Starting phenix.real_space_refine on Tue Aug 6 03:48:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxk_18730/08_2024/8qxk_18730.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxk_18730/08_2024/8qxk_18730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxk_18730/08_2024/8qxk_18730.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxk_18730/08_2024/8qxk_18730.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxk_18730/08_2024/8qxk_18730.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxk_18730/08_2024/8qxk_18730.cif" } resolution = 2.66 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= 0.003 sd= 0.158 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 36 5.49 5 Mg 12 5.21 5 S 80 5.16 5 C 9694 2.51 5 N 2646 2.21 5 O 2851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 127": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A GLU 496": "OE1" <-> "OE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C GLU 417": "OE1" <-> "OE2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B GLU 459": "OE1" <-> "OE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "D GLU 459": "OE1" <-> "OE2" Residue "D GLU 496": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15323 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3738 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3729 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 3742 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 458, 3734 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 458, 3734 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 3813 Chain: "D" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3738 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 94 Unusual residues: {' FE': 1, ' MG': 3, 'DCP': 1, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 94 Unusual residues: {' FE': 1, ' MG': 3, 'DCP': 1, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 94 Unusual residues: {' FE': 1, ' MG': 3, 'DCP': 1, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 94 Unusual residues: {' FE': 1, ' MG': 3, 'DCP': 1, 'DTP': 1, 'GTP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 10.46, per 1000 atoms: 0.68 Number of scatterers: 15323 At special positions: 0 Unit cell: (119.88, 104.76, 93.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 80 16.00 P 36 15.00 Mg 12 11.99 O 2851 8.00 N 2646 7.00 C 9694 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.36 Conformation dependent library (CDL) restraints added in 3.2 seconds 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3442 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 16 sheets defined 60.3% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 144 through 147 removed outlier: 3.518A pdb=" N ILE A 147 " --> pdb=" O LEU A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 144 through 147' Processing helix chain 'A' and resid 150 through 156 removed outlier: 3.766A pdb=" N TYR A 154 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 186 removed outlier: 4.000A pdb=" N HIS A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 190 removed outlier: 3.524A pdb=" N GLN A 190 " --> pdb=" O PRO A 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 190' Processing helix chain 'A' and resid 192 through 205 Processing helix chain 'A' and resid 214 through 220 removed outlier: 4.146A pdb=" N ASP A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.598A pdb=" N LEU A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 248 Processing helix chain 'A' and resid 250 through 257 removed outlier: 3.574A pdb=" N TYR A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 274 removed outlier: 4.113A pdb=" N CYS A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 removed outlier: 3.856A pdb=" N SER A 295 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE A 296 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU A 299 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 300 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 324 removed outlier: 3.683A pdb=" N TRP A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 324 " --> pdb=" O CYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 337 Processing helix chain 'A' and resid 355 through 373 Processing helix chain 'A' and resid 376 through 394 Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 410 through 414 removed outlier: 4.200A pdb=" N ILE A 413 " --> pdb=" O SER A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 424 through 432 removed outlier: 4.131A pdb=" N LEU A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 438 through 450 Processing helix chain 'A' and resid 469 through 473 removed outlier: 3.911A pdb=" N TYR A 473 " --> pdb=" O ARG A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.716A pdb=" N VAL A 537 " --> pdb=" O THR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 573 removed outlier: 3.541A pdb=" N ARG