Starting phenix.real_space_refine on Wed Feb 14 18:31:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfs_30346/02_2024/7cfs_30346.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfs_30346/02_2024/7cfs_30346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfs_30346/02_2024/7cfs_30346.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfs_30346/02_2024/7cfs_30346.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfs_30346/02_2024/7cfs_30346.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cfs_30346/02_2024/7cfs_30346.pdb" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians S 81 5.16 5 Na 1 4.78 5 C 6402 2.51 5 N 1631 2.21 5 O 1859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 219": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "C GLU 219": "OE1" <-> "OE2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C GLU 375": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9974 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3249 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 407} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 112 Chain: "B" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3267 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 407} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3268 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 407} Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 83 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' NA': 1, 'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.55, per 1000 atoms: 0.56 Number of scatterers: 9974 At special positions: 0 Unit cell: (97.344, 96.33, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 81 16.00 Na 1 11.00 O 1859 8.00 N 1631 7.00 C 6402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 314 " - pdb=" SG CYS A 361 " distance=2.33 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 314 " - pdb=" SG CYS B 361 " distance=2.33 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 325 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 367 " distance=2.02 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 314 " - pdb=" SG CYS C 361 " distance=2.33 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 325 " - pdb=" SG CYS C 337 " 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 NAG-ASN " NAG A 601 " - " ASN A 395 " " NAG A 602 " - " ASN A 368 " " NAG B 601 " - " ASN B 395 " " NAG B 602 " - " ASN B 368 " " NAG C 601 " - " ASN C 395 " " NAG C 602 " - " ASN C 368 " Time building additional restraints: 4.08 Conformation dependent library (CDL) restraints added in 1.8 seconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 15 sheets defined 35.2% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 45 through 61 removed outlier: 4.264A pdb=" N LEU A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.511A pdb=" N HIS A 70 " --> pdb=" O TYR A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.830A pdb=" N VAL A 103 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.543A pdb=" N HIS A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 140 removed outlier: 3.581A pdb=" N ILE A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.706A pdb=" N ARG A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 180 through 184 removed outlier: 3.583A pdb=" N ASP A 183 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 184 " --> pdb=" O ALA A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 184' Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.810A pdb=" N TYR A 229 " --> pdb=" O GLN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.559A pdb=" N TYR A 318 " --> pdb=" O CYS A 314 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.784A pdb=" N LYS A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.548A pdb=" N PHE A 352 " --> pdb=" O PRO A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 removed outlier: 3.620A pdb=" N ALA A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 404 removed outlier: 3.513A pdb=" N GLY A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 443 removed outlier: 4.012A pdb=" N GLY A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET A 439 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 462 removed outlier: 3.822A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 61 removed outlier: 4.263A pdb=" N LEU B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 removed outlier: 3.509A pdb=" N HIS B 70 " --> pdb=" O TYR B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.830A pdb=" N VAL B 103 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 removed outlier: 3.542A pdb=" N HIS B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 140 removed outlier: 3.582A pdb=" N ILE B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU B 138 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.707A pdb=" N ARG B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 180 through 184 removed outlier: 3.582A pdb=" N ASP B 183 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 184 " --> pdb=" O ALA B 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 184' Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.810A pdb=" N TYR B 229 " --> pdb=" O GLN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.559A pdb=" N TYR B 318 " --> pdb=" O CYS B 314 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.784A pdb=" N LYS B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 removed outlier: 3.548A