdb=" O ASN F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 228 Processing helix chain 'F' and resid 243 through 263 removed outlier: 3.571A pdb=" N GLU F 263 " --> pdb=" O ARG F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 284 Processing helix chain 'F' and resid 299 through 309 removed outlier: 4.047A pdb=" N PHE F 303 " --> pdb=" O ALA F 300 " (cutoff:3.500A) Proline residue: F 304 - end of helix Processing helix chain 'F' and resid 333 through 343 Processing helix chain 'F' and resid 354 through 358 Processing helix chain 'F' and resid 375 through 378 No H-bonds generated for 'chain 'F' and resid 375 through 378' Processing helix chain 'F' and resid 381 through 396 removed outlier: 4.144A pdb=" N ALA F 395 " --> pdb=" O ARG F 391 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASP F 396 " --> pdb=" O LYS F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 412 removed outlier: 3.658A pdb=" N ALA F 411 " --> pdb=" O LEU F 407 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 419 Processing sheet with id= A, first strand: chain 'A' and resid 62 through 65 Processing sheet with id= B, first strand: chain 'A' and resid 74 through 76 Processing sheet with id= C, first strand: chain 'A' and resid 348 through 351 Processing sheet with id= D, first strand: chain 'A' and resid 319 through 324 removed outlier: 6.828A pdb=" N LYS A 209 " --> pdb=" O MET A 268 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N LEU A 270 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE A 211 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ASP A 272 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU A 213 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU A 233 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LEU A 214 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE A 235 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ASP A 216 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N SER A 237 " --> pdb=" O ASP A 216 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 109 through 111 removed outlier: 5.479A pdb=" N ARG A 111 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU A 122 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 62 through 64 Processing sheet with id= G, first strand: chain 'B' and resid 74 through 76 Processing sheet with id= H, first strand: chain 'B' and resid 180 through 183 removed outlier: 6.207A pdb=" N MET B 348 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL B 183 " --> pdb=" O MET B 348 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU B 350 " --> pdb=" O VAL B 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 319 through 324 removed outlier: 6.802A pdb=" N LYS B 209 " --> pdb=" O MET B 268 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU B 270 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 211 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ASP B 272 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B 213 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU B 233 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N LEU B 214 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE B 235 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N ASP B 216 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N SER B 237 " --> pdb=" O ASP B 216 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 62 through 64 Processing sheet with id= K, first strand: chain 'C' and resid 74 through 76 Processing sheet with id= L, first strand: chain 'C' and resid 348 through 351 Processing sheet with id= M, first strand: chain 'C' and resid 319 through 324 removed outlier: 6.748A pdb=" N LYS C 209 " --> pdb=" O MET C 268 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU C 270 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE C 211 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ASP C 272 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU C 213 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU C 233 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LEU C 214 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE C 235 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ASP C 216 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N SER C 237 " --> pdb=" O ASP C 216 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 109 through 111 removed outlier: 3.580A pdb=" N LYS C 124 " --> pdb=" O GLN C 109 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ARG C 111 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LEU C 122 " --> pdb=" O ARG C 111 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 62 through 65 Processing sheet with id= P, first strand: chain 'D' and resid 66 through 68 Processing sheet with id= Q, first strand: chain 'D' and resid 348 through 351 Processing sheet with id= R, first strand: chain 'D' and resid 319 through 324 removed outlier: 6.811A pdb=" N LYS D 209 " --> pdb=" O MET D 268 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU D 270 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE D 211 " --> pdb=" O LEU D 270 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ASP D 272 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU D 213 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU D 