A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 137 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 144 through 147 removed outlier: 3.517A pdb=" N ILE C 147 " --> pdb=" O LEU C 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 144 through 147' Processing helix chain 'C' and resid 150 through 156 removed outlier: 3.765A pdb=" N TYR C 154 " --> pdb=" O GLY C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 186 removed outlier: 3.998A pdb=" N HIS C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 190 removed outlier: 3.653A pdb=" N GLN C 190 " --> pdb=" O PRO C 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 190' Processing helix chain 'C' and resid 192 through 205 Processing helix chain 'C' and resid 214 through 220 removed outlier: 4.189A pdb=" N ASP C 218 " --> pdb=" O SER C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 226 removed outlier: 3.590A pdb=" N LEU C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 248 Processing helix chain 'C' and resid 250 through 257 removed outlier: 3.590A pdb=" N TYR C 257 " --> pdb=" O VAL C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 274 removed outlier: 4.233A pdb=" N CYS C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 300 removed outlier: 3.906A pdb=" N SER C 295 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N PHE C 296 " --> pdb=" O ASN C 293 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU C 299 " --> pdb=" O PHE C 296 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE C 300 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 324 removed outlier: 3.681A pdb=" N TRP C 313 " --> pdb=" O ASP C 309 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY C 324 " --> pdb=" O CYS C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 337 Processing helix chain 'C' and resid 355 through 373 Processing helix chain 'C' and resid 376 through 394 Processing helix chain 'C' and resid 409 through 414 removed outlier: 3.615A pdb=" N ALA C 412 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE C 413 " --> pdb=" O SER C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 421 through 423 No H-bonds generated for 'chain 'C' and resid 421 through 423' Processing helix chain 'C' and resid 424 through 432 removed outlier: 4.123A pdb=" N LEU C 428 " --> pdb=" O ASP C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 437 No H-bonds generated for 'chain 'C' and resid 435 through 437' Processing helix chain 'C' and resid 438 through 450 Processing helix chain 'C' and resid 475 through 482 Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 533 through 538 removed outlier: 3.656A pdb=" N VAL C 537 " --> pdb=" O THR C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 574 removed outlier: 3.635A pdb=" N ALA C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 144 through 147 removed outlier: 3.514A pdb=" N ILE B 147 " --> pdb=" O LEU B 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 147' Processing helix chain 'B' and resid 150 through 156 removed outlier: 3.766A pdb=" N TYR B 154 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 186 removed outlier: 3.997A pdb=" N HIS B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 190 removed outlier: 3.618A pdb=" N GLN B 190 " --> pdb=" O PRO B 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 187 through 190' Processing helix chain 'B' and resid 192 through 205 Processing helix chain 'B' and resid 214 through 220 removed outlier: 4.180A pdb=" N ASP B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.601A pdb=" N LEU B 224 " --> pdb=" O ARG B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 248 Processing helix chain 'B' and resid 250 through 257 removed outlier: 3.567A pdb=" N TYR B 257 " --> pdb=" O VAL B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 274 removed outlier: 4.148A pdb=" N CYS B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.884A pdb=" N SER B 295 " --> pdb=" O GLU B 292 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N PHE B 296 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B 299 " --> pdb=" O PHE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 324 removed outlier: 3.699A pdb=" N TRP B 313 " --> pdb=" O ASP B 309 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B 324 " --> pdb=" O CYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 337 Processing helix chain 'B' and resid 355 through 373 Processing helix chain 'B' and resid 376 through 394 Processing helix chain 'B' and resid 409 through 414 removed outlier: 3.628A pdb=" N ALA B 412 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE B 413 " --> pdb=" O SER B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 421 through 423 No H-bonds generated for 'chain 'B' and resid 421 through 423' Processing helix chain 'B' and resid 424 through 432 removed outlier: 4.124A pdb=" N LEU B 428 " --> pdb=" O ASP B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 438 