Starting phenix.real_space_refine on Sat Jul 4 20:13:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e4t_30987/07_2026/7e4t_30987.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e4t_30987/07_2026/7e4t_30987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e4t_30987/07_2026/7e4t_30987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e4t_30987/07_2026/7e4t_30987.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7e4t_30987/07_2026/7e4t_30987.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e4t_30987/07_2026/7e4t_30987.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e4t_30987/07_2026/7e4t_30987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e4t_30987/07_2026/7e4t_30987.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.176 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 Ca 4 9.91 5 Zn 4 6.06 5 P 8 5.49 5 S 116 5.16 5 C 14632 2.51 5 N 3564 2.21 5 O 3948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22276 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5412 Classifications: {'peptide': 664} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 639} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1148 SG CYS A 176 14.234 43.015 61.526 1.00172.12 S ATOM 1162 SG CYS A 178 13.069 40.045 59.271 1.00194.88 S ATOM 1184 SG CYS A 181 16.749 40.871 59.364 1.00197.66 S Restraints were copied for chains: B, C, D Time building chain proxies: 5.19, per 1000 atoms: 0.23 Number of scatterers: 22276 At special positions: 0 Unit cell: (113.905, 113.905, 136.895, 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) Zn 4 29.99 Ca 4 19.99 S 116 16.00 P 8 15.00 O 3948 8.00 N 3564 7.00 C 14632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.03 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 176 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 181 " pdb=" ZN B 804 " pdb="ZN ZN B 804 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 176 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 178 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 181 " pdb=" ZN C 804 " pdb="ZN ZN C 804 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 176 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 181 " pdb=" ZN D 804 " pdb="ZN ZN D 804 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 176 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 178 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 181 " Number of angles added : 12 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5120 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 4 sheets defined 77.3% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 44 through 59 removed outlier: 3.693A pdb=" N ILE A 57 " --> pdb=" O GLN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 164 removed outlier: 3.810A pdb=" N LYS A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 188 through 204 removed outlier: 3.504A pdb=" N SER A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 237 through 258 removed outlier: 3.889A pdb=" N TYR A 241 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 362 through 385 removed outlier: 3.913A pdb=" N SER A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 426 Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 427 through 432 Processing helix chain 'A' and resid 435 through 460 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 493 through 500 removed outlier: 3.782A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 540 removed outlier: 4.102A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing helix chain 'A' and resid 567 through 580 removed outlier: 3.695A pdb=" N VAL A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 588 removed outlier: 3.636A pdb=" N VAL A 587 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 613 Processing helix chain 'A' and resid 614 through 633 removed outlier: 3.812A pdb=" N ASN A 618 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN A 629 " --> pdb=" O ASN A 625 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 630 " --> pdb=" O ASN A 626 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP A 633 " --> pdb=" O GLN A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 650 removed outlier: 3.700A pdb=" N TYR A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 731 Processing helix chain 'A' and resid 740 through 761 Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.693A pdb=" N ILE B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 98 through 106 Processing helix chain 'B' and resid 108 through 118 Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 164 removed outlier: 3.810A pdb=" N LYS B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 188 through 204 removed outlier: 3.503A pdb=" N SER