Starting phenix.real_space_refine on Sat Mar 16 16:57:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/03_2024/6huo_0282_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/03_2024/6huo_0282.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/03_2024/6huo_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_0282/03_2024/6huo_0282_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/03_2024/6huo_0282_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/03_2024/6huo_0282.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/03_2024/6huo_0282.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/03_2024/6huo_0282_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huo_0282/03_2024/6huo_0282_updated.pdb" } resolution = 3.26 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= 0.001 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 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. 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 21 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 dihedrals: 6 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: 18 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 dihedrals: 6 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: 15 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 dihedrals: 6 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: 18 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: 8.23, per 1000 atoms: 0.54 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: 5.92 Conformation dependent library (CDL) restraints added in 2.7 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: 2.78 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: 4.57 Time building geometry restraints manager: 6.42 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 - 28.28: 9392 28.28 - 56.56: 79 56.56 - 84.84: 32 84.84 - 113.12: 20 113.12 - 141.40: 3 Dihedral angle restraints: 9526 sinusoidal: 4204 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 9523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.205: 2446 0.205 - 0.411: 16 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 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: 0.920 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: 4.240 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 41.430 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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 : 0.006 0.064 15610 Z= 0.368 Angle : 0.886 15.779 21213 Z= 0.456 Chirality : 0.062 1.027 2467 Planarity : 0.007 0.063 2576 Dihedral : 11.906 141.400 6086 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 % Allowed : 1.74 % Favored : 98.26 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 95 HIS 0.012 0.002 HIS B 107 PHE 0.038 0.003 PHE C 113 TYR 0.021 0.002 TYR E 66 ARG 0.008 0.001 ARG A 249 *********************** 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 : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 MET cc_start: 0.8058 (tpp) cc_final: 0.7707 (tpt) REVERT: A 114 MET cc_start: 0.7816 (mmm) cc_final: 0.7469 (mmm) REVERT: A 250 GLU cc_start: 0.8534 (mp0) cc_final: 0.8287 (mp0) REVERT: A 287 ASP cc_start: 0.7746 (m-30) cc_final: 0.7510 (m-30) REVERT: A 391 LYS cc_start: 0.8019 (mtmt) cc_final: 0.7778 (mptt) REVERT: B 9 MET cc_start: 0.8369 (tpp) cc_final: 0.8153 (tpp) REVERT: B 101 ASP cc_start: 0.7238 (t70) cc_final: 0.6596 (p0) REVERT: B 217 ASN cc_start: 0.8606 (m-40) cc_final: 0.8338 (m-40) REVERT: B 235 LEU cc_start: 0.8870 (mt) cc_final: 0.8600 (mt) REVERT: C 88 LYS cc_start: 0.8545 (mttt) cc_final: 0.8343 (mttt) REVERT: C 130 MET cc_start: 0.8239 (tmt) cc_final: 0.7977 (tmm) REVERT: C 157 ASN cc_start: 0.6401 (m-40) cc_final: 0.6171 (m110) REVERT: D 20 ASP cc_start: 0.8590 (m-30) cc_final: 0.8060 (m-30) REVERT: D 189 ASN cc_start: 0.8322 (m-40) cc_final: 0.8033 (m110) REVERT: D 209 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6817 (mt-10) REVERT: D 267 THR cc_start: 0.8560 (m) cc_final: 0.8278 (p) REVERT: E 163 ASP cc_start: 0.7588 (m-30) cc_final: 0.7285 (m-30) REVERT: E 286 MET cc_start: 0.7556 (mtm) cc_final: 0.7194 (mmt) REVERT: G 514 SER cc_start: 0.8286 (p) cc_final: 0.8067 (p) REVERT: G 516 TYR cc_start: 0.9009 (m-80) cc_final: 0.8581 (m-80) outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.3492 time to fit residues: 222.0755 Evaluate side-chains 263 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.691 ------------------------------------------------------------------------------- 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: 2.9990 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 99 ASN C 122 HIS D 190 GLN D 417 ASN E 54 ASN E 113 ASN ** G 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15610 Z= 0.261 Angle : 0.617 7.866 21213 Z= 0.325 Chirality : 0.045 0.239 2467 Planarity : 0.005 0.048 2576 Dihedral : 12.097 142.211 2693 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.67 % Allowed : 7.94 % Favored : 89.39 % 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: -2.04 (0.18), residues: 1784 helix: -0.71 (0.20), residues: 552 sheet: -1.34 (0.21), residues: 498 loop : -1.72 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 92 HIS 0.009 0.001 HIS G 517 PHE 0.019 0.002 PHE C 113 TYR 0.025 0.002 TYR D 309 ARG 0.006 0.001 ARG E 68 *********************** 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 311 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 268 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.7605 (mmm) cc_final: 0.7347 (mmm) REVERT: A 391 LYS cc_start: 0.8011 (mtmt) cc_final: 0.7799 (mptt) REVERT: B 101 ASP cc_start: 0.7183 (t70) cc_final: 0.6671 (p0) REVERT: B 251 VAL cc_start: 0.9098 (t) cc_final: 0.8838 (t) REVERT: C 130 MET cc_start: 0.8085 (tmt) cc_final: 0.7839 (tmm) REVERT: D 160 TYR cc_start: 0.8666 (t80) cc_final: 0.8331 (t80) REVERT: D 209 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6023 (mt-10) REVERT: E 243 ASN cc_start: 0.7299 (t0) cc_final: 0.6879 (t0) REVERT: E 275 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8230 (pp) REVERT: E 286 MET cc_start: 0.7415 (mtm) cc_final: 0.6961 (mmt) outliers start: 43 outliers final: 28 residues processed: 297 average time/residue: 0.2846 time to fit residues: 121.8873 Evaluate side-chains 268 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 239 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain G residue 427 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 162 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 chunk 145 optimal weight: 0.0870 chunk 161 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 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 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 ASN D 417 ASN E 64 GLN E 65 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: 0.8133 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15610 Z= 0.168 Angle : 0.543 8.931 21213 Z= 0.279 Chirality : 0.043 0.242 2467 Planarity : 0.004 0.047 2576 Dihedral : 11.062 142.236 2693 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.86 % Allowed : 9.99 % Favored : 88.15 % 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: -1.08 (0.19), residues: 1784 helix: 0.63 (0.22), residues: 550 sheet: -1.06 (0.22), residues: 493 loop : -1.41 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 92 HIS 0.011 0.001 HIS G 517 PHE 0.014 0.001 PHE D 226 TYR 0.023 0.001 TYR E 299 ARG 0.010 0.000 ARG E 68 *********************** 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 291 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 261 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.7571 (mmm) cc_final: 0.7303 (mmm) REVERT: A 391 LYS cc_start: 0.8029 (mtmt) cc_final: 0.7815 (mptt) REVERT: B 101 ASP cc_start: 0.7138 (t70) cc_final: 0.6678 (p0) REVERT: B 165 GLU cc_start: 0.7502 (tt0) cc_final: 0.7230 (tt0) REVERT: B 251 VAL cc_start: 0.9109 (t) cc_final: 0.8855 (t) REVERT: C 118 LYS cc_start: 0.8196 (mmmt) cc_final: 0.7981 (tptp) REVERT: C 239 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7785 (tm-30) REVERT: D 131 MET cc_start: 0.8756 (ptm) cc_final: 0.8466 (ptt) REVERT: D 160 TYR cc_start: 0.8520 (t80) cc_final: 0.8149 (t80) REVERT: D 199 ASP cc_start: 0.7654 (p0) cc_final: 0.7442 (p0) REVERT: D 204 GLN cc_start: 0.8407 (tp40) cc_final: 0.8170 (tp40) REVERT: E 163 ASP cc_start: 0.7682 (m-30) cc_final: 0.7477 (m-30) REVERT: E 243 ASN cc_start: 0.7171 (t0) cc_final: 0.6774 (t0) REVERT: E 275 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8202 (pp) REVERT: G 427 SER cc_start: 0.8424 (OUTLIER) cc_final: 0.8073 (p) outliers start: 30 outliers final: 26 residues processed: 279 average time/residue: 0.2699 time to fit residues: 110.0952 Evaluate side-chains 262 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 234 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain G residue 427 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 0.1980 chunk 122 optimal weight: 0.0370 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.8262 ------------------------------------------------------------------------------- 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** C 80 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: 0.8156 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15610 Z= 0.186 Angle : 0.538 8.690 21213 Z= 0.272 Chirality : 0.043 0.242 2467 Planarity : 0.004 0.047 2576 Dihedral : 10.356 142.549 2693 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.54 % Allowed : 10.42 % Favored : 87.03 % 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: -0.53 (0.20), residues: 1784 helix: 1.31 (0.23), residues: 543 sheet: -0.83 (0.22), residues: 481 loop : -1.21 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 92 HIS 0.010 0.001 HIS G 517 PHE 0.016 0.001 PHE D 226 TYR 0.023 0.001 TYR E 299 ARG 0.007 0.000 ARG E 68 *********************** 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 286 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 245 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.7600 (mmm) cc_final: 0.7321 (mmm) REVERT: A 209 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7157 (tt0) REVERT: A 391 LYS cc_start: 0.8063 (mtmt) cc_final: 0.7859 (mptt) REVERT: B 101 ASP cc_start: 0.7217 (t70) cc_final: 0.6774 (p0) REVERT: B 165 GLU cc_start: 0.7543 (tt0) cc_final: 0.7261 (tt0) REVERT: B 251 VAL cc_start: 0.9150 (t) cc_final: 0.8887 (t) REVERT: C 239 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7940 (tm-30) REVERT: C 246 LEU cc_start: 0.7812 (mt) cc_final: 0.7600 (mt) REVERT: D 131 MET cc_start: 0.8798 (ptm) cc_final: 0.8435 (ptp) REVERT: D 160 TYR cc_start: 0.8579 (t80) cc_final: 0.8181 (t80) REVERT: D 204 GLN cc_start: 0.8327 (tp40) cc_final: 0.7921 (tp40) REVERT: E 243 ASN cc_start: 0.7161 (t0) cc_final: 0.6918 (t0) REVERT: E 275 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8226 (pp) REVERT: G 427 SER cc_start: 0.8432 (OUTLIER) cc_final: 0.8172 (p) outliers start: 41 outliers final: 33 residues processed: 271 average time/residue: 0.2935 time to fit residues: 114.5249 Evaluate side-chains 265 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 230 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain G residue 423 SER Chi-restraints excluded: chain G residue 427 SER Chi-restraints excluded: chain G residue 467 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 144 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15610 Z= 0.187 Angle : 0.545 13.401 21213 Z= 0.271 Chirality : 0.043 0.257 2467 Planarity : 0.004 0.048 2576 Dihedral : 9.941 142.529 2693 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.85 % Allowed : 10.92 % Favored : 86.23 % 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: 1.65 (0.23), residues: 547 sheet: -0.71 (0.23), residues: 485 loop : -1.02 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 67 HIS 0.012 0.001 HIS G 517 PHE 0.016 0.001 PHE A 101 TYR 0.023 0.001 TYR E 299 ARG 0.007 0.000 ARG B 129 *********************** 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 295 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 249 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.7582 (mmm) cc_final: 0.7273 (mmm) REVERT: A 391 LYS cc_start: 0.8022 (mtmt) cc_final: 0.7803 (mptt) REVERT: B 101 ASP cc_start: 0.7058 (t70) cc_final: 0.6719 (p0) REVERT: B 165 GLU cc_start: 0.7564 (tt0) cc_final: 0.7298 (tt0) REVERT: B 251 VAL cc_start: 0.9158 (t) cc_final: 