through 450 Processing helix chain 'B' and resid 469 through 474 removed outlier: 4.107A pdb=" N TYR B 473 " --> pdb=" O ARG B 470 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLU B 474 " --> pdb=" O GLU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 482 Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 533 through 538 removed outlier: 3.684A pdb=" N VAL B 537 " --> pdb=" O THR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 573 Processing helix chain 'D' and resid 129 through 137 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 144 through 147 removed outlier: 3.516A pdb=" N ILE D 147 " --> pdb=" O LEU D 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 144 through 147' Processing helix chain 'D' and resid 150 through 156 removed outlier: 3.761A pdb=" N TYR D 154 " --> pdb=" O GLY D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 186 removed outlier: 3.996A pdb=" N HIS D 167 " --> pdb=" O ASN D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 190 removed outlier: 3.551A pdb=" N GLN D 190 " --> pdb=" O PRO D 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 190' Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 214 through 220 removed outlier: 4.129A pdb=" N ASP D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 226 removed outlier: 3.602A pdb=" N LEU D 224 " --> pdb=" O ARG D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 248 Processing helix chain 'D' and resid 250 through 257 removed outlier: 3.578A pdb=" N TYR D 257 " --> pdb=" O VAL D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 274 removed outlier: 4.309A pdb=" N CYS D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 300 removed outlier: 3.882A pdb=" N SER D 295 " --> pdb=" O GLU D 292 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N PHE D 296 " --> pdb=" O ASN D 293 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU D 299 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE D 300 " --> pdb=" O LEU D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 324 removed outlier: 3.682A pdb=" N TRP D 313 " --> pdb=" O ASP D 309 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY D 324 " --> pdb=" O CYS D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 337 Processing helix chain 'D' and resid 355 through 373 Processing helix chain 'D' and resid 376 through 394 Processing helix chain 'D' and resid 402 through 404 No H-bonds generated for 'chain 'D' and resid 402 through 404' Processing helix chain 'D' and resid 410 through 414 removed outlier: 4.171A pdb=" N ILE D 413 " --> pdb=" O SER D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 421 through 423 No H-bonds generated for 'chain 'D' and resid 421 through 423' Processing helix chain 'D' and resid 424 through 432 removed outlier: 4.135A pdb=" N LEU D 428 " --> pdb=" O ASP D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 437 No H-bonds generated for 'chain 'D' and resid 435 through 437' Processing helix chain 'D' and resid 438 through 450 Processing helix chain 'D' and resid 469 through 473 removed outlier: 3.947A pdb=" N TYR D 473 " --> pdb=" O ARG D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 482 Processing helix chain 'D' and resid 494 through 496 No H-bonds generated for 'chain 'D' and resid 494 through 496' Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 533 through 538 removed outlier: 3.699A pdb=" N VAL D 537 " --> pdb=" O THR D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 574 removed outlier: 3.650A pdb=" N ALA D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 120 Processing sheet with id=AA2, first strand: chain 'A' and resid 339 through 342 removed outlier: 8.343A pdb=" N TYR A 521 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA A 351 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 400 Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 459 removed outlier: 6.994A pdb=" N VAL A 552 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU A 459 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE A 550 " --> pdb=" O GLU A 459 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 116 through 120 Processing sheet with id=AA6, first strand: chain 'C' and resid 339 through 342 removed outlier: 8.333A pdb=" N TYR C 521 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 351 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 399 through 400 Processing sheet with id=AA8, first strand: chain 'C' and resid 455 through 459 removed outlier: 6.980A pdb=" N VAL C 552 " --> pdb=" O VAL C 457 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU C 459 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE C 550 " --> pdb=" O GLU C 459 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 120 Processing sheet with id=AB1, first strand: chain 'B' and resid 339 through 343 removed outlier: 8.342A pdb=" N TYR B 521 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA B 351 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AB3, first strand: chain 'B' and resid 455 through 459 removed outlier: 6.986A pdb=" N VAL B 552 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU B 459 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE B 550 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 116 through 120 Processing sheet with id=AB5, first strand: chain 'D' and resid 339 through 342 removed outlier: 8.341A pdb=" N TYR D 521 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA D 351 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 399 through 400 Processing sheet with id=AB7, first strand: chain 'D' and resid 455 through 459 removed outlier: 6.975A pdb=" N VAL D 552 " --> pdb=" O VAL D 457 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU D 459 " --> pdb=" O ILE D 550 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE D 550 " --> pdb=" O GLU D 459 " (cutoff:3.500A) 704 hydrogen bonds defined for protein. 1908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.39 Time building geometry restraints manager: 5.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4943 1.34 - 1.46: 3456 1.46 - 1.58: 7104 1.58 - 1.69: 57 1.69 - 1.81: 120 Bond restraints: 15680 Sorted by residual: bond pdb=" C4 DCP C 706 " pdb=" C5 DCP C 706 " ideal model delta sigma weight residual 1.426 1.388 0.038 1.20e-02 6.94e+03 1.00e+01 bond pdb=" C4 DCP A 706 " pdb=" C5 DCP A 706 " ideal model delta sigma weight residual 1.426 1.388 0.038 1.20e-02 6.94e+03 9.90e+00 bond pdb=" O1A DCP B 707 " pdb=" PA DCP B 707 " ideal model delta sigma weight residual 1.477 1.508 -0.031 1.00e-02 1.00e+04 9.86e+00 bond pdb=" C4 DCP B 707 " pdb=" C5 DCP B 707 " ideal model delta sigma weight residual 1.426 1.389 0.037 1.20e-02 6.94e+03 9.74e+00 bond pdb=" C4 DCP D 707 " pdb=" C5 DCP D 707 " ideal model delta sigma weight residual 1.426 1.389 0.037 1.20e-02 6.94e+03 9.69e+00 ... (remaining 15675 not shown) Histogram of bond angle deviations from ideal: 98.51 - 106.78: 528 106.78 - 115.05: 9356 115.05 - 123.32: 10824 123.32 - 131.58: 506 131.58 - 139.85: 36 Bond angle restraints: 21250 Sorted by residual: angle pdb=" PB DCP D 707 " pdb=" O3B DCP D 707 " pdb=" PG DCP D 707 " ideal model delta sigma weight residual 139.87 120.17 19.70 1.00e+00 1.00e+00 3.88e+02 angle pdb=" PB DCP B 707 " pdb=" O3B DCP B 707 " pdb=" PG DCP B 707 " ideal model delta sigma weight residual 139.87 120.36 19.51 1.00e+00 1.00e+00 3.81e+02 angle pdb=" PB DCP A 706 " pdb=" O3B DCP A 706 " pdb=" PG DCP A 706 " ideal model delta sigma weight residual 139.87 120.50 19.37 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB DCP C 706 " pdb=" O3B DCP C 706 " pdb=" PG DCP C 706 " ideal model delta sigma weight residual 139.87 120.57 19.30 1.00e+00 1.00e+00 3.73e+02 angle pdb=" PA DCP C 706 " pdb=" O3A DCP C 706 " pdb=" PB DCP C 706 " ideal model delta sigma weight residual 136.83 122.46 14.37 1.00e+00 1.00e+00 2.06e+02 ... (remaining 21245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.50: 9116 33.50 - 67.01: 321 67.01 - 100.51: 61 100.51 - 134.01: 4 134.01 - 167.51: 4 Dihedral angle restraints: 9506 sinusoidal: 4146 harmonic: 5360 Sorted by residual: dihedral pdb=" O3A GTP D 702 " pdb=" O3B GTP D 702 " pdb=" PB GTP D 702 " pdb=" PG GTP D 702 " ideal model delta sinusoidal sigma weight residual 303.79 136.28 167.51 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O3A GTP B 702 " pdb=" O3B GTP B 702 " pdb=" PB GTP B 702 " pdb=" PG GTP B 702 " ideal model delta sinusoidal sigma weight residual 303.79 136.57 167.22 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O3A GTP C 701 " pdb=" O3B GTP C 701 " pdb=" PB GTP C 701 " pdb=" PG GTP C 701 " ideal model delta sinusoidal sigma weight residual 303.79 136.99 166.80 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 9503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1768 0.048 - 0.096: 341 0.096 - 0.145: 115 0.145 - 0.193: 9 0.193 - 0.241: 8 Chirality restraints: 2241 Sorted by residual: chirality pdb=" C3' DTP D 701 " pdb=" C2' DTP D 701 " pdb=" C4' DTP D 701 " pdb=" O3' DTP D 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.92 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C3' DTP C 707 " pdb=" C2' DTP C 707 " pdb=" C4' DTP C 707 " pdb=" O3' DTP C 707 " both_signs ideal model delta sigma weight residual False -2.68 -2.92 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C3' DTP B 701 " pdb=" C2' DTP B 701 " pdb=" C4' DTP B 701 " pdb=" O3' DTP B 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.92 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 2238 not shown) Planarity restraints: 2688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DCP B 707 " -0.017 2.00e-02 2.50e+03 6.56e-02 9.68e+01 pdb=" C2 DCP B 707 " 0.016 2.00e-02 2.50e+03 pdb=" C4 DCP B 707 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DCP B 707 " -0.116 2.00e-02 2.50e+03 