pdb=" N PHE B 352 " --> pdb=" O PRO B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 394 removed outlier: 3.620A pdb=" N ALA B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 404 removed outlier: 3.513A pdb=" N GLY B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 443 removed outlier: 4.012A pdb=" N GLY B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET B 439 " --> pdb=" O ILE B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 462 removed outlier: 3.822A pdb=" N LEU B 451 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B 458 " --> pdb=" O PHE B 454 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 462 " --> pdb=" O TYR B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 removed outlier: 4.263A pdb=" N LEU C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 removed outlier: 3.510A pdb=" N HIS C 70 " --> pdb=" O TYR C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 removed outlier: 3.830A pdb=" N VAL C 103 " --> pdb=" O PHE C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 111 removed outlier: 3.543A pdb=" N HIS C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.581A pdb=" N ILE C 137 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU C 138 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 removed outlier: 3.707A pdb=" N ARG C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 180 through 184 removed outlier: 3.583A pdb=" N ASP C 183 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C 184 " --> pdb=" O ALA C 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 184' Processing helix chain 'C' and resid 225 through 229 removed outlier: 3.811A pdb=" N TYR C 229 " --> pdb=" O GLN C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.560A pdb=" N TYR C 318 " --> pdb=" O CYS C 314 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.783A pdb=" N LYS C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 removed outlier: 3.547A pdb=" N PHE C 352 " --> pdb=" O PRO C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 394 removed outlier: 3.620A pdb=" N ALA C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 404 removed outlier: 3.513A pdb=" N GLY C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 443 removed outlier: 4.013A pdb=" N GLY C 433 " --> pdb=" O ALA C 429 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET C 439 " --> pdb=" O ILE C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 462 removed outlier: 3.822A pdb=" N LEU C 451 " --> pdb=" O ILE C 447 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR C 458 " --> pdb=" O PHE C 454 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS C 462 " --> pdb=" O TYR C 458 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 81 removed outlier: 10.264A pdb=" N PHE A 269 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N ILE A 410 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR A 271 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE A 412 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N VAL A 273 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N VAL A 414 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS A 275 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN A 416 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU A 277 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 274 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN A 276 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 278 " --> pdb=" O ARG A 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 221 through 223 removed outlier: 10.264A pdb=" N PHE A 269 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N ILE A 410 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR A 271 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE A 412 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N VAL A 273 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N VAL A 414 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS A 275 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN A 416 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU A 277 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 189 removed outlier: 7.261A pdb=" N LYS A 193 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASN A 94 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A 250 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 81 removed outlier: 10.264A pdb=" N PHE B 269 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N ILE B 410 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR B 271 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE B 412 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N VAL B 273 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N VAL B 414 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS B 275 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN B 416 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLU B 277 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 274 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 276 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 278 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 221 through 223 removed outlier: 10.264A pdb=" N PHE B 269 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N ILE B 410 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR B 271 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE B 412 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N