0.8894 (t) REVERT: C 246 LEU cc_start: 0.7953 (mt) cc_final: 0.7720 (mt) REVERT: D 85 ARG cc_start: 0.7799 (mpp-170) cc_final: 0.7568 (mtm-85) REVERT: D 131 MET cc_start: 0.8788 (ptm) cc_final: 0.8480 (ptp) REVERT: D 160 TYR cc_start: 0.8578 (t80) cc_final: 0.8160 (t80) REVERT: D 204 GLN cc_start: 0.8372 (tp40) cc_final: 0.7958 (tp40) REVERT: E 243 ASN cc_start: 0.7167 (t0) cc_final: 0.6940 (t0) REVERT: E 275 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8244 (pp) REVERT: G 427 SER cc_start: 0.8435 (OUTLIER) cc_final: 0.8193 (p) outliers start: 46 outliers final: 34 residues processed: 278 average time/residue: 0.2814 time to fit residues: 114.0087 Evaluate side-chains 274 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 238 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain G residue 423 SER Chi-restraints excluded: chain G residue 427 SER Chi-restraints excluded: chain G residue 467 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 173 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 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: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 GLN G 5 GLN G 517 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15610 Z= 0.173 Angle : 0.527 10.966 21213 Z= 0.265 Chirality : 0.043 0.259 2467 Planarity : 0.004 0.049 2576 Dihedral : 9.647 142.616 2693 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.04 % Allowed : 11.41 % Favored : 85.55 % 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: 0.02 (0.20), residues: 1784 helix: 1.93 (0.23), residues: 540 sheet: -0.62 (0.23), residues: 486 loop : -0.91 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 256 HIS 0.006 0.001 HIS A 142 PHE 0.014 0.001 PHE D 226 TYR 0.023 0.001 TYR E 299 ARG 0.008 0.000 ARG C 284 *********************** 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 299 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 250 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.7552 (mmm) cc_final: 0.7248 (mmm) REVERT: A 144 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7713 (mm-30) REVERT: A 250 GLU cc_start: 0.8615 (mp0) cc_final: 0.8333 (mp0) REVERT: A 391 LYS cc_start: 0.8035 (mtmt) cc_final: 0.7817 (mptt) REVERT: B 101 ASP cc_start: 0.7112 (t70) cc_final: 0.6765 (p0) REVERT: B 165 GLU cc_start: 0.7575 (tt0) cc_final: 0.7349 (tt0) REVERT: B 251 VAL cc_start: 0.9153 (t) cc_final: 0.8869 (t) REVERT: C 246 LEU cc_start: 0.8073 (mt) cc_final: 0.7871 (mt) REVERT: D 85 ARG cc_start: 0.7783 (mpp-170) cc_final: 0.7559 (mtm-85) REVERT: D 131 MET cc_start: 0.8780 (ptm) cc_final: 0.8457 (ptp) REVERT: D 294 TYR cc_start: 0.8149 (t80) cc_final: 0.7918 (t80) REVERT: E 243 ASN cc_start: 0.7174 (t0) cc_final: 0.6961 (t0) REVERT: E 275 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8165 (pp) REVERT: G 13 GLN cc_start: 0.6910 (mt0) cc_final: 0.6709 (mt0) outliers start: 49 outliers final: 39 residues processed: 280 average time/residue: 0.2796 time to fit residues: 114.1683 Evaluate side-chains 272 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 232 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 151 HIS Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain G residue 423 SER Chi-restraints excluded: chain G residue 467 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 172 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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** ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 517 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15610 Z= 0.274 Angle : 0.572 11.840 21213 Z= 0.285 Chirality : 0.044 0.265 2467 Planarity : 0.004 0.050 2576 Dihedral : 9.648 142.700 2693 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.10 % Allowed : 11.85 % Favored : 85.05 % 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: 0.04 (0.20), residues: 1784 helix: 1.91 (0.23), residues: 540 sheet: -0.63 (0.23), residues: 486 loop : -0.86 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 256 HIS 0.007 0.001 HIS A 151 PHE 0.020 0.002 PHE A 101 TYR 0.026 0.002 TYR E 299 ARG 0.008 0.000 ARG E 68 *********************** 