Starting phenix.real_space_refine (version: dev) on Tue Feb 21 15:39:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/02_2023/6huo_0282_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/02_2023/6huo_0282.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/02_2023/6huo_0282_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/02_2023/6huo_0282_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/02_2023/6huo_0282_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/02_2023/6huo_0282.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/02_2023/6huo_0282.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/02_2023/6huo_0282_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/02_2023/6huo_0282_updated.pdb" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.007 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 Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "C ARG 324": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 180": "NH1" <-> "NH2" Residue "E ARG 269": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 15227 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 329} Chain breaks: 1 Chain: "B" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2758 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain breaks: 1 Chain: "C" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2720 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 2780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2780 Classifications: {'peptide': 343} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 328} Chain breaks: 1 Chain: "E" Number of atoms: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2740 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 1 Chain: "G" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 7 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ABU': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'08H': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.47, per 1000 atoms: 0.56 Number of scatterers: 15227 At special positions: 0 Unit cell: (100.58, 123.05, 136.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 83 16.00 P 6 15.00 O 2815 8.00 N 2475 7.00 C 9847 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.04 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.04 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS G 428 " - pdb=" SG CYS G 501 " distance=2.03 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=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 7 " " MAN F 4 " - " MAN F 5 " " BMA I 3 " - " MAN I 6 " " MAN I 4 " - " MAN I 5 " " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 6 " " MAN M 4 " - " MAN M 5 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 6 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 5 " " BMA M 3 " - " MAN M 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " NAG-ASN " NAG F 1 " - " ASN A 111 " " NAG H 1 " - " ASN B 80 " " NAG I 1 " - " ASN B 149 " " NAG J 1 " - " ASN C 208 " " NAG K 1 " - " ASN D 111 " " NAG L 1 " - " ASN E 80 " " NAG M 1 " - " ASN E 149 " Time building additional restraints: 6.94 Conformation dependent library (CDL) restraints added in 2.2 seconds 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3422 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 17 sheets defined 32.2% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.574A pdb=" N ILE A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 252 through 274 removed outlier: 3.589A pdb=" N THR A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 262 " --> pdb=" O PHE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 310 removed outlier: 3.519A pdb=" N PHE A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 415 removed outlier: 4.029A pdb=" N ILE A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Proline residue: A 401 - end of helix removed outlier: 3.511A pdb=" N ALA A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 415 " --> pdb=" O TYR A 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 219 through 222 No H-bonds generated for 'chain 'B' and resid 219 through 222' Processing helix chain 'B' and resid 226 through 240 removed outlier: 3.832A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 270 removed outlier: 4.107A pdb=" N ALA B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 307 removed outlier: 3.831A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 445 removed outlier: 3.887A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix removed outlier: 3.502A pdb=" N LEU B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 233 through 237 removed outlier: 3.837A pdb=" N THR C 237 " --> pdb=" O GLY C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 256 removed outlier: 4.401A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TRP C 256 " --> pdb=" O TRP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 286 removed outlier: 3.601A pdb=" N THR C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 286 " --> pdb=" O ILE C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 321 removed outlier: 3.711A pdb=" N LEU C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 434 removed outlier: 4.071A pdb=" N ILE C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.637A pdb=" N VAL C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 434 " --> pdb=" O TRP C 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 22 removed outlier: 3.512A pdb=" N ARG D 21 " --> pdb=" O ARG D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 