pdb=" C6 DCP B 707 " 0.061 2.00e-02 2.50e+03 pdb=" N1 DCP B 707 " 0.059 2.00e-02 2.50e+03 pdb=" N3 DCP B 707 " 0.098 2.00e-02 2.50e+03 pdb=" N4 DCP B 707 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DCP B 707 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DCP C 706 " 0.019 2.00e-02 2.50e+03 6.50e-02 9.50e+01 pdb=" C2 DCP C 706 " -0.016 2.00e-02 2.50e+03 pdb=" C4 DCP C 706 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DCP C 706 " 0.115 2.00e-02 2.50e+03 pdb=" C6 DCP C 706 " -0.062 2.00e-02 2.50e+03 pdb=" N1 DCP C 706 " -0.059 2.00e-02 2.50e+03 pdb=" N3 DCP C 706 " -0.096 2.00e-02 2.50e+03 pdb=" N4 DCP C 706 " 0.004 2.00e-02 2.50e+03 pdb=" O2 DCP C 706 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DCP A 706 " -0.016 2.00e-02 2.50e+03 6.49e-02 9.47e+01 pdb=" C2 DCP A 706 " 0.015 2.00e-02 2.50e+03 pdb=" C4 DCP A 706 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DCP A 706 " -0.115 2.00e-02 2.50e+03 pdb=" C6 DCP A 706 " 0.059 2.00e-02 2.50e+03 pdb=" N1 DCP A 706 " 0.057 2.00e-02 2.50e+03 pdb=" N3 DCP A 706 " 0.098 2.00e-02 2.50e+03 pdb=" N4 DCP A 706 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DCP A 706 " -0.089 2.00e-02 2.50e+03 ... (remaining 2685 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 110 2.55 - 3.14: 11263 3.14 - 3.73: 22390 3.73 - 4.31: 33339 4.31 - 4.90: 55855 Nonbonded interactions: 122957 Sorted by model distance: nonbonded pdb=" O1B GTP C 701 " pdb="MG MG C 705 " model vdw 1.965 2.170 nonbonded pdb=" O1B GTP A 701 " pdb="MG MG A 705 " model vdw 1.968 2.170 nonbonded pdb=" O1B GTP D 702 " pdb="MG MG D 706 " model vdw 1.969 2.170 nonbonded pdb=" O1B GTP B 702 " pdb="MG MG B 706 " model vdw 1.969 2.170 nonbonded pdb=" OG1 THR B 463 " pdb=" OE1 GLN B 465 " model vdw 1.990 3.040 ... (remaining 122952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 114 through 469 or (resid 470 and (name N or name CA or na \ me C or name O or name CB )) or resid 471 through 483 or (resid 484 and (name N \ or name CA or name C or name O or name CB )) or resid 485 through 527 or resid 5 \ 29 through 576 or (resid 577 and (name N or name CA or name C or name O or name \ CB )) or resid 578 or resid 704 through 705)) selection = (chain 'B' and (resid 114 through 469 or (resid 470 and (name N or name CA or na \ me C or name O or name CB )) or resid 471 through 527 or resid 529 through 576 o \ r (resid 577 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 78 or resid 704 through 705)) selection = (chain 'C' and (resid 114 through 483 or (resid 484 and (name N or name CA or na \ me C or name O or name CB )) or resid 485 through 527 or resid 529 through 578 o \ r resid 704 through 705)) selection = (chain 'D' and (resid 114 through 469 or (resid 470 and (name N or name CA or na \ me C or name O or name CB )) or resid 471 through 483 or (resid 484 and (name N \ or name CA or name C or name O or name CB )) or resid 485 through 527 or resid 5 \ 29 through 576 or (resid 577 and (name N or name CA or name C or name O or name \ CB )) or resid 578 or resid 704 through 705)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 43.300 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 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 : 0.003 0.044 15680 Z= 0.228 Angle : 0.736 19.702 21250 Z= 0.506 Chirality : 0.046 0.241 2241 Planarity : 0.005 0.066 2688 Dihedral : 17.510 167.514 6064 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.20), residues: 1817 helix: 0.63 (0.19), residues: 896 sheet: 1.15 (0.48), residues: 120 loop : -1.20 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 572 HIS 0.005 0.001 HIS A 233 PHE 0.015 0.001 PHE B 165 TYR 0.021 0.002 TYR B 473 ARG 0.005 0.000 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.691 Fit side-chains REVERT: A 311 ASP cc_start: 0.8353 (t0) cc_final: 0.8120 (t0) REVERT: A 461 GLN cc_start: 0.7502 (tt0) cc_final: 0.7125 (tt0) REVERT: B 311 ASP cc_start: 0.8356 (t0) cc_final: 0.8068 (t0) REVERT: B 372 ARG cc_start: 0.7675 (mtm180) cc_final: 0.7127 (mtm180) REVERT: D 311 ASP cc_start: 0.8433 (t0) cc_final: 0.8226 (t0) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 1.5858 time to fit residues: 396.2100 Evaluate side-chains 180 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 0.0870 chunk 105 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 293 ASN A 527 ASN A 548 GLN C 293 ASN C 527 ASN B 293 ASN B 527 ASN D 215 HIS D 293 ASN D 527 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15680 Z= 0.239 Angle : 0.647 8.405 21250 Z= 0.343 Chirality : 0.047 0.203 2241 Planarity : 0.005 0.043 2688 Dihedral : 15.685 171.716 2306 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.52 % Rotamer: Outliers : 1.18 % Allowed : 8.05 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.19), residues: 1817 helix: 0.89 (0.18), residues: 900 sheet: 1.51 (0.47), residues: 120 loop : -1.17 