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 283 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 233 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.7568 (mmm) cc_final: 0.7290 (mmm) REVERT: A 258 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.7362 (t80) REVERT: A 391 LYS cc_start: 0.8126 (mtmt) cc_final: 0.7890 (mptt) REVERT: B 101 ASP cc_start: 0.7174 (t70) cc_final: 0.6729 (p0) REVERT: B 251 VAL cc_start: 0.9153 (t) cc_final: 0.8867 (t) REVERT: D 131 MET cc_start: 0.8841 (ptm) cc_final: 0.8524 (ptt) REVERT: E 40 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7687 (mtt) REVERT: E 55 MET cc_start: 0.9127 (mmt) cc_final: 0.8677 (mmt) REVERT: E 243 ASN cc_start: 0.7221 (t0) cc_final: 0.7017 (t0) REVERT: E 275 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8203 (pp) outliers start: 50 outliers final: 41 residues processed: 263 average time/residue: 0.2811 time to fit residues: 107.3254 Evaluate side-chains 273 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 229 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain G residue 423 SER Chi-restraints excluded: chain G residue 467 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 517 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15610 Z= 0.182 Angle : 0.542 11.958 21213 Z= 0.271 Chirality : 0.043 0.256 2467 Planarity : 0.003 0.048 2576 Dihedral : 9.404 142.638 2693 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.92 % Allowed : 12.41 % Favored : 84.68 % 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: 0.21 (0.21), residues: 1784 helix: 2.10 (0.23), residues: 536 sheet: -0.54 (0.23), residues: 484 loop : -0.77 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 256 HIS 0.005 0.001 HIS G 517 PHE 0.015 0.001 PHE C 158 TYR 0.023 0.001 TYR E 299 ARG 0.007 0.000 ARG E 68 *********************** 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 285 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 238 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 MET cc_start: 0.7983 (tpp) cc_final: 0.7437 (tpp) REVERT: A 114 MET cc_start: 0.7547 (mmm) cc_final: 0.7236 (mmm) REVERT: A 258 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.7667 (t80) REVERT: A 391 LYS cc_start: 0.8055 (mtmt) cc_final: 0.7796 (mptt) REVERT: B 101 ASP cc_start: 0.7169 (t70) cc_final: 0.6716 (p0) REVERT: B 251 VAL cc_start: 0.9152 (t) cc_final: 0.8872 (t) REVERT: D 85 ARG cc_start: 0.7804 (mpp-170) cc_final: 0.7550 (mtm-85) REVERT: E 40 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7643 (mtt) REVERT: E 275 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8196 (pp) outliers start: 47 outliers final: 35 residues processed: 267 average time/residue: 0.2806 time to fit residues: 108.8933 Evaluate side-chains 272 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 234 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 420 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 160 optimal weight: 0.3980 chunk 96 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 126 optimal weight: 0.2980 chunk 49 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 B 267 HIS ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 517 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15610 Z= 0.189 Angle : 0.542 12.943 21213 Z= 0.270 Chirality : 0.043 0.259 2467 Planarity : 0.004 0.050 2576 Dihedral : 9.061 142.590 2693 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.54 % Allowed : 12.59 % Favored : 84.86 % 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: 0.29 (0.21), residues: 1784 helix: 2.11 (0.23), residues: 537 sheet: -0.49 (0.23), residues: 484 loop : -0.68 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 256 HIS 0.004 0.001 HIS G 517 PHE 0.016 0.001 PHE A 101 TYR 0.023 0.001 TYR E 299 ARG 0.007 0.000 ARG E 68 *********************** 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 283 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 242 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.7559 (mmm) cc_final: 0.7256 (mmm) REVERT: A 258 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.7642 (t80) REVERT: A 391 LYS cc_start: 0.8064 (mtmt) cc_final: 0.7802 (mptt) REVERT: B 101 ASP cc_start: 0.7192 (t70) cc_final: 0.6740 (p0) REVERT: B 251 VAL cc_start: 0.9141 (t) cc_final: 0.8855 (t) REVERT: D 85 ARG cc_start: 0.7795 (mpp-170) cc_final: 0.7541 (mtm-85) REVERT: E 40 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7635 (mtt) REVERT: E 55 MET cc_start: 0.9113 (mmt) cc_final: 0.8647 (mmt) REVERT: E 153 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7656 (mm-30) REVERT: E 275 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8225 (pp) REVERT: G 514 SER cc_start: 0.8287 (m) cc_final: 0.7769 (t) outliers start: 41 outliers final: 35 residues processed: 269 average time/residue: 0.2797 time to fit residues: 109.7938 Evaluate side-chains 269 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 231 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 420 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 151 optimal weight: 0.0770 overall best weight: 0.7140 ------------------------------------------------------------------------------- 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 ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 517 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15610 Z= 0.169 Angle : 0.536 12.206 21213 Z= 0.267 Chirality : 0.043 0.255 2467 Planarity : 0.004 0.049 2576 Dihedral : 8.837 142.592 2693 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.42 % Allowed : 13.03 % Favored : 84.55 % 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: 2.07 (0.23), residues: 545 sheet: -0.44 (0.23), residues: 484 loop : -0.63 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 256 HIS 0.004 0.001 HIS A 142 PHE 0.014 0.001 PHE D 226 TYR 0.022 0.001 TYR E 299 ARG 0.008 0.000 ARG E 68 ********************** 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 274 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 235 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 MET cc_start: 0.7875 (tpp) cc_final: 0.7348 (tpp) REVERT: A 114 MET cc_start: 0.7611 (mmm) cc_final: 0.7328 (mmm) REVERT: A 258 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.7648 (t80) REVERT: A 391 LYS cc_start: 0.8052 (mtmt) cc_final: 0.7792 (mptt) REVERT: B 101 ASP cc_start: 0.7162 (t70) cc_final: 0.6718 (p0) REVERT: B 251 VAL cc_start: 0.9141 (t) cc_final: 0.8861 (t) REVERT: E 9 MET cc_start: 0.6565 (tmm) cc_final: 0.5785 (tmm) REVERT: E 40 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7614 (mtt) REVERT: E 55 MET cc_start: 0.9093 (mmt) cc_final: 0.8630 (mmt) REVERT: E 275 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8237 (pp) REVERT: G 514 SER cc_start: 0.8280 (m) cc_final: 0.7755 (t) outliers start: 39 outliers final: 34 residues processed: 260 average time/residue: 0.2889 time to fit residues: 109.1080 Evaluate side-chains 266 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 229 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 192 ASP Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 420 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 0.0980 chunk 130 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 C 99 ASN ** E 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 517 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.116244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.101708 restraints weight = 22332.044| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.71 r_work: 0.3069 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15610 Z= 0.171 Angle : 0.533 12.319 21213 Z= 0.266 Chirality : 0.043 0.253 2467 Planarity : 0.004 0.050 2576 Dihedral : 8.772 142.643 2693 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.67 % Allowed : 12.84 % Favored : 84.49 % 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: 0.39 (0.21), residues: 1784 helix: 2.11 (0.23), residues: 544 sheet: -0.40 (0.23), residues: 483 loop : -0.61 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 256 HIS 0.004 0.001 HIS A 142 PHE 0.015 0.001 PHE A 101 TYR 0.022 0.001 TYR E 299 ARG 0.007 0.000 ARG E 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3517.51 seconds wall clock time: 64 minutes 15.35 seconds (3855.35 seconds total)