233 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU D 214 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE D 235 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ASP D 216 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N SER D 237 " --> pdb=" O ASP D 216 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 62 through 64 Processing sheet with id= T, first strand: chain 'E' and resid 74 through 76 removed outlier: 3.526A pdb=" N ALA E 88 " --> pdb=" O LEU E 76 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 180 through 183 removed outlier: 6.230A pdb=" N MET E 348 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL E 183 " --> pdb=" O MET E 348 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU E 350 " --> pdb=" O VAL E 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'E' and resid 319 through 324 removed outlier: 6.662A pdb=" N LYS E 209 " --> pdb=" O MET E 268 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LEU E 270 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE E 211 " --> pdb=" O LEU E 270 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ASP E 272 " --> pdb=" O ILE E 211 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU E 213 " --> pdb=" O ASP E 272 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU E 233 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU E 214 " --> pdb=" O GLU E 233 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE E 235 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ASP E 216 " --> pdb=" O ILE E 235 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N SER E 237 " --> pdb=" O ASP E 216 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 63 through 65 Processing sheet with id= X, first strand: chain 'F' and resid 66 through 68 Processing sheet with id= Y, first strand: chain 'F' and resid 348 through 352 Processing sheet with id= Z, first strand: chain 'F' and resid 319 through 324 removed outlier: 6.767A pdb=" N LYS F 209 " --> pdb=" O MET F 268 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU F 270 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE F 211 " --> pdb=" O LEU F 270 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ASP F 272 " --> pdb=" O ILE F 211 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU F 213 " --> pdb=" O ASP F 272 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU F 233 " --> pdb=" O VAL F 212 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU F 214 " --> pdb=" O GLU F 233 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE F 235 " --> pdb=" O LEU F 214 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N ASP F 216 " --> pdb=" O ILE F 235 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N SER F 237 " --> pdb=" O ASP F 216 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1620 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: 5.30 Time building geometry restraints manager: 6.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5908 1.34 - 1.46: 3223 1.46 - 1.58: 8275 1.58 - 1.69: 18 1.69 - 1.81: 84 Bond restraints: 17508 Sorted by residual: bond pdb=" BE BEF C1002 " pdb=" F2 BEF C1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" BE BEF A1002 " pdb=" F2 BEF A1002 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" BE BEF B1002 " pdb=" F2 BEF B1002 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" BE BEF D1002 " pdb=" F2 BEF D1002 " ideal model delta sigma weight residual 1.476 1.558 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" BE BEF E1002 " pdb=" F2 BEF E1002 " ideal model delta sigma weight residual 1.476 1.557 -0.081 2.00e-02 2.50e+03 1.65e+01 ... (remaining 17503 not shown) Histogram of bond angle deviations from ideal: 98.88 - 106.42: 585 106.42 - 113.96: 10152 113.96 - 121.49: 8723 121.49 - 129.03: 4153 129.03 - 136.57: 75 Bond angle restraints: 23688 Sorted by residual: angle pdb=" C ALA B 136 " pdb=" N LYS B 137 " pdb=" CA LYS B 137 " ideal model delta sigma weight residual 120.28 131.12 -10.84 1.44e+00 4.82e-01 5.66e+01 angle pdb=" OG1 THR A 288 " pdb=" CB THR A 288 " pdb=" CG2 THR A 288 " ideal model delta sigma weight residual 109.30 120.07 -10.77 2.00e+00 2.50e-01 2.90e+01 angle pdb=" CA THR A 288 " pdb=" CB THR A 288 " pdb=" CG2 THR A 288 " ideal model delta sigma weight residual 110.50 119.02 -8.52 1.70e+00 3.46e-01 2.51e+01 angle pdb=" F2 BEF C1002 " pdb=" BE BEF C1002 " pdb=" F3 BEF C1002 " ideal model delta sigma weight residual 119.96 105.35 14.61 3.00e+00 1.11e-01 2.37e+01 angle pdb=" F2 BEF F1002 " pdb=" BE BEF F1002 " pdb=" F3 BEF F1002 " ideal model delta sigma weight residual 119.96 107.18 12.78 3.00e+00 1.11e-01 1.81e+01 ... (remaining 23683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 10598 35.40 - 70.80: 210 70.80 - 106.20: 12 106.20 - 141.60: 6 141.60 - 177.00: 4 Dihedral angle restraints: 10830 sinusoidal: 4602 harmonic: 6228 Sorted by residual: dihedral pdb=" O1B ADP C1000 " pdb=" O3A ADP C1000 " pdb=" PB ADP C1000 " pdb=" PA ADP C1000 " ideal model delta sinusoidal sigma weight residual -60.00 117.00 -177.00 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP D1000 " pdb=" O3A ADP D1000 " pdb=" PB ADP D1000 " pdb=" PA ADP D1000 " ideal model delta sinusoidal sigma weight residual 300.00 130.52 169.48 