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 572 HIS 0.007 0.002 HIS A 233 PHE 0.016 0.002 PHE B 165 TYR 0.033 0.002 TYR B 315 ARG 0.004 0.000 ARG D 339 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 178 time to evaluate : 1.700 Fit side-chains REVERT: A 461 GLN cc_start: 0.7538 (tt0) cc_final: 0.7146 (tt0) REVERT: A 475 SER cc_start: 0.7242 (OUTLIER) cc_final: 0.6993 (t) outliers start: 19 outliers final: 6 residues processed: 194 average time/residue: 1.5756 time to fit residues: 331.6506 Evaluate side-chains 176 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 169 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain D residue 365 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN C 527 ASN C 535 ASN B 345 ASN B 527 ASN D 215 HIS D 527 ASN D 535 ASN D 548 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15680 Z= 0.283 Angle : 0.667 9.241 21250 Z= 0.351 Chirality : 0.048 0.176 2241 Planarity : 0.005 0.040 2688 Dihedral : 15.518 173.981 2306 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.97 % Favored : 96.97 % Rotamer: Outliers : 2.11 % Allowed : 9.67 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.19), residues: 1817 helix: 0.77 (0.18), residues: 904 sheet: 1.47 (0.47), residues: 120 loop : -1.12 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 572 HIS 0.007 0.002 HIS C 162 PHE 0.015 0.002 PHE B 165 TYR 0.031 0.002 TYR B 315 ARG 0.004 0.001 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 185 time to evaluate : 1.847 Fit side-chains REVERT: A 372 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.6762 (mtp180) REVERT: A 461 GLN cc_start: 0.7568 (tt0) cc_final: 0.7187 (tt0) REVERT: A 475 SER cc_start: 0.7493 (p) cc_final: 0.7141 (t) REVERT: B 429 GLU cc_start: 0.7571 (tt0) cc_final: 0.7351 (tm-30) REVERT: D 429 GLU cc_start: 0.7474 (tt0) cc_final: 0.7156 (tm-30) outliers start: 34 outliers final: 15 residues processed: 209 average time/residue: 1.5151 time to fit residues: 344.3014 Evaluate side-chains 191 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 175 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 155 optimal weight: 0.1980 chunk 46 optimal weight: 3.9990 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 527 ASN A 536 GLN C 527 ASN C 535 ASN C 536 GLN C 539 GLN B 527 ASN B 535 ASN B 536 GLN D 215 HIS D 527 ASN D 535 ASN D 536 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15680 Z= 0.238 Angle : 0.622 9.043 21250 Z= 0.327 Chirality : 0.046 0.166 2241 Planarity : 0.005 0.039 2688 Dihedral : 15.226 179.165 2306 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.52 % Rotamer: Outliers : 2.17 % Allowed : 10.97 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.19), residues: 1817 helix: 0.99 (0.18), residues: 880 sheet: 1.46 (0.48), residues: 120 loop : -1.04 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 285 HIS 0.007 0.002 HIS A 233 PHE 0.015 0.002 PHE B 165 TYR 0.029 0.002 TYR B 315 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 180 time to evaluate : 1.793 Fit side-chains REVERT: A 372 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.6691 (mtp180) REVERT: A 475 SER cc_start: 0.7520 (p) cc_final: 0.7109 (t) REVERT: B 429 GLU cc_start: 0.7560 (tt0) cc_final: 0.7339 (tm-30) REVERT: D 429 GLU cc_start: 0.7465 (tt0) cc_final: 0.7154 (tm-30) outliers start: 35 outliers final: 14 residues processed: 205 average time/residue: 1.4436 time to fit residues: 322.8778 Evaluate side-chains 184 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 169 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 148 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN C 527 ASN C 535 ASN C 539 GLN B 345 ASN B 527 ASN B 535 ASN D 527 ASN D 535 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15680 Z= 0.211 Angle : 0.598 8.688 21250 Z= 0.313 Chirality : 0.045 0.156 2241 Planarity : 0.004 0.039 2688 Dihedral : 14.790 175.438 2306 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.48 % Favored : 97.47 % Rotamer: Outliers : 2.42 % Allowed : 11.71 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.20), residues: 1817 helix: 1.10 (0.18), residues: 880 sheet: 1.50 (0.48), residues: 120 loop : -0.96 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 572 HIS 0.007 0.002 HIS A 233 PHE 0.014 0.002 PHE B 165 TYR 0.027 0.002 TYR B 315 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 179 time to evaluate : 1.851 Fit side-chains REVERT: A 242 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7167 (tm-30) REVERT: A 372 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.6666 (mtp180) REVERT: A 475 SER cc_start: 0.7493 (OUTLIER) cc_final: 0.7143 (t) REVERT: B 429 GLU cc_start: 0.7548 (tt0) cc_final: 0.7312 (tm-30) REVERT: D 429 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7133 (tm-30) REVERT: D 478 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.7183 (mttt) outliers start: 39 outliers final: 19 residues processed: 209 