B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 215 through 234 Processing helix chain 'B' and resid 237 through 258 removed outlier: 3.889A pdb=" N TYR B 241 " --> pdb=" O PHE B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 362 through 385 removed outlier: 3.913A pdb=" N SER B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 426 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 427 through 432 Processing helix chain 'B' and resid 435 through 460 Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 473 through 492 Processing helix chain 'B' and resid 493 through 500 removed outlier: 3.782A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 540 removed outlier: 4.101A pdb=" N LEU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 567 through 580 removed outlier: 3.695A pdb=" N VAL B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE B 580 " --> pdb=" O PHE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 588 removed outlier: 3.636A pdb=" N VAL B 587 " --> pdb=" O ASN B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 613 Processing helix chain 'B' and resid 614 through 633 removed outlier: 3.813A pdb=" N ASN B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN B 629 " --> pdb=" O ASN B 625 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 630 " --> pdb=" O ASN B 626 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 650 removed outlier: 3.700A pdb=" N TYR B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 731 Processing helix chain 'B' and resid 740 through 761 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 44 through 59 removed outlier: 3.693A pdb=" N ILE C 57 " --> pdb=" O GLN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 98 through 106 Processing helix chain 'C' and resid 108 through 118 Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 164 removed outlier: 3.810A pdb=" N LYS C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 204 removed outlier: 3.504A pdb=" N SER C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 215 through 234 Processing helix chain 'C' and resid 237 through 258 removed outlier: 3.889A pdb=" N TYR C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 326 through 340 Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'C' and resid 362 through 385 removed outlier: 3.912A pdb=" N SER C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 426 Proline residue: C 409 - end of helix Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 435 through 460 Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 473 through 492 Processing helix chain 'C' and resid 493 through 500 removed outlier: 3.782A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 540 removed outlier: 4.101A pdb=" N LEU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 567 through 580 removed outlier: 3.695A pdb=" N VAL C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE C 580 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 588 removed outlier: 3.636A pdb=" N VAL C 587 " --> pdb=" O ASN C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 613 Processing helix chain 'C' and resid 614 through 633 removed outlier: 3.812A pdb=" N ASN C 618 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN C 629 " --> pdb=" O ASN C 625 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 630 " --> pdb=" O ASN C 626 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 631 " --> pdb=" O SER C 627 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP C 633 " --> pdb=" O GLN C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 650 removed outlier: 3.701A pdb=" N TYR C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 731 Processing helix chain 'C' and resid 740 through 761 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 44 through 59 removed outlier: 3.693A pdb=" N ILE D 57 " --> pdb=" O GLN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 108 through 118 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 164 removed outlier: 3.810A pdb=" N LYS D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 188 through 204 removed outlier: 3.504A pdb=" N SER D 193 " --> pdb=" O SER D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 211 Processing helix chain 'D' and resid 215 through 234 Processing helix chain 'D' and resid 237 through 258 removed outlier: 3.888A pdb=" N TYR D 241 " --> pdb=" O PHE D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 326 through 340 Processing helix chain 'D' and resid 340 through 351 Processing helix chain 'D' and resid 362 through 385 removed outlier: 3.912A pdb=" N SER D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 426 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 427 through 432 Processing helix chain 'D' and resid 435 