224 through 229 removed outlier: 3.734A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 246 removed outlier: 4.298A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N TRP D 246 " --> pdb=" O GLN D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 276 removed outlier: 3.525A pdb=" N VAL D 257 " --> pdb=" O PRO D 253 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D 262 " --> pdb=" O PHE D 258 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D 263 " --> pdb=" O GLY D 259 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D 274 " --> pdb=" O SER D 270 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN D 275 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 308 removed outlier: 3.759A pdb=" N LEU D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 414 removed outlier: 3.526A pdb=" N LEU D 395 " --> pdb=" O LYS D 391 " (cutoff:3.500A) Proline residue: D 401 - end of helix Processing helix chain 'E' and resid 10 through 19 Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 85 through 90 Processing helix chain 'E' and resid 140 through 142 No H-bonds generated for 'chain 'E' and resid 140 through 142' Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 219 through 224 Processing helix chain 'E' and resid 226 through 235 removed outlier: 3.517A pdb=" N THR E 233 " --> pdb=" O SER E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 240 No H-bonds generated for 'chain 'E' and resid 238 through 240' Processing helix chain 'E' and resid 247 through 269 Processing helix chain 'E' and resid 280 through 306 removed outlier: 3.727A pdb=" N PHE E 291 " --> pdb=" O GLY E 287 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA E 300 " --> pdb=" O LEU E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 445 removed outlier: 4.323A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Proline residue: E 432 - end of helix removed outlier: 3.533A pdb=" N LEU E 444 " --> pdb=" O LEU E 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 493 through 495 No H-bonds generated for 'chain 'G' and resid 493 through 495' Processing helix chain 'G' and resid 513 through 515 No H-bonds generated for 'chain 'G' and resid 513 through 515' Processing sheet with id= A, first strand: chain 'A' and resid 167 through 171 removed outlier: 5.903A pdb=" N THR A 39 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU A 170 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL A 41 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU A 40 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS A 71 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASP A 63 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU A 119 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.085A pdb=" N SER A 159 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL A 211 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY A 195 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LYS A 220 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU A 193 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.183A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.756A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.836A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 179 through 183 removed outlier: 5.874A pdb=" N THR C 51 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N GLN C 182 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE C 53 " --> pdb=" O GLN C 182 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU C 52 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASP C 75 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 57 through 59 Processing sheet with id= I, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.592A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY C 205 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER C 230 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N PHE C 203 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 116 through 121 removed outlier: 6.735A pdb=" N ASP C 148 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA C 119 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR C 146 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 167 through 171 removed outlier: 6.314A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE D 46 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 133 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE D 121 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 150 through 158 Processing sheet with id= M, first strand: chain 'D' and resid 196 through 205 Processing sheet with id= N, first strand: chain 'E' and resid 164 through 168 removed outlier: 6.349A pdb=" N VAL E 36 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N TYR E 167 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL E 38 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.668A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 5 through 7 Processing sheet with id= Q, first strand: chain 'G' and resid 498 through 504 removed outlier: 3.789A pdb=" N MET G 440 " --> pdb=" O MET G 457 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ARG G 444 " --> pdb=" O PHE G 453 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N PHE G 453 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ALA G 446 " --> pdb=" O ARG G 451 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG G 451 " --> pdb=" O ALA G 446 " (cutoff:3.500A) 589 hydrogen bonds defined for protein. 