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O1B ADP E1000 " pdb=" O3A ADP E1000 " pdb=" PB ADP E1000 " pdb=" PA ADP E1000 " ideal model delta sinusoidal sigma weight residual -60.00 85.53 -145.53 1 2.00e+01 2.50e-03 4.38e+01 ... (remaining 10827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 2716 0.270 - 0.539: 1 0.539 - 0.809: 0 0.809 - 1.079: 0 1.079 - 1.348: 1 Chirality restraints: 2718 Sorted by residual: chirality pdb=" CB THR A 288 " pdb=" CA THR A 288 " pdb=" OG1 THR A 288 " pdb=" CG2 THR A 288 " both_signs ideal model delta sigma weight residual False 2.55 1.20 1.35 2.00e-01 2.50e+01 4.55e+01 chirality pdb=" CA SER C 164 " pdb=" N SER C 164 " pdb=" C SER C 164 " pdb=" CB SER C 164 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA VAL E 106 " pdb=" N VAL E 106 " pdb=" C VAL E 106 " pdb=" CB VAL E 106 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.70e-01 ... (remaining 2715 not shown) Planarity restraints: 3084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 286 " -0.089 5.00e-02 4.00e+02 1.36e-01 2.96e+01 pdb=" N PRO E 287 " 0.235 5.00e-02 4.00e+02 pdb=" CA PRO E 287 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO E 287 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 286 " -0.086 5.00e-02 4.00e+02 1.31e-01 2.75e+01 pdb=" N PRO A 287 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 286 " -0.075 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO B 287 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO B 287 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO B 287 " -0.063 5.00e-02 4.00e+02 ... (remaining 3081 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 224 2.41 - 3.03: 11922 3.03 - 3.66: 26549 3.66 - 4.28: 39964 4.28 - 4.90: 62921 Nonbonded interactions: 141580 Sorted by model distance: nonbonded pdb=" OE1 GLU C 217 " pdb="MG MG C1001 " model vdw 1.788 2.170 nonbonded pdb=" O1A ADP D1000 " pdb="MG MG D1001 " model vdw 1.792 2.170 nonbonded pdb=" O5' ADP C1000 " pdb="MG MG C1001 " model vdw 1.798 2.170 nonbonded pdb=" O5' ADP E1000 " pdb="MG MG E1001 " model vdw 1.820 2.170 nonbonded pdb=" O1A ADP A1000 " pdb="MG MG A1001 " model vdw 1.850 2.170 ... (remaining 141575 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.790 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 47.600 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.100 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 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 0.087 17508 Z= 0.299 Angle : 0.801 14.612 23688 Z= 0.428 Chirality : 0.049 1.348 2718 Planarity : 0.007 0.136 3084 Dihedral : 14.726 176.999 6798 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.71 % Favored : 95.96 % Rotamer: Outliers : 4.93 % Allowed : 8.99 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.81 (0.18), residues: 2154 helix: -0.24 (0.17), residues: 870 sheet: -0.48 (0.29), residues: 342 loop : -0.67 (0.20), residues: 942 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 454 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 16 residues processed: 528 average time/residue: 0.4377 time to fit residues: 306.8430 Evaluate side-chains 242 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 226 time to evaluate : 2.016 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2649 time to fit residues: 9.2121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 196 optimal weight: 1.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 246 HIS B 70 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN D 148 GLN D 246 HIS ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 ASN E 230 GLN ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 HIS E 254 HIS ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 17508 Z= 0.303 Angle : 0.848 10.091 23688 Z= 0.411 Chirality : 0.047 0.218 2718 Planarity : 0.007 0.136 3084 Dihedral : 11.075 169.508 2466 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 23.69 Ramachandran Plot: Outliers : 0.37 % Allowed : 2.88 % Favored : 96.75 % Rotamer: Outliers : 3.89 % Allowed : 16.17 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: -0.53 (0.17), residues: 2154 helix: -0.23 (0.17), residues: 834 sheet: 0.19 (0.30), residues: 330 loop : -0.49 (0.19), residues: 990 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 241 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 38 residues processed: 299 average time/residue: 0.3877 time to fit residues: 160.7780 Evaluate side-chains 228 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 190 time to evaluate : 2.034 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.2017 time to fit residues: 15.7250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 163 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 196 optimal weight: 0.4980 chunk 212 optimal weight: 0.0570 chunk 175 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 overall best weight: 1.2900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 GLN ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 ASN ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 17508 Z= 0.235 Angle : 0.754 8.395 23688 Z= 0.367 Chirality : 0.045 0.230 2718 Planarity : 0.007 0.130 3084 Dihedral : 10.458 155.668 2466 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 23.78 