through 460 Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 473 through 492 Processing helix chain 'D' and resid 493 through 500 removed outlier: 3.782A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 540 removed outlier: 4.102A pdb=" N LEU D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP D 516 " --> pdb=" O ARG D 512 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE D 522 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 567 through 580 removed outlier: 3.695A pdb=" N VAL D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE D 580 " --> pdb=" O PHE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 588 removed outlier: 3.635A pdb=" N VAL D 587 " --> pdb=" O ASN D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 613 Processing helix chain 'D' and resid 614 through 633 removed outlier: 3.812A pdb=" N ASN D 618 " --> pdb=" O VAL D 614 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN D 629 " --> pdb=" O ASN D 625 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 630 " --> pdb=" O ASN D 626 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE D 631 " --> pdb=" O SER D 627 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP D 633 " --> pdb=" O GLN D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 650 removed outlier: 3.701A pdb=" N TYR D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 731 Processing helix chain 'D' and resid 740 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.149A pdb=" N VAL B 166 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 removed outlier: 4.148A pdb=" N VAL A 166 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 18 through 20 removed outlier: 4.148A pdb=" N VAL C 166 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 18 through 20 removed outlier: 4.149A pdb=" N VAL D 166 " --> pdb=" O LEU C 20 " (cutoff:3.500A) 1432 hydrogen bonds defined for protein. 4200 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: 3.71 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3500 1.32 - 1.44: 6112 1.44 - 1.57: 12960 1.57 - 1.69: 16 1.69 - 1.81: 188 Bond restraints: 22776 Sorted by residual: bond pdb=" C12 YZY D 806 " pdb=" C13 YZY D 806 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C12 YZY A 806 " pdb=" C13 YZY A 806 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C12 YZY C 806 " pdb=" C13 YZY C 806 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C12 YZY B 806 " pdb=" C13 YZY B 806 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C28 YZY B 806 " pdb=" C29 YZY B 806 " ideal model delta sigma weight residual 1.332 1.504 -0.172 2.00e-02 2.50e+03 7.40e+01 ... (remaining 22771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.11: 30604 4.11 - 8.22: 128 8.22 - 12.32: 36 12.32 - 16.43: 12 16.43 - 20.54: 4 Bond angle restraints: 30784 Sorted by residual: angle pdb=" C27 YZY D 806 " pdb=" C28 YZY D 806 " pdb=" C29 YZY D 806 " ideal model delta sigma weight residual 128.13 107.59 20.54 3.00e+00 1.11e-01 4.69e+01 angle pdb=" C27 YZY A 806 " pdb=" C28 YZY A 806 " pdb=" C29 YZY A 806 " ideal model delta sigma weight residual 128.13 107.62 20.51 3.00e+00 1.11e-01 4.68e+01 angle pdb=" C27 YZY C 806 " pdb=" C28 YZY C 806 " pdb=" C29 YZY C 806 " ideal model delta sigma weight residual 128.13 107.64 20.49 3.00e+00 1.11e-01 4.67e+01 angle pdb=" C27 YZY B 806 " pdb=" C28 YZY B 806 " pdb=" C29 YZY B 806 " ideal model delta sigma weight residual 128.13 107.65 20.48 3.00e+00 1.11e-01 4.66e+01 angle pdb=" C21 YZY C 806 " pdb=" C20 YZY C 806 " pdb=" O4 YZY C 806 " ideal model delta sigma weight residual 111.77 126.25 -14.48 3.00e+00 1.11e-01 2.33e+01 ... (remaining 30779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 13352 34.84 - 69.68: 212 69.68 - 104.52: 16 104.52 - 139.36: 8 139.36 - 174.21: 12 Dihedral angle restraints: 13600 sinusoidal: 5736 harmonic: 7864 Sorted by residual: dihedral pdb=" C26 YZY B 806 " pdb=" C27 YZY B 806 " pdb=" C28 YZY B 806 " pdb=" C29 YZY B 806 " ideal model delta sinusoidal sigma weight residual 119.11 -66.68 -174.21 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C26 YZY A 806 " pdb=" C27 YZY A 806 " pdb=" C28 YZY A 806 " pdb=" C29 YZY A 806 " ideal model delta sinusoidal sigma weight residual 119.11 -66.70 -174.19 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C26 YZY C 806 " pdb=" C27 YZY C 806 " pdb=" C28 YZY C 806 " pdb=" C29 YZY C 806 " ideal model delta sinusoidal sigma weight residual 119.11 -66.70 -174.19 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 13597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2832 0.046 - 0.092: 520 0.092 - 0.138: 76 0.138 - 0.185: 8 0.185 - 0.231: 8 Chirality restraints: 3444 Sorted by residual: chirality pdb=" CBI Y01 A 803 " pdb=" CAU Y01 A 