1713 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: 4.49 Time building geometry restraints manager: 7.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2560 1.33 - 1.45: 4506 1.45 - 1.57: 8392 1.57 - 1.70: 8 1.70 - 1.82: 144 Bond restraints: 15610 Sorted by residual: bond pdb=" N PRO A 140 " pdb=" CD PRO A 140 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.65e+01 bond pdb=" C2C PIO D 502 " pdb=" O2C PIO D 502 " ideal model delta sigma weight residual 1.399 1.463 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1B PIO A 502 " pdb=" O3C PIO A 502 " ideal model delta sigma weight residual 1.399 1.336 0.063 2.00e-02 2.50e+03 9.97e+00 bond pdb=" C1B PIO D 502 " pdb=" O3C PIO D 502 " ideal model delta sigma weight residual 1.399 1.336 0.063 2.00e-02 2.50e+03 9.87e+00 bond pdb=" C2C PIO A 502 " pdb=" O2C PIO A 502 " ideal model delta sigma weight residual 1.399 1.461 -0.062 2.00e-02 2.50e+03 9.74e+00 ... (remaining 15605 not shown) Histogram of bond angle deviations from ideal: 92.74 - 100.99: 52 100.99 - 109.24: 1508 109.24 - 117.49: 9832 117.49 - 125.74: 9546 125.74 - 133.99: 275 Bond angle restraints: 21213 Sorted by residual: angle pdb=" N ALA G 505 " pdb=" CA ALA G 505 " pdb=" C ALA G 505 " ideal model delta sigma weight residual 108.52 92.74 15.78 1.63e+00 3.76e-01 9.37e+01 angle pdb=" C4 PIO D 502 " pdb=" O4 PIO D 502 " pdb=" P4 PIO D 502 " ideal model delta sigma weight residual 118.46 132.38 -13.92 3.00e+00 1.11e-01 2.15e+01 angle pdb=" C4 PIO A 502 " pdb=" O4 PIO A 502 " pdb=" P4 PIO A 502 " ideal model delta sigma weight residual 118.46 132.08 -13.62 3.00e+00 1.11e-01 2.06e+01 angle pdb=" C GLY G 509 " pdb=" N LEU G 510 " pdb=" CA LEU G 510 " ideal model delta sigma weight residual 121.54 130.15 -8.61 1.91e+00 2.74e-01 2.03e+01 angle pdb=" C ASP C 192 " pdb=" N THR C 193 " pdb=" CA THR C 193 " ideal model delta sigma weight residual 121.54 129.05 -7.51 1.91e+00 2.74e-01 1.55e+01 ... (remaining 21208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.72: 8647 13.72 - 27.44: 410 27.44 - 41.16: 60 41.16 - 54.88: 19 54.88 - 68.60: 3 Dihedral angle restraints: 9139 sinusoidal: 3817 harmonic: 5322 Sorted by residual: dihedral pdb=" CB CYS E 136 " pdb=" SG CYS E 136 " pdb=" SG CYS E 150 " pdb=" CB CYS E 150 " ideal model delta sinusoidal sigma weight residual 93.00 161.60 -68.60 1 1.00e+01 1.00e-02 6.10e+01 dihedral pdb=" CA ALA B 280 " pdb=" C ALA B 280 " pdb=" N ILE B 281 " pdb=" CA ILE B 281 " ideal model delta harmonic sigma weight residual 180.00 153.04 26.96 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CB CYS C 151 " pdb=" SG CYS C 151 " pdb=" SG CYS C 165 " pdb=" CB CYS C 165 " ideal model delta sinusoidal sigma weight residual 93.00 52.35 40.65 1 1.00e+01 1.00e-02 2.32e+01 ... (remaining 9136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.205: 2450 0.205 - 0.411: 12 0.411 - 0.616: 3 0.616 - 0.821: 1 0.821 - 1.027: 1 Chirality restraints: 2467 Sorted by residual: chirality pdb=" C1 MAN F 4 " pdb=" O6 BMA F 3 " pdb=" C2 MAN F 4 " pdb=" O5 MAN F 4 " both_signs ideal model delta sigma weight residual False 2.40 1.37 1.03 2.00e-02 2.50e+03 2.64e+03 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-02 2.50e+03 3.53e+02 chirality pdb=" C1 MAN M 5 " pdb=" O3 MAN M 4 " pdb=" C2 MAN M 5 " pdb=" O5 MAN M 5 " both_signs ideal model delta sigma weight residual False 2.40 2.10 0.30 2.00e-02 2.50e+03 2.32e+02 ... (remaining 2464 not shown) Planarity restraints: 2583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " 0.039 2.00e-02 2.50e+03 3.25e-02 1.32e+01 pdb=" C7 NAG K 1 " -0.014 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " 0.031 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " -0.050 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 431 " 0.042 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO B 432 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 432 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 432 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 146 " -0.040 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO D 147 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 147 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 147 " -0.030 5.00e-02 4.00e+02 ... (remaining 2580 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3449 2.79 - 3.31: 12784 3.31 - 3.84: 25342 3.84 - 4.37: 30720 4.37 - 4.90: 52650 Nonbonded interactions: 124945 Sorted by model distance: nonbonded pdb=" OD1 ASP B 101 " pdb=" OG1 THR B 132 " model vdw 2.257 2.440 nonbonded pdb=" OG1 THR A 99 " pdb=" OH TYR A 169 " model vdw 2.290 2.440 nonbonded pdb=" OD1 ASP D 98 " pdb=" OG SER D 159 " model vdw 2.292 2.440 nonbonded pdb=" OD1 ASP E 101 " pdb=" OG1 THR E 132 " model vdw 2.297 2.440 nonbonded pdb=" OG1 THR C 111 " pdb=" OH TYR C 181 " model vdw 2.304 2.440 ... (remaining 124940 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' and (resid 13 through 320 or resid 384 through 418 or resid 502)) selection = (chain 'D' and (resid 13 through 418 or resid 502)) } ncs_group { reference = (chain 'B' and (resid 8 through 312 or resid 419 through 447)) selection = (chain 'E' and resid 8 through 447) } ncs_group { reference = (chain 'F' and (resid 2 or resid 5 through 7)) selection = (chain 'I' and (resid 1 or resid 4 through 6)) selection = (chain 'M' and (resid 1 or resid 4 through 6)) } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 83 5.16 5 Cl 1 4.86 5 C 9847 2.51 5 N 2475 2.21 5 O 2815 