VAL B 273 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N VAL B 414 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS B 275 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN B 416 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLU B 277 " --> pdb=" O ASN B 416 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 185 through 189 removed outlier: 7.262A pdb=" N LYS B 193 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASN B 94 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS B 250 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 174 Processing sheet with id=AB2, first strand: chain 'C' and resid 73 through 81 removed outlier: 10.264A pdb=" N PHE C 269 " --> pdb=" O LEU C 408 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N ILE C 410 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR C 271 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE C 412 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N VAL C 273 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N VAL C 414 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS C 275 " --> pdb=" O VAL C 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN C 416 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU C 277 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 274 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN C 276 " --> pdb=" O GLY C 373 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 278 " --> pdb=" O ARG C 371 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 221 through 223 removed outlier: 10.264A pdb=" N PHE C 269 " --> pdb=" O LEU C 408 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N ILE C 410 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR C 271 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE C 412 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N VAL C 273 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N VAL C 414 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS C 275 " --> pdb=" O VAL C 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN C 416 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU C 277 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB5, first strand: chain 'C' and resid 185 through 189 removed outlier: 7.262A pdb=" N LYS C 193 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASN C 94 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS C 250 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 173 through 174 303 hydrogen bonds defined for protein. 810 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: 2.70 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3154 1.34 - 1.45: 1745 1.45 - 1.57: 5202 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 10209 Sorted by residual: bond pdb=" CAI Y01 B 603 " pdb=" CAK Y01 B 603 " ideal model delta sigma weight residual 1.492 1.386 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" CAI Y01 C 603 " pdb=" CAK Y01 C 603 " ideal model delta sigma weight residual 1.492 1.386 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" CAI Y01 A 603 " pdb=" CAK Y01 A 603 " ideal model delta sigma weight residual 1.492 1.387 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" CAI Y01 C 603 " pdb=" CAZ Y01 C 603 " ideal model delta sigma weight residual 1.332 1.380 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" CAI Y01 A 603 " pdb=" CAZ Y01 A 603 " ideal model delta sigma weight residual 1.332 1.380 -0.048 2.00e-02 2.50e+03 5.78e+00 ... (remaining 10204 not shown) Histogram of bond angle deviations from ideal: 96.80 - 104.23: 175 104.23 - 111.65: 4341 111.65 - 119.08: 3783 119.08 - 126.51: 5464 126.51 - 133.94: 119 Bond angle restraints: 13882 Sorted by residual: angle pdb=" N ILE A 381 " pdb=" CA ILE A 381 " pdb=" C ILE A 381 " ideal model delta sigma weight residual 108.88 117.02 -8.14 2.16e+00 2.14e-01 1.42e+01 angle pdb=" N ILE C 381 " pdb=" CA ILE C 381 " pdb=" C ILE C 381 " ideal model delta sigma weight residual 108.88 116.98 -8.10 2.16e+00 2.14e-01 1.41e+01 angle pdb=" N ILE B 381 " pdb=" CA ILE B 381 " pdb=" C ILE B 381 " ideal model delta sigma weight residual 108.88 116.97 -8.09 2.16e+00 2.14e-01 1.40e+01 angle pdb=" CA ILE C 381 " pdb=" C ILE C 381 " pdb=" N PRO C 382 " ideal model delta sigma weight residual 118.88 124.19 -5.31 1.54e+00 4.22e-01 1.19e+01 angle pdb=" CA ILE B 381 " pdb=" C ILE B 381 " pdb=" N PRO B 382 " ideal model delta sigma weight residual 118.88 124.17 -5.29 1.54e+00 4.22e-01 1.18e+01 ... (remaining 13877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 5486 16.89 - 33.78: 656 33.78 - 50.68: 141 50.68 - 67.57: 39 67.57 - 84.46: 21 Dihedral angle restraints: 6343 sinusoidal: 2607 harmonic: 3736 Sorted by residual: dihedral pdb=" CB CYS C 323 " pdb=" SG CYS C 323 " pdb=" SG CYS C 345 " pdb=" CB CYS C 345 " ideal model delta sinusoidal sigma weight residual -86.00 -170.46 84.46 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS B 323 " pdb=" SG CYS B 323 " pdb=" SG CYS B 345 " pdb=" CB CYS B 345 " ideal model delta sinusoidal sigma weight residual -86.00 -170.45 84.45 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS A 323 " pdb=" SG CYS A 323 " pdb=" SG CYS A 345 " pdb=" CB CYS A 345 " ideal model delta sinusoidal sigma weight residual -86.00 -170.45 84.45 1 1.00e+01 1.00e-02 8.67e+01 ... (remaining 6340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1248 0.067 - 0.135: 270 0.135 - 