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.11 % Favored : 96.52 % Rotamer: Outliers : 3.40 % Allowed : 18.53 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: -0.30 (0.18), residues: 2154 helix: -0.02 (0.17), residues: 834 sheet: 0.18 (0.30), residues: 330 loop : -0.33 (0.20), residues: 990 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 201 time to evaluate : 1.983 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 outliers start: 62 outliers final: 30 residues processed: 250 average time/residue: 0.3592 time to fit residues: 127.7272 Evaluate side-chains 191 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 2.048 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1604 time to fit residues: 11.8301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 197 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 186 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 130 ASN ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 17508 Z= 0.224 Angle : 0.738 8.476 23688 Z= 0.358 Chirality : 0.044 0.171 2718 Planarity : 0.007 0.126 3084 Dihedral : 10.003 147.996 2466 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 23.63 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.39 % Favored : 96.24 % Rotamer: Outliers : 1.97 % Allowed : 20.34 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: -0.26 (0.18), residues: 2154 helix: 0.03 (0.17), residues: 834 sheet: 0.21 (0.30), residues: 330 loop : -0.33 (0.20), residues: 990 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 179 time to evaluate : 2.015 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 outliers start: 36 outliers final: 17 residues processed: 201 average time/residue: 0.3594 time to fit residues: 104.1450 Evaluate side-chains 177 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 160 time to evaluate : 2.053 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1811 time to fit residues: 8.5752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 178 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 106 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 GLN ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.5937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 17508 Z= 0.245 Angle : 0.725 8.115 23688 Z= 0.350 Chirality : 0.044 0.192 2718 Planarity : 0.007 0.120 3084 Dihedral : 9.589 141.062 2466 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 24.44 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.16 % Favored : 96.47 % Rotamer: Outliers : 1.43 % Allowed : 22.04 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: -0.30 (0.18), residues: 2154 helix: -0.00 (0.17), residues: 834 sheet: 0.08 (0.30), residues: 330 loop : -0.30 (0.20), residues: 990 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 169 time to evaluate : 2.033 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 outliers start: 26 outliers final: 8 residues processed: 192 average time/residue: 0.3232 time to fit residues: 91.3365 Evaluate side-chains 152 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 1.913 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1620 time to fit residues: 5.1459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.9990 chunk 188 optimal weight: 0.7980 chunk 41 optimal weight: 0.0970 chunk 122 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN D 281 ASN ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.6291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 17508 Z= 0.204 Angle : 0.701 8.534 23688 Z= 0.336 Chirality : 0.044 0.182 2718 Planarity : 0.006 0.116 3084 Dihedral : 9.075 131.962 2466 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.25 % Favored : 96.38 % Rotamer: Outliers : 1.54 % Allowed : 21.98 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: -0.23 (0.18), residues: 2154 helix: 0.13 (0.17), residues: 828 sheet: -0.03 (0.31), residues: 306 loop : -0.29 (0.20), residues: 1020 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 176 time to evaluate : 1.946 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 outliers start: 28 outliers final: 19 residues processed: 190 average time/residue: 0.3591 time to fit residues: 98.7856 Evaluate side-chains 168 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 2.056 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1810 time to fit residues: 9.0197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 118 optimal weight: 0.0670 chunk 175 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 208 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.6609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 17508 Z= 0.197 Angle : 0.695 9.391 23688 Z= 0.334 Chirality : 0.044 0.206 2718 Planarity : 0.006 0.110 3084 Dihedral : 8.746 123.172 2466 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.25 % Favored : 96.38 % Rotamer: Outliers : 0.88 % Allowed : 22.42 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.18), residues: 2154 helix: 0.16 (0.18), residues: 834 sheet: -0.21 (0.29), residues: 354 loop : -0.08 (0.21), residues: 966 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 2.073 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 outliers start: 16 outliers final: 7 residues processed: 176 average time/residue: 0.3411 time to fit residues: 89.8934 Evaluate side-chains 155 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 2.115 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1712 time to fit residues: 4.9767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.0870 chunk 83 optimal weight: 8.9990 chunk 124 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 163 optimal weight: 0.7980 chunk 189 optimal weight: 4.