average time/residue: 1.4492 time to fit residues: 333.6713 Evaluate side-chains 196 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 172 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 80 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 91 optimal weight: 0.0470 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN C 527 ASN C 535 ASN C 539 GLN B 527 ASN B 535 ASN D 215 HIS D 527 ASN D 535 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15680 Z= 0.144 Angle : 0.529 7.463 21250 Z= 0.275 Chirality : 0.043 0.135 2241 Planarity : 0.004 0.037 2688 Dihedral : 13.196 162.383 2306 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.20 % Favored : 97.74 % Rotamer: Outliers : 1.73 % Allowed : 12.83 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1817 helix: 1.45 (0.18), residues: 880 sheet: 1.70 (0.48), residues: 120 loop : -0.77 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 313 HIS 0.005 0.001 HIS A 233 PHE 0.014 0.001 PHE B 165 TYR 0.024 0.001 TYR B 315 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 189 time to evaluate : 1.675 Fit side-chains REVERT: A 242 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7227 (tm-30) REVERT: A 372 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6568 (mtp180) REVERT: A 429 GLU cc_start: 0.7449 (tt0) cc_final: 0.7247 (tm-30) REVERT: A 461 GLN cc_start: 0.7498 (tt0) cc_final: 0.7117 (tt0) REVERT: A 475 SER cc_start: 0.7437 (p) cc_final: 0.7029 (t) REVERT: C 429 GLU cc_start: 0.7519 (tt0) cc_final: 0.7287 (tm-30) REVERT: B 429 GLU cc_start: 0.7501 (tt0) cc_final: 0.7278 (tm-30) REVERT: D 429 GLU cc_start: 0.7421 (tt0) cc_final: 0.7107 (tm-30) REVERT: D 478 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.7159 (mttt) outliers start: 28 outliers final: 15 residues processed: 212 average time/residue: 1.4330 time to fit residues: 331.6874 Evaluate side-chains 194 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 176 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 527 ASN C 535 ASN C 539 GLN B 527 ASN B 535 ASN B 539 GLN D 527 ASN D 535 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15680 Z= 0.209 Angle : 0.597 8.364 21250 Z= 0.311 Chirality : 0.045 0.150 2241 Planarity : 0.004 0.038 2688 Dihedral : 13.324 159.667 2306 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.58 % Rotamer: Outliers : 1.98 % Allowed : 13.20 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 1817 helix: 1.30 (0.18), residues: 880 sheet: 1.74 (0.49), residues: 120 loop : -0.84 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 572 HIS 0.006 0.001 HIS A 233 PHE 0.013 0.002 PHE B 165 TYR 0.026 0.002 TYR B 315 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 180 time to evaluate : 1.784 Fit side-chains REVERT: A 242 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7119 (tm-30) REVERT: A 372 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.6644 (mtp180) REVERT: A 475 SER cc_start: 0.7475 (OUTLIER) cc_final: 0.7132 (t) REVERT: C 429 GLU cc_start: 0.7526 (tt0) cc_final: 0.7296 (tm-30) REVERT: B 429 GLU cc_start: 0.7520 (tt0) cc_final: 0.7303 (tm-30) REVERT: D 429 GLU cc_start: 0.7441 (tt0) cc_final: 0.7125 (tm-30) REVERT: D 478 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.7188 (mttt) outliers start: 32 outliers final: 18 residues processed: 206 average time/residue: 1.3568 time to fit residues: 306.6534 Evaluate side-chains 195 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 173 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 0.0570 chunk 33 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN C 328 ASN C 527 ASN C 535 ASN C 539 GLN B 527 ASN B 535 ASN B 539 GLN D 527 ASN D 535 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15680 Z= 0.174 Angle : 0.563 7.736 21250 Z= 0.293 Chirality : 0.044 0.137 2241 Planarity : 0.004 0.037 2688 Dihedral : 12.621 158.869 2306 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.15 % Favored : 97.80 % Rotamer: Outliers : 1.80 % Allowed : 13.57 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1817 helix: 1.41 (0.18), residues: 880 sheet: 1.83 (0.49), residues: 120 loop : -0.76 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 572 HIS 0.006 0.001 HIS A 233 PHE 0.013 0.001 PHE B 165 TYR 0.027 0.002 TYR C 331 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 173 time to evaluate : 1.606 Fit side-chains REVERT: A 242 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7179 (tm-30) REVERT: A 372 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.6562 (mtp180) REVERT: A 475 SER cc_start: 0.7443 (OUTLIER) cc_final: 0.7023 (t) REVERT: C 315 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.7640 (p90) REVERT: C 429 GLU cc_start: 0.7513 (tt0) cc_final: 0.7275 (tm-30) REVERT: B 429 GLU cc_start: 0.7514 (tt0) cc_final: 0.7277 (tm-30) REVERT: D 429 GLU cc_start: 0.7428 (tt0) cc_final: 0.7105 (tm-30) REVERT: D 478 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.7174 (mttt) outliers start: 29 outliers final: 18 residues processed: 199 average time/residue: 1.3683 time to fit residues: 298.6111 Evaluate side-chains 191 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 168 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 126 optimal weight: 0.0970 chunk 49 optimal weight: 0.0970 chunk 146 optimal weight: 0.1980 chunk 152 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN C 527 ASN C 535 ASN C 539 GLN B 527 ASN B 535 ASN B 539 GLN D 527 ASN D 535 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15680 Z= 0.165 Angle : 0.552 7.505 21250 Z= 0.287 Chirality : 0.044 0.135 2241 Planarity : 0.004 0.037 2688 Dihedral : 12.156 158.005 2306 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.20 % Favored : 97.74 % Rotamer: Outliers : 1.98 % Allowed : 13.82 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.20), residues: 1817 helix: 1.43 (0.18), residues: 884 sheet: 1.86 (0.49), residues: 120 loop : -0.71 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 572 HIS 0.006 0.001 HIS A 233 PHE 0.014 0.001 PHE B 165 TYR 0.026 0.002 TYR A 331 ARG 0.002 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 172 time to evaluate : 1.884 Fit side-chains REVERT: A 242 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7195 (tm-30) REVERT: A 262 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.5999 (mp0) REVERT: A 372 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.6505 (mtp180) REVERT: A 475 SER cc_start: 0.7456 (OUTLIER) cc_final: 0.7042 (t) REVERT: C 315 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7651 (p90) REVERT: C 429 GLU cc_start: 0.7462 (tt0) cc_final: 0.7220 (tm-30) REVERT: B 429 GLU cc_start: 0.7507 (tt0) cc_final: 0.7256 (tm-30) REVERT: D 429 GLU cc_start: 0.7423 (tt0) cc_final: 0.7097 (tm-30) REVERT: D 478 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.7160 (mttt) outliers start: 32 outliers final: 20 residues processed: 200 average time/residue: 1.3729 time to fit residues: 300.9438 Evaluate side-chains 196 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 110 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN C 328 ASN C 527 ASN C 535 ASN C 539 GLN B 527 ASN B 535 ASN B 539 GLN D 527 ASN D 535 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15680 Z= 0.181 Angle : 0.571 7.514 21250 Z= 0.297 Chirality : 0.044 0.139 2241 Planarity : 0.004 0.038 2688 Dihedral : 12.219 158.115 2306 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.20 % Favored : 97.74 % Rotamer: Outliers : 1.86 % Allowed : 14.13 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.20), residues: 1817 helix: 1.42 (0.18), residues: 880 sheet: 1.75 (0.48), residues: 120 loop : -0.77 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 572 HIS 0.007 0.001 HIS A 233 PHE 0.013 0.001 PHE B 165 TYR 0.028 0.002 TYR C 331 ARG 0.003 0.000 ARG A 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 170 time to evaluate : 1.635 Fit side-chains REVERT: A 242 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7180 (tm-30) REVERT: A 372 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.6570 (mtp180) REVERT: A 429 GLU cc_start: 0.7445 (tt0) cc_final: 0.7211 (tm-30) REVERT: A 475 SER cc_start: 0.7464 (OUTLIER) cc_final: 0.7034 (t) REVERT: C 315 TYR cc_start: 0.7965 (OUTLIER) cc_final: 0.7660 (p90) REVERT: C 429 GLU cc_start: 0.7507 (tt0) cc_final: 0.7264 (tm-30) REVERT: B 429 GLU cc_start: 0.7495 (tt0) cc_final: 0.7267 (tm-30) REVERT: D 429 GLU cc_start: 0.7432 (tt0) cc_final: 0.7105 (tm-30) REVERT: D 478 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.7158 (mttt) outliers start: 30 outliers final: 21 residues processed: 196 average time/residue: 1.3863 time to fit residues: 297.2815 Evaluate side-chains 192 residues out of total 1623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN C 527 ASN C 535 ASN C 539 GLN B 527 ASN B 535 ASN B 539 GLN D 527 ASN D 535 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.163867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.134246 restraints weight = 20650.601| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.68 r_work: 0.3194 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15680 Z= 0.193 Angle : 0.582 7.769 21250 Z= 0.303 Chirality : 0.045 0.142 2241 Planarity : 0.004 0.038 2688 Dihedral : 12.305 158.467 2306 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.26 % Favored : 97.69 % Rotamer: Outliers : 1.98 % Allowed : 13.94 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.20), residues: 1817 helix: 1.37 (0.18), residues: 880 sheet: 1.71 (0.48), residues: 120 loop : -0.78 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 572 HIS 0.006 0.001 HIS A 233 PHE 0.013 0.001 PHE B 165 TYR 0.028 0.002 TYR A 331 ARG 0.003 0.000 ARG D 305 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5624.99 seconds wall clock time: 98 minutes 56.30 seconds (5936.30 seconds total)