0.202: 33 0.202 - 0.270: 0 0.270 - 0.337: 6 Chirality restraints: 1557 Sorted by residual: chirality pdb=" CBG Y01 C 603 " pdb=" CAQ Y01 C 603 " pdb=" CBD Y01 C 603 " pdb=" CBI Y01 C 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.67 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CBG Y01 B 603 " pdb=" CAQ Y01 B 603 " pdb=" CBD Y01 B 603 " pdb=" CBI Y01 B 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.67 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CBG Y01 A 603 " pdb=" CAQ Y01 A 603 " pdb=" CBD Y01 A 603 " pdb=" CBI Y01 A 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.66 0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 1554 not shown) Planarity restraints: 1795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 338 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO B 339 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 339 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 339 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 338 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A 339 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 338 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO C 339 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 339 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 339 " -0.026 5.00e-02 4.00e+02 ... (remaining 1792 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 25 2.45 - 3.06: 5484 3.06 - 3.67: 14301 3.67 - 4.29: 20002 4.29 - 4.90: 33905 Nonbonded interactions: 73717 Sorted by model distance: nonbonded pdb=" CE1 HIS C 73 " pdb=" OE1 GLN C 422 " model vdw 1.835 3.260 nonbonded pdb=" ND1 HIS C 73 " pdb=" OE1 GLN C 422 " model vdw 1.971 2.520 nonbonded pdb=" CD2 HIS A 73 " pdb=" OE1 GLN A 422 " model vdw 1.990 3.260 nonbonded pdb=" CD2 HIS B 73 " pdb=" OE1 GLN B 422 " model vdw 2.116 3.260 nonbonded pdb=" OD1 ASP A 434 " pdb="NA NA A 604 " model vdw 2.251 2.470 ... (remaining 73712 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 40 through 87 or (resid 88 through 89 and (name N or name \ CA or name C or name O or name CB )) or resid 90 through 198 or (resid 199 and ( \ name N or name CA or name C or name O or name CB )) or resid 200 through 290 or \ (resid 291 through 300 and (name N or name CA or name C or name O or name CB )) \ or resid 301 through 452 or (resid 453 through 455 and (name N or name CA or nam \ e C or name O or name CB )) or resid 456 through 464 or (resid 465 and (name N o \ r name CA or name C or name O or name CB )) or resid 601 through 603)) selection = (chain 'B' and (resid 40 through 42 or (resid 43 through 44 and (name N or name \ CA or name C or name O or name CB )) or resid 45 through 146 or (resid 147 throu \ gh 148 and (name N or name CA or name C or name O or name CB )) or resid 149 thr \ ough 181 or (resid 182 and (name N or name CA or name C or name O or name CB )) \ or resid 183 through 290 or (resid 291 through 300 and (name N or name CA or nam \ e C or name O or name CB )) or resid 301 through 314 or (resid 315 and (name N o \ r name CA or name C or name O or name CB )) or resid 316 through 363 or (resid 3 \ 64 and (name N or name CA or name C or name O or name CB )) or resid 365 through \ 452 or (resid 453 through 455 and (name N or name CA or name C or name O or nam \ e CB )) or resid 456 through 465 or resid 601 through 603)) selection = (chain 'C' and (resid 40 through 87 or (resid 88 through 89 and (name N or name \ CA or name C or name O or name CB )) or resid 90 through 146 or (resid 147 throu \ gh 148 and (name N or name CA or name C or name O or name CB )) or resid 149 thr \ ough 181 or (resid 182 and (name N or name CA or name C or name O or name CB )) \ or resid 183 through 198 or (resid 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 234 or (resid 235 and (name N or name CA or \ name C or name O or name CB )) or resid 236 through 314 or (resid 315 and (name \ N or name CA or name C or name O or name CB )) or resid 316 through 363 or (res \ id 364 and (name N or name CA or name C or name O or name CB )) or resid 365 thr \ ough 457 or (resid 458 through 459 and (name N or name CA or name C or name O or \ name CB )) or resid 460 through 465 or resid 601 through 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 2.220 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 29.410 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 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 : 0.008 0.106 10209 Z= 0.495 Angle : 0.936 9.704 13882 Z= 0.481 Chirality : 0.058 0.337 1557 Planarity : 0.005 0.047 1789 Dihedral : 15.513 84.427 3880 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.60 % Allowed : 8.97 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.35 (0.18), residues: 1272 helix: -4.61 (0.10), residues: 342 sheet: -3.63 (0.23), residues: 300 loop : -2.77 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 46 HIS 0.004 0.001 HIS B 329 PHE 0.018 0.002 PHE B 263 TYR 0.016 0.001 TYR C 426 ARG 0.003 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 182 time to evaluate : 1.204 Fit side-chains REVERT: A 50 PHE cc_start: 0.8789 (t80) cc_final: 0.8562 (t80) REVERT: A 219 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6821 (mt-10) REVERT: A 313 ASP cc_start: 0.8171 (t70) cc_final: 0.7848 (t0) REVERT: A 327 MET cc_start: 0.8442 (mtp) cc_final: 0.8171 (mtm) REVERT: A 330 MET cc_start: 0.9331 (mtt) cc_final: 0.8551 (mtt) REVERT: A 342 TYR cc_start: 0.8976 (OUTLIER) cc_final: 0.7043 (t80) REVERT: A 351 ASP cc_start: 0.8245 (t0) cc_final: 0.7928 (t0) REVERT: B 291 LYS cc_start: 0.8194 (tppt) cc_final: 0.7774 (tttp) REVERT: B 313 ASP cc_start: 0.8265 (t70) cc_final: 0.8018 (t0) REVERT: B 330 MET cc_start: 0.9270 (mtt) cc_final: 0.8499 (mtt) REVERT: B 342 TYR cc_start: 0.9029 (OUTLIER) cc_final: 0.8499 (t80) REVERT: C 63 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7203 (tm-30) REVERT: C 313 ASP cc_start: 0.8246 (t70) cc_final: 0.7835 (t0) REVERT: C 330 MET cc_start: 0.9240 (mtt) cc_final: 0.8682 (mtt) REVERT: C 342 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.7071 (t80) outliers start: 6 outliers final: 0 residues processed: 188 average time/residue: 0.2656 time to fit residues: 66.2579 Evaluate side-chains 134 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain C residue 342 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN A 329 HIS ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS B 276 GLN B 438 GLN C 276 GLN C 329 HIS ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10209 Z= 0.245 Angle : 0.584 7.591 13882 Z= 0.298 Chirality : 0.041 0.128 1557 Planarity : 0.004 0.039 1789 Dihedral : 6.838 58.531 1727 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.52 % Allowed : 16.23 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.20), residues: 1272 helix: -2.75 (0.20), residues: 390 sheet: -3.52 (0.25), residues: 279 loop : -2.20 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 46 HIS 0.006 0.001 HIS B 73 PHE 0.017 0.001 PHE A 301 TYR 0.018 0.001 TYR C 67 ARG 0.003 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 158 time to evaluate : 1.275 Fit side-chains revert: symmetry clash REVERT: A 219 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6708 (mt-10) REVERT: A 313 ASP cc_start: 0.7610 (t70) cc_final: 0.7235 (t0) REVERT: A 327 MET cc_start: 0.8445 (mtp) cc_final: 0.8177 (mtm) REVERT: A 330 MET cc_start: 0.9296 (mtt) cc_final: 0.8430 (mtt) REVERT: A 342 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.7168 (t80) REVERT: A 351 ASP cc_start: 0.8226 (t0) cc_final: 0.7883 (t0) REVERT: B 63 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7423 (tm-30) REVERT: B 291 LYS cc_start: 0.8204 (tppt) cc_final: 0.7777 (tttm) REVERT: B 330 MET cc_start: 0.9259 (mtt) cc_final: 0.8526 (mtt) REVERT: B 342 TYR cc_start: 0.9088 (OUTLIER) cc_final: 0.8647 (t80) REVERT: C 63 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7369 (tm-30) REVERT: C 211 LYS cc_start: 0.8424 (mtmt) cc_final: 0.7964 (mtpp) REVERT: C 313 ASP cc_start: 0.7486 (t70) cc_final: 0.7095 (t0) REVERT: C 342 TYR cc_start: 0.9115 (OUTLIER) cc_final: 0.7284 (t80) REVERT: C 351 ASP cc_start: 0.8191 (t0) cc_final: 0.7939 (t0) outliers start: 25 outliers final: 14 residues processed: 181 average time/residue: 0.1832 time to fit residues: 48.8615 Evaluate side-chains 148 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 423 LYS Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.0980 chunk 35 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN A 438 GLN B 66 GLN C 72 HIS C 252 GLN C 438 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10209 Z= 0.191 Angle : 0.536 8.072 13882 Z= 0.273 Chirality : 0.040 0.130 1557 Planarity : 0.003 0.037 1789 Dihedral : 6.300 59.118 1727 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.63 % Allowed : 18.55 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.22), residues: 1272 helix: -1.68 (0.24), residues: 390 sheet: -3.13 (0.29), residues: 237 loop : -1.84 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 46 HIS 0.003 0.001 HIS A 73 PHE 0.008 0.001 PHE C 98 TYR 0.016 0.001 TYR C 67 ARG 0.005 0.000 ARG B 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 143 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: A 313 ASP cc_start: 0.7575 (t70) cc_final: 0.7265 (t0) REVERT: A 327 MET cc_start: 0.8316 (mtp) cc_final: 0.7981 (mtm) REVERT: A 330 MET cc_start: 0.9185 (mtt) cc_final: 0.8310 (mtt) REVERT: A 342 TYR cc_start: 0.9007 (OUTLIER) cc_final: 0.7144 (t80) REVERT: A 351 ASP cc_start: 0.8191 (t0) cc_final: 0.7932 (t0) REVERT: B 63 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7333 (tm-30) REVERT: B 291 LYS cc_start: 0.8239 (tppt) cc_final: 0.8019 (ttmt) REVERT: B 327 MET cc_start: 0.8557 (mtp) cc_final: 0.8271 (mtp) REVERT: B 330 MET cc_start: 0.9198 (mtt) cc_final: 0.8475 (mtt) REVERT: B 342 TYR cc_start: 0.9029 (OUTLIER) cc_final: 0.8674 (t80) REVERT: B 399 GLN cc_start: 0.8063 (tm-30) cc_final: 0.7764 (tm-30) REVERT: C 211 LYS cc_start: 0.8495 (mtmt) cc_final: 0.7999 (mtpp) REVERT: C 313 ASP cc_start: 0.7457 (t70) cc_final: 0.7124 (t0) REVERT: C 342 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.7170 (t80) REVERT: C 351 ASP cc_start: 0.8234 (t0) cc_final: 0.7965 (t0) outliers start: 36 outliers final: 18 residues processed: 165 average time/residue: 0.1782 time to fit residues: 44.1720 Evaluate side-chains 160 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 423 LYS Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 0.0050 chunk 121 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 72 HIS C 66 GLN C 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10209 Z= 0.318 Angle : 0.583 8.462 13882 Z= 0.296 Chirality : 0.042 0.139 1557 Planarity : 0.003 0.035 1789 Dihedral : 6.282 58.945 1727 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.64 % Allowed : 17.84 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.23), residues: 1272 helix: -0.87 (0.27), residues: 372 sheet: -3.05 (0.27), residues: 303 loop : -1.62 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 46 HIS 0.005 0.001 HIS A 73 PHE 0.011 0.001 PHE C 442 TYR 0.013 0.001 TYR C 67 ARG 0.004 0.000 ARG C 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 138 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: A 313 ASP cc_start: 0.7564 (t70) cc_final: 0.7222 (t0) REVERT: A 327 MET cc_start: 0.8437 (mtp) cc_final: 0.8123 (mtm) REVERT: A 330 MET cc_start: 0.9258 (mtt) cc_final: 0.8409 (mtt) REVERT: A 342 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.7173 (t80) REVERT: A 345 CYS cc_start: 0.5776 (m) cc_final: 0.5337 (m) REVERT: A 351 ASP cc_start: 0.8263 (t0) cc_final: 0.7999 (t0) REVERT: B 63 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7350 (tm-30) REVERT: B 179 CYS cc_start: 0.6437 (OUTLIER) cc_final: 0.6061 (m) REVERT: B 291 LYS cc_start: 0.8219 (tppt) cc_final: 0.7997 (ttmt) REVERT: B 330 MET cc_start: 0.9171 (mtt) cc_final: 0.8468 (mtt) REVERT: B 342 TYR cc_start: 0.9007 (OUTLIER) cc_final: 0.8605 (t80) REVERT: B 345 CYS cc_start: 0.5492 (m) cc_final: 0.5113 (m) REVERT: B 351 ASP cc_start: 0.8061 (t0) cc_final: 0.7842 (t0) REVERT: B 399 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7831 (tm-30) REVERT: C 211 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8059 (mtpp) REVERT: C 313 ASP cc_start: 0.7465 (t70) cc_final: 0.7151 (t0) REVERT: C 342 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.7166 (t80) REVERT: C 351 ASP cc_start: 0.8245 (t0) cc_final: 0.7956 (t0) outliers start: 46 outliers final: 34 residues processed: 171 average time/residue: 0.1666 time to fit residues: 43.3534 Evaluate side-chains 168 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 130 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 423 LYS Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 103 optimal weight: 0.0670 chunk 84 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 438 GLN B 252 GLN B 438 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10209 Z= 0.166 Angle : 0.515 8.633 13882 Z= 0.257 Chirality : 0.040 0.130 1557 Planarity : 0.003 0.035 1789 Dihedral : 5.831 59.770 1727 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.03 % Allowed : 19.35 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.24), residues: 1272 helix: -0.66 (0.27), residues: 390 sheet: -2.91 (0.28), residues: 285 loop : -1.33 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 46 HIS 0.004 0.000 HIS A 73 PHE 0.011 0.001 PHE C 442 TYR 0.012 0.001 TYR A 417 ARG 0.003 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 151 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 58 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8271 (mm) REVERT: A 313 ASP cc_start: 0.7519 (t70) cc_final: 0.7180 (t0) REVERT: A 327 MET cc_start: 0.8305 (mtp) cc_final: 0.7962 (mtt) REVERT: A 330 MET cc_start: 0.9247 (mtt) cc_final: 0.8414 (mtt) REVERT: A 342 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.7254 (t80) REVERT: A 351 ASP cc_start: 0.8242 (t0) cc_final: 0.7934 (t0) REVERT: B 63 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7334 (tm-30) REVERT: B 291 LYS cc_start: 0.8238 (tppt) cc_final: 0.8031 (ttmt) REVERT: B 327 MET cc_start: 0.8599 (mtp) cc_final: 0.8329 (mtp) REVERT: B 330 MET cc_start: 0.9190 (mtt) cc_final: 0.8484 (mtt) REVERT: B 342 TYR cc_start: 0.9039 (OUTLIER) cc_final: 0.8493 (t80) REVERT: B 351 ASP cc_start: 0.7927 (t0) cc_final: 0.7714 (t0) REVERT: B 399 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7799 (tm-30) REVERT: C 211 LYS cc_start: 0.8512 (mtmt) cc_final: 0.8046 (mtpp) REVERT: C 313 ASP cc_start: 0.7387 (t70) cc_final: 0.7120 (t0) REVERT: C 342 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.7139 (t80) REVERT: C 351 ASP cc_start: 0.8181 (t0) cc_final: 0.7939 (t0) outliers start: 40 outliers final: 22 residues processed: 181 average time/residue: 0.1686 time to fit residues: 46.7994 Evaluate side-chains 169 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 423 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 9.9990 chunk 109 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10209 Z= 0.144 Angle : 0.494 7.712 13882 Z= 0.248 Chirality : 0.039 0.128 1557 Planarity : 0.003 0.035 1789 Dihedral : 5.632 59.274 1727 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.73 % Allowed : 20.36 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.25), residues: 1272 helix: -0.37 (0.28), residues: 390 sheet: -2.89 (0.28), residues: 297 loop : -1.00 (0.28), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 233 HIS 0.003 0.000 HIS A 73 PHE 0.011 0.001 PHE C 442 TYR 0.011 0.001 TYR B 417 ARG 0.003 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 153 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8194 (mm) REVERT: A 313 ASP cc_start: 0.7459 (t70) cc_final: 0.7174 (t0) REVERT: A 327 MET cc_start: 0.8271 (mtp) cc_final: 0.7918 (mtt) REVERT: A 330 MET cc_start: 0.9192 (mtt) cc_final: 0.8250 (mtt) REVERT: A 342 TYR cc_start: 0.8993 (OUTLIER) cc_final: 0.7143 (t80) REVERT: A 351 ASP cc_start: 0.8176 (t0) cc_final: 0.7963 (t0) REVERT: B 46 TRP cc_start: 0.8119 (OUTLIER) cc_final: 0.7386 (m100) REVERT: B 63 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7382 (tm-30) REVERT: B 291 LYS cc_start: 0.8311 (tppt) cc_final: 0.8098 (ttmt) REVERT: B 330 MET cc_start: 0.9110 (mtt) cc_final: 0.8333 (mtt) REVERT: B 342 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.8635 (t80) REVERT: B 351 ASP cc_start: 0.7965 (t0) cc_final: 0.7740 (t0) REVERT: B 399 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7795 (tm-30) REVERT: C 211 LYS cc_start: 0.8502 (mtmt) cc_final: 0.8044 (mtpp) REVERT: C 313 ASP cc_start: 0.7290 (t70) cc_final: 0.7025 (t0) REVERT: C 342 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.7099 (t80) REVERT: C 351 ASP cc_start: 0.8195 (t0) cc_final: 0.7939 (t0) outliers start: 37 outliers final: 25 residues processed: 179 average time/residue: 0.1741 time to fit residues: 47.8069 Evaluate side-chains 170 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 140 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 423 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 chunk 121 optimal weight: 0.0980 chunk 76 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10209 Z= 0.134 Angle : 0.486 7.019 13882 Z= 0.243 Chirality : 0.040 0.228 1557 Planarity : 0.003 0.042 1789 Dihedral : 5.486 58.842 1727 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.73 % Allowed : 21.47 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.25), residues: 1272 helix: -0.41 (0.27), residues: 414 sheet: -2.68 (0.35), residues: 201 loop : -1.01 (0.26), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 233 HIS 0.002 0.000 HIS A 73 PHE 0.011 0.001 PHE C 442 TYR 0.012 0.001 TYR A 417 ARG 0.002 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 155 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8159 (mm) REVERT: A 313 ASP cc_start: 0.7441 (t70) cc_final: 0.7151 (t0) REVERT: A 327 MET cc_start: 0.8005 (mtp) cc_final: 0.7436 (mtp) REVERT: A 330 MET cc_start: 0.9099 (mtt) cc_final: 0.8047 (mtt) REVERT: A 342 TYR cc_start: 0.9014 (OUTLIER) cc_final: 0.7163 (t80) REVERT: A 351 ASP cc_start: 0.8182 (t0) cc_final: 0.7958 (t0) REVERT: B 46 TRP cc_start: 0.8192 (OUTLIER) cc_final: 0.7391 (m100) REVERT: B 58 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7259 (pp) REVERT: B 63 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7371 (tm-30) REVERT: B 291 LYS cc_start: 0.8284 (tppt) cc_final: 0.8068 (ttmt) REVERT: B 330 MET cc_start: 0.9011 (mtt) cc_final: 0.8272 (mtt) REVERT: B 342 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.8530 (t80) REVERT: B 399 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7705 (tm-30) REVERT: C 211 LYS cc_start: 0.8458 (mtmt) cc_final: 0.8063 (mtpp) REVERT: C 342 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.7186 (t80) REVERT: C 351 ASP cc_start: 0.8145 (t0) cc_final: 0.7896 (t0) outliers start: 37 outliers final: 25 residues processed: 182 average time/residue: 0.1636 time to fit residues: 45.7219 Evaluate side-chains 173 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 423 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.2980 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 110 optimal weight: 0.4980 chunk 116 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 GLN C 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10209 Z= 0.136 Angle : 0.500 8.444 13882 Z= 0.245 Chirality : 0.040 0.260 1557 Planarity : 0.003 0.040 1789 Dihedral : 5.393 59.019 1727 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.93 % Allowed : 21.47 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.24), residues: 1272 helix: -0.34 (0.27), residues: 420 sheet: -2.79 (0.33), residues: 222 loop : -0.99 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 233 HIS 0.002 0.000 HIS A 73 PHE 0.007 0.001 PHE C 98 TYR 0.011 0.001 TYR A 417 ARG 0.002 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ASP cc_start: 0.7364 (t70) cc_final: 0.7087 (t0) REVERT: A 327 MET cc_start: 0.7945 (mtp) cc_final: 0.7391 (mtp) REVERT: A 330 MET cc_start: 0.9102 (mtt) cc_final: 0.8121 (mtt) REVERT: A 342 TYR cc_start: 0.9003 (OUTLIER) cc_final: 0.7158 (t80) REVERT: A 351 ASP cc_start: 0.8145 (t0) cc_final: 0.7921 (t0) REVERT: B 46 TRP cc_start: 0.8227 (OUTLIER) cc_final: 0.7409 (m100) REVERT: B 63 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7396 (tm-30) REVERT: B 291 LYS cc_start: 0.8314 (tppt) cc_final: 0.8079 (ttmt) REVERT: B 330 MET cc_start: 0.9022 (mtt) cc_final: 0.8251 (mtt) REVERT: B 342 TYR cc_start: 0.9005 (OUTLIER) cc_final: 0.8574 (t80) REVERT: B 399 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7723 (tm-30) REVERT: C 211 LYS cc_start: 0.8437 (mtmt) cc_final: 0.8050 (mtpp) REVERT: C 342 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.7119 (t80) REVERT: C 351 ASP cc_start: 0.8116 (t0) cc_final: 0.7862 (t0) outliers start: 39 outliers final: 28 residues processed: 182 average time/residue: 0.1640 time to fit residues: 45.7718 Evaluate side-chains 178 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 146 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 46 TRP Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 377 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 0.0970 chunk 102 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 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 329 HIS B 438 GLN C 252 GLN C 438 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10209 Z= 0.144 Angle : 0.502 8.583 13882 Z= 0.245 Chirality : 0.040 0.278 1557 Planarity : 0.003 0.042 1789 Dihedral : 5.341 59.109 1727 