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.6863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 17508 Z= 0.189 Angle : 0.706 11.810 23688 Z= 0.334 Chirality : 0.044 0.217 2718 Planarity : 0.007 0.106 3084 Dihedral : 8.440 122.279 2466 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.30 % Favored : 96.38 % Rotamer: Outliers : 0.66 % Allowed : 23.52 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: -0.11 (0.18), residues: 2154 helix: 0.22 (0.18), residues: 834 sheet: 0.05 (0.30), residues: 318 loop : -0.22 (0.20), residues: 1002 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 166 time to evaluate : 2.177 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 outliers start: 12 outliers final: 5 residues processed: 173 average time/residue: 0.3284 time to fit residues: 84.6356 Evaluate side-chains 149 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 2.121 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1934 time to fit residues: 4.5718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 0.6980 chunk 181 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 116 optimal weight: 0.0050 chunk 84 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 59 optimal weight: 0.0980 chunk 175 optimal weight: 8.9990 chunk 183 optimal weight: 0.0000 chunk 193 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 HIS C 244 GLN ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.7157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 17508 Z= 0.181 Angle : 0.713 12.006 23688 Z= 0.334 Chirality : 0.044 0.217 2718 Planarity : 0.006 0.101 3084 Dihedral : 8.061 122.076 2466 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.81 % Favored : 95.87 % Rotamer: Outliers : 0.88 % Allowed : 23.85 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: -0.17 (0.18), residues: 2154 helix: 0.31 (0.18), residues: 828 sheet: -0.15 (0.28), residues: 384 loop : -0.33 (0.21), residues: 942 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 2.021 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 outliers start: 16 outliers final: 6 residues processed: 174 average time/residue: 0.3263 time to fit residues: 84.5604 Evaluate side-chains 152 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 146 time to evaluate : 2.010 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1725 time to fit residues: 4.6376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 215 optimal weight: 0.0060 chunk 198 optimal weight: 0.7980 chunk 171 optimal weight: 0.2980 chunk 17 optimal weight: 0.0170 chunk 132 optimal weight: 0.2980 chunk 105 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 overall best weight: 0.2834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.7380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 17508 Z= 0.179 Angle : 0.716 12.524 23688 Z= 0.335 Chirality : 0.044 0.215 2718 Planarity : 0.006 0.096 3084 Dihedral : 7.766 126.781 2466 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.25 % Favored : 96.43 % Rotamer: Outliers : 0.33 % Allowed : 24.23 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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 (0.18), residues: 2154 helix: 0.23 (0.18), residues: 840 sheet: -0.13 (0.28), residues: 384 loop : -0.34 (0.21), residues: 930 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 164 time to evaluate : 2.204 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 outliers start: 6 outliers final: 0 residues processed: 167 average time/residue: 0.3445 time to fit residues: 84.1619 Evaluate side-chains 150 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.853 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 8.9990 chunk 52 optimal weight: 0.5980 chunk 158 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 ASN D 79 ASN ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.117851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.092876 restraints weight = 70544.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.095000 restraints weight = 48205.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.096441 restraints weight = 37548.639| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.7583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 17508 Z= 0.235 Angle : 0.743 11.314 23688 Z= 0.351 Chirality : 0.044 0.233 2718 Planarity : 0.006 0.091 3084 Dihedral : 7.710 120.303 2466 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 23.86 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.57 % Favored : 96.15 % Rotamer: Outliers : 1.10 % Allowed : 23.96 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: -0.24 (0.18), residues: 2154 helix: 0.26 (0.18), residues: 822 sheet: -0.27 (0.27), residues: 414 loop : -0.32 (0.21), residues: 918 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3479.59 seconds wall clock time: 64 minutes 16.93 seconds (3856.93 seconds total)