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.700 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: 4.770 Check model and map are aligned: 0.230 Process input model: 40.230 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.130 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.005 0.064 15610 Z= 0.347 Angle : 0.864 15.779 21213 Z= 0.454 Chirality : 0.061 1.027 2467 Planarity : 0.007 0.063 2576 Dihedral : 8.565 60.539 5699 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -4.15 (0.15), residues: 1784 helix: -3.84 (0.10), residues: 558 sheet: -1.81 (0.21), residues: 487 loop : -2.29 (0.20), residues: 739 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 467 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.3428 time to fit residues: 217.7074 Evaluate side-chains 264 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 1.679 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 190 GLN A 308 ASN B 64 GLN B 185 GLN B 243 ASN C 66 ASN C 80 GLN C 99 ASN C 122 HIS C 157 ASN D 189 ASN D 190 GLN D 417 ASN E 54 ASN E 65 GLN E 113 ASN ** G 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 15610 Z= 0.365 Angle : 0.654 8.098 21213 Z= 0.349 Chirality : 0.047 0.354 2467 Planarity : 0.006 0.047 2576 Dihedral : 6.088 50.358 2306 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 2.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -2.05 (0.18), residues: 1784 helix: -0.77 (0.20), residues: 553 sheet: -1.37 (0.21), residues: 503 loop : -1.65 (0.22), residues: 728 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 262 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 34 residues processed: 295 average time/residue: 0.2878 time to fit residues: 123.6722 Evaluate side-chains 266 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 232 time to evaluate : 1.687 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1568 time to fit residues: 11.7633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 162 optimal weight: 1.9990 chunk 175 optimal weight: 0.2980 chunk 145 optimal weight: 0.8980 chunk 161 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN D 417 ASN E 64 GLN ** G 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 517 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 15610 Z= 0.183 Angle : 0.542 8.909 21213 Z= 0.284 Chirality : 0.043 0.338 2467 Planarity : 0.004 0.049 2576 Dihedral : 5.693 51.168 2306 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.20), residues: 1784 helix: 0.63 (0.22), residues: 544 sheet: -1.09 (0.22), residues: 488 loop : -1.35 (0.22), residues: 752 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 265 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 273 average time/residue: 0.2862 time to fit residues: 113.5952 Evaluate side-chains 241 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 233 time to evaluate : 1.749 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1372 time to fit residues: 4.3977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 84 optimal weight: 0.0770 chunk 18 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 163 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN D 229 GLN D 275 ASN D 417 ASN E 64 GLN ** G 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 517 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 15610 Z= 0.241 Angle : 0.547 9.065 21213 Z= 0.285 Chirality : 0.044 0.341 2467 Planarity : 0.004 0.046 2576 Dihedral : 5.582 52.285 2306 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -0.55 (0.20), residues: 1784 helix: 1.30 (0.23), residues: 542 sheet: -0.85 (0.22), residues: 482 loop : -1.20 (0.23), residues: 760 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 241 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 25 residues processed: 259 average time/residue: 0.2986 time to fit residues: 112.4306 Evaluate side-chains 253 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 228 time to evaluate : 1.876 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1437 time to fit residues: 9.1987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 144 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 147 optimal weight: 0.0980 chunk 119 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN D 204 GLN E 64 GLN ** G 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 517 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 15610 Z= 0.168 Angle : 0.519 8.479 21213 Z= 0.268 Chirality : 0.043 0.393 2467 Planarity : 0.004 0.049 2576 Dihedral : 5.425 52.867 2306 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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 (0.20), residues: 1784 helix: 1.66 (0.23), residues: 541 sheet: -0.68 (0.23), residues: 473 loop : -1.02 (0.23), residues: 770 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 253 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 262 average time/residue: 0.2946 time to fit residues: 112.0456 Evaluate side-chains 227 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 222 time to evaluate : 1.762 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1451 time to fit residues: 3.6022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 101 optimal weight: 0.0010 chunk 42 optimal weight: 0.5980 chunk 173 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN E 64 GLN ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN G 517 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 15610 Z= 0.197 Angle : 0.525 8.922 21213 Z= 0.271 Chirality : 0.043 0.348 2467 Planarity : 0.004 0.049 2576 Dihedral : 5.386 53.202 2306 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -0.01 (0.20), residues: 1784 helix: 1.84 (0.23), residues: 539 sheet: -0.58 (0.23), residues: 477 loop : -0.91 (0.23), residues: 768 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 239 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 252 average time/residue: 0.2949 time to fit residues: 108.5964 Evaluate side-chains 244 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 228 time to evaluate : 1.710 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1482 time to fit residues: 6.7682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 0.5980 chunk 19 optimal weight: 0.0770 chunk 98 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 172 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN E 64 GLN E 303 ASN G 517 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 15610 Z= 0.163 Angle : 0.506 10.122 21213 Z= 0.261 Chirality : 0.043 0.392 2467 Planarity : 0.004 0.049 2576 Dihedral : 5.274 53.878 2306 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: 1784 helix: 2.03 (0.23), residues: 537 sheet: -0.49 (0.23), residues: 481 loop : -0.77 (0.23), residues: 766 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 248 time to evaluate : 1.881 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 252 average time/residue: 0.3014 time to fit residues: 111.1129 Evaluate side-chains 241 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 236 time to evaluate : 1.732 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2144 time to fit residues: 4.2724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 156 optimal weight: 0.3980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN G 517 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 15610 Z= 0.248 Angle : 0.542 12.143 21213 Z= 0.278 Chirality : 0.044 0.400 2467 Planarity : 0.004 0.050 2576 Dihedral : 5.367 54.033 2306 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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 (0.20), residues: 1784 helix: 1.96 (0.23), residues: 540 sheet: -0.47 (0.23), residues: 478 loop : -0.71 (0.23), residues: 766 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 233 time to evaluate : 1.614 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 237 average time/residue: 0.2941 time to fit residues: 101.3791 Evaluate side-chains 233 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 228 time to evaluate : 1.737 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1496 time to fit residues: 3.6455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 0.8980 chunk 150 optimal weight: 0.3980 chunk 160 optimal weight: 0.5980 chunk 96 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 126 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN G 517 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 15610 Z= 0.166 Angle : 0.515 12.388 21213 Z= 0.263 Chirality : 0.042 0.390 2467 Planarity : 0.003 0.050 2576 Dihedral : 5.272 54.452 2306 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: 0.34 (0.21), residues: 1784 helix: 2.08 (0.23), residues: 537 sheet: -0.33 (0.23), residues: 472 loop : -0.69 (0.23), residues: 775 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 235 time to evaluate : 1.892 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 236 average time/residue: 0.2968 time to fit residues: 102.2443 Evaluate side-chains 235 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 233 time to evaluate : 1.754 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1443 time to fit residues: 2.9219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN B 267 HIS G 517 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 15610 Z= 0.287 Angle : 0.569 12.494 21213 Z= 0.291 Chirality : 0.045 0.378 2467 Planarity : 0.004 0.051 2576 Dihedral : 5.437 54.661 2306 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: 0.24 (0.21), residues: 1784 helix: 1.90 (0.23), residues: 540 sheet: -0.43 (0.23), residues: 481 loop : -0.65 (0.23), residues: 763 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 230 time to evaluate : 1.756 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 232 average time/residue: 0.3007 time to fit residues: 102.1311 Evaluate side-chains 226 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 221 time to evaluate : 1.937 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1763 time to fit residues: 4.0481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 0.5980 chunk 130 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 146 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 124 optimal weight: 0.0030 chunk 8 optimal weight: 0.9980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN G 517 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.101516 restraints weight = 22256.597| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.72 r_work: 0.3050 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 15610 Z= 0.163 Angle : 0.519 11.845 21213 Z= 0.265 Chirality : 0.042 0.382 2467 Planarity : 0.003 0.050 2576 Dihedral : 5.320 56.242 2306 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: 0.36 (0.21), residues: 1784 helix: 1.97 (0.23), residues: 546 sheet: -0.27 (0.24), residues: 469 loop : -0.64 (0.23), residues: 769 =============================================================================== Job complete usr+sys time: 3282.59 seconds wall clock time: 60 minutes 21.59 seconds (3621.59 seconds total)