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.83 % Allowed : 21.88 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.25), residues: 1272 helix: -0.21 (0.27), residues: 417 sheet: -2.69 (0.33), residues: 222 loop : -0.95 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 233 HIS 0.002 0.000 HIS C 73 PHE 0.007 0.001 PHE C 98 TYR 0.011 0.001 TYR A 417 ARG 0.002 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 152 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 CYS cc_start: 0.6112 (OUTLIER) cc_final: 0.5580 (m) REVERT: A 313 ASP cc_start: 0.7384 (t70) cc_final: 0.7109 (t0) REVERT: A 327 MET cc_start: 0.7924 (mtp) cc_final: 0.7358 (mtp) REVERT: A 330 MET cc_start: 0.9100 (mtt) cc_final: 0.8111 (mtt) REVERT: A 342 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.7168 (t80) REVERT: A 351 ASP cc_start: 0.8133 (t0) cc_final: 0.7912 (t0) REVERT: B 46 TRP cc_start: 0.8205 (OUTLIER) cc_final: 0.7341 (m100) REVERT: B 63 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7402 (tm-30) REVERT: B 238 GLU cc_start: 0.7598 (pp20) cc_final: 0.7151 (tm-30) REVERT: B 291 LYS cc_start: 0.8314 (tppt) cc_final: 0.8072 (ttmt) REVERT: B 330 MET cc_start: 0.8972 (mtt) cc_final: 0.8047 (mtt) REVERT: B 342 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.8287 (t80) REVERT: B 399 GLN cc_start: 0.7964 (tm-30) cc_final: 0.7705 (tm-30) REVERT: C 211 LYS cc_start: 0.8452 (mtmt) cc_final: 0.8043 (mtpp) REVERT: C 313 ASP cc_start: 0.7089 (t0) cc_final: 0.6872 (t0) REVERT: C 342 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.7135 (t80) REVERT: C 351 ASP cc_start: 0.8146 (t0) cc_final: 0.7875 (t0) REVERT: C 382 PRO cc_start: 0.6752 (Cg_exo) cc_final: 0.6434 (Cg_endo) outliers start: 38 outliers final: 31 residues processed: 177 average time/residue: 0.1664 time to fit residues: 45.4592 Evaluate side-chains 179 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 143 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 46 TRP Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 377 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 115 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 61 optimal weight: 0.0040 chunk 79 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10209 Z= 0.144 Angle : 0.502 9.066 13882 Z= 0.246 Chirality : 0.041 0.297 1557 Planarity : 0.003 0.051 1789 Dihedral : 5.376 59.327 1727 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.73 % Allowed : 22.08 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.25), residues: 1272 helix: -0.18 (0.27), residues: 417 sheet: -2.63 (0.33), residues: 222 loop : -0.90 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 233 HIS 0.002 0.000 HIS C 73 PHE 0.010 0.001 PHE C 442 TYR 0.011 0.001 TYR A 417 ARG 0.002 0.000 ARG A 201 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 145 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 CYS cc_start: 0.6085 (OUTLIER) cc_final: 0.5554 (m) REVERT: A 313 ASP cc_start: 0.7388 (t70) cc_final: 0.7120 (t0) REVERT: A 327 MET cc_start: 0.7909 (mtp) cc_final: 0.7338 (mtp) REVERT: A 330 MET cc_start: 0.9065 (mtt) cc_final: 0.8082 (mtt) REVERT: A 342 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.7167 (t80) REVERT: A 351 ASP cc_start: 0.8098 (t0) cc_final: 0.7882 (t0) REVERT: B 46 TRP cc_start: 0.8206 (OUTLIER) cc_final: 0.7328 (m100) REVERT: B 238 GLU cc_start: 0.7577 (pp20) cc_final: 0.7084 (tm-30) REVERT: B 291 LYS cc_start: 0.8307 (tppt) cc_final: 0.8066 (ttmt) REVERT: B 330 MET cc_start: 0.9039 (mtt) cc_final: 0.8027 (mtt) REVERT: B 342 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.8368 (t80) REVERT: B 399 GLN cc_start: 0.7988 (tm-30) cc_final: 0.7725 (tm-30) REVERT: C 211 LYS cc_start: 0.8443 (mtmt) cc_final: 0.8045 (mtpp) REVERT: C 313 ASP cc_start: 0.7106 (t0) cc_final: 0.6878 (t0) REVERT: C 342 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.7083 (t80) REVERT: C 351 ASP cc_start: 0.8066 (t0) cc_final: 0.7817 (t0) REVERT: C 382 PRO cc_start: 0.6841 (Cg_exo) cc_final: 0.6526 (Cg_endo) outliers start: 37 outliers final: 30 residues processed: 169 average time/residue: 0.1581 time to fit residues: 41.6698 Evaluate side-chains 178 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 143 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 378 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 chunk 100 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 5 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.163045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.119694 restraints weight = 12999.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.123298 restraints weight = 7286.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.125417 restraints weight = 5370.432| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10209 Z= 0.131 Angle : 0.496 8.648 13882 Z= 0.242 Chirality : 0.040 0.284 1557 Planarity : 0.003 0.049 1789 Dihedral : 5.293 59.175 1727 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.83 % Allowed : 21.57 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.25), residues: 1272 helix: 0.00 (0.27), residues: 429 sheet: -2.55 (0.34), residues: 222 loop : -0.85 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP C 233 HIS 0.002 0.000 HIS C 73 PHE 0.008 0.001 PHE C 442 TYR 0.011 0.001 TYR A 417 ARG 0.002 0.000 ARG A 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2028.76 seconds wall clock time: 37 minutes 23.50 seconds (2243.50 seconds total)