803 " pdb=" CBE Y01 A 803 " pdb=" CBG Y01 A 803 " both_signs ideal model delta sigma weight residual False 2.94 2.71 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CBI Y01 B 803 " pdb=" CAU Y01 B 803 " pdb=" CBE Y01 B 803 " pdb=" CBG Y01 B 803 " both_signs ideal model delta sigma weight residual False 2.94 2.71 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CBI Y01 C 803 " pdb=" CAU Y01 C 803 " pdb=" CBE Y01 C 803 " pdb=" CBG Y01 C 803 " both_signs ideal model delta sigma weight residual False 2.94 2.71 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 3441 not shown) Planarity restraints: 3784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 573 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C GLN C 573 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN C 573 " 0.008 2.00e-02 2.50e+03 pdb=" N SER C 574 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 573 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C GLN B 573 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN B 573 " 0.008 2.00e-02 2.50e+03 pdb=" N SER B 574 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 573 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C GLN D 573 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN D 573 " 0.008 2.00e-02 2.50e+03 pdb=" N SER D 574 " 0.007 2.00e-02 2.50e+03 ... (remaining 3781 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 5587 2.80 - 3.33: 21748 3.33 - 3.85: 37197 3.85 - 4.38: 44011 4.38 - 4.90: 75825 Nonbonded interactions: 184368 Sorted by model distance: nonbonded pdb=" OG1 THR B 140 " pdb=" OD1 ASP B 142 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR D 140 " pdb=" OD1 ASP D 142 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR C 140 " pdb=" OD1 ASP C 142 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR A 140 " pdb=" OD1 ASP A 142 " model vdw 2.279 3.040 nonbonded pdb=" OD1 ASP C 215 " pdb=" OH TYR C 713 " model vdw 2.328 3.040 ... (remaining 184363 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.620 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 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 : 0.007 0.204 22796 Z= 0.345 Angle : 0.791 20.541 30804 Z= 0.323 Chirality : 0.036 0.231 3444 Planarity : 0.003 0.029 3784 Dihedral : 13.887 174.205 8468 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.01 % Allowed : 3.21 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.15), residues: 2608 helix: 0.88 (0.11), residues: 1948 sheet: None (None), residues: 0 loop : -0.35 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 222 TYR 0.010 0.001 TYR A 524 PHE 0.014 0.001 PHE D 341 TRP 0.008 0.001 TRP B 639 HIS 0.001 0.000 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.34 (22776) covalent geometry : angle 0.78570 / 0.32 (30784) SS BOND : bond 0.00035 / 0.02 ( 4) SS BOND : angle 0.34789 / 0.21 ( 8) hydrogen bonds : bond 0.11980 / 8.29 ( 1432) hydrogen bonds : angle 4.63947 / 3.39 ( 4200) metal coordination : bond 0.06300 / 4.98 ( 16) metal coordination : angle 4.89818 / 3.75 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 484 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.6611 (mt-10) cc_final: 0.6372 (mt-10) REVERT: A 42 LYS cc_start: 0.6697 (mtmt) cc_final: 0.6411 (mmtt) REVERT: A 54 GLU cc_start: 0.6850 (tt0) cc_final: 0.5948 (tm-30) REVERT: A 56 GLU cc_start: 0.6000 (mt-10) cc_final: 0.5578 (tm-30) REVERT: A 75 LEU cc_start: 0.5853 (mp) cc_final: 0.5484 (mp) REVERT: A 79 GLU cc_start: 0.7629 (tt0) cc_final: 0.7005 (mp0) REVERT: A 170 ARG cc_start: 0.6102 (mtp180) cc_final: 0.5362 (ptp90) REVERT: A 191 ARG cc_start: 0.6848 (ttm-80) cc_final: 0.5850 (tpp-160) REVERT: A 214 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7482 (mp0) REVERT: A 237 PHE cc_start: 0.6873 (m-80) cc_final: 0.6649 (m-80) REVERT: A 337 ILE cc_start: 0.6925 (mm) cc_final: 0.6716 (mt) REVERT: A 393 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6514 (mp) REVERT: A 422 MET cc_start: 0.6625 (tpt) cc_final: 0.6289 (ttp) REVERT: A 512 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.7546 (mmm160) REVERT: A 551 ASN cc_start: 0.8531 (t0) cc_final: 0.8065 (t0) REVERT: A 634 HIS cc_start: 0.6683 (m90) cc_final: 0.6454 (m170) REVERT: A 653 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7349 (pm20) REVERT: A 715 GLU cc_start: 0.6827 (tt0) cc_final: 0.6614 (pt0) REVERT: B 33 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6608 (mt-10) REVERT: B 42 LYS cc_start: 0.6698 (mtmt) cc_final: 0.6412 (mmtt) REVERT: B 54 GLU cc_start: 0.6809 (tt0) cc_final: 0.5907 (tm-30) REVERT: B 56 GLU cc_start: 0.5994 (mt-10) cc_final: 0.5574 (tm-30) REVERT: B 75 LEU cc_start: 0.5855 (mp) cc_final: 0.5476 (OUTLIER) REVERT: B 79 GLU cc_start: 0.7598 (tt0) cc_final: 0.6986 (mp0) REVERT: B 87 GLU cc_start: 0.7564 (tt0) cc_final: 0.6832 (tp30) REVERT: B 91 ASN cc_start: 0.8098 (m-40) cc_final: 0.7646 (m-40) REVERT: B 170 ARG cc_start: 0.6104 (mtp180) cc_final: 0.5366 (ptp90) REVERT: B 191 ARG cc_start: 0.6849 (ttm-80) cc_final: 0.5848 (tpp-160) REVERT: B 214 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7483 (mp0) REVERT: B 237 PHE cc_start: 0.6873 (m-80) cc_final: 0.6648 (m-80) REVERT: B 337 ILE cc_start: 0.6925 (mm) cc_final: 0.6715 (mt) REVERT: B 393 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.6470 (mt) REVERT: B 422 MET cc_start: 0.6619 (tpt) cc_final: 0.6285 (ttp) REVERT: B 512 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.7547 (mmm160) REVERT: B 551 ASN cc_start: 0.8531 (t0) cc_final: 0.8063 (t0) REVERT: B 634 HIS cc_start: 0.6681 (m90) cc_final: 0.6454 (m170) REVERT: B 653 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7367 (pm20) REVERT: B 715 GLU cc_start: 0.6841 (tt0) cc_final: 0.6551 (pt0) REVERT: C 33 GLU cc_start: 0.6617 (mt-10) cc_final: 0.6379 (mt-10) REVERT: C 42 LYS cc_start: 0.6707 (mtmt) cc_final: 0.6417 (mmtt) REVERT: C 54 GLU cc_start: 0.6771 (tt0) cc_final: 0.5881 (tm-30) REVERT: C 56 GLU cc_start: 0.5993 (mt-10) cc_final: 0.5553 (tm-30) REVERT: C 75 LEU cc_start: 0.5854 (mp) cc_final: 0.5476 (OUTLIER) REVERT: C 79 GLU cc_start: 0.7597 (tt0) cc_final: 0.6986 (mp0) REVERT: C 170 ARG cc_start: 0.5949 (mtp180) cc_final: 0.5236 (ptp90) REVERT: C 191 ARG cc_start: 0.6845 (ttm-80) cc_final: 0.5844 (tpp-160) REVERT: C 214 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7398 (mp0) REVERT: C 237 PHE cc_start: 0.6909 (m-80) cc_final: 0.6693 (m-80) REVERT: C 337 ILE cc_start: 0.6929 (mm) cc_final: 0.6720 (mt) REVERT: C 393 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6399 (mt) REVERT: C 422 MET cc_start: 0.6558 (tpt) cc_final: 0.6256 (ttp) REVERT: C 512 ARG cc_start: 0.7790 (mmm-85) cc_final: 0.7541 (mmm160) REVERT: C 551 ASN cc_start: 0.8513 (t0) cc_final: 0.8032 (t0) REVERT: C 634 HIS cc_start: 0.6670 (m90) cc_final: 0.6440 (m170) REVERT: C 653 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7403 (pm20) REVERT: C 715 GLU cc_start: 0.6825 (tt0) cc_final: 0.6615 (pt0) REVERT: D 33 GLU cc_start: 0.6610 (mt-10) cc_final: 0.6372 (mt-10) REVERT: D 42 LYS cc_start: 0.6708 (mtmt) cc_final: 0.6419 (mmtt) REVERT: D 54 GLU cc_start: 0.6825 (tt0) cc_final: 0.5917 (tm-30) REVERT: D 56 GLU cc_start: 0.5996 (mt-10) cc_final: 0.5575 (tm-30) REVERT: D 75 LEU cc_start: 0.5851 (mp) cc_final: 0.5474 (OUTLIER) REVERT: D 79 GLU cc_start: 0.7597 (tt0) cc_final: 0.6984 (mp0) REVERT: D 170 ARG cc_start: 0.6120 (mtp180) cc_final: 0.5389 (ptp90) REVERT: D 191 ARG cc_start: 0.6844 (ttm-80) cc_final: 0.5845 (tpp-160) REVERT: D 214 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7397 (mp0) REVERT: D 237 PHE cc_start: 0.6870 (m-80) cc_final: 0.6651 (m-80) REVERT: D 359 PHE cc_start: 0.7325 (t80) cc_final: 0.6778 (t80) REVERT: D 393 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6412 (mt) REVERT: D 422 MET cc_start: 0.6562 (tpt) cc_final: 0.6253 (ttp) REVERT: D 512 ARG cc_start: 0.7795 (mmm-85) cc_final: 0.7541 (mmm160) REVERT: D 551 ASN cc_start: 0.8502 (t0) cc_final: 0.8020 (t0) REVERT: D 593 ARG cc_start: 0.7985 (mtp180) cc_final: 0.7634 (mtp-110) REVERT: D 595 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6432 (mp0) REVERT: D 634 HIS cc_start: 0.6694 (m90) cc_final: 0.6463 (m170) REVERT: D 653 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7347 (pm20) REVERT: D 715 GLU cc_start: 0.6825 (tt0) cc_final: 0.6616 (pt0) outliers start: 24 outliers final: 10 residues processed: 500 average time/residue: 0.6377 time to fit residues: 360.5842 Evaluate side-chains 294 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 283 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 619 MET Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 631 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN A 609 ASN ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN B 609 ASN ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 GLN C 609 ASN C 626 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.157469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.120171 restraints weight = 25079.871| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.65 r_work: 0.3248 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22796 Z= 0.163 Angle : 0.515 7.250 30804 Z= 0.258 Chirality : 0.036 0.149 3444 Planarity : 0.004 0.038 3784 Dihedral : 14.068 176.478 3265 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.63 % Allowed : 9.59 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.16), residues: 2608 helix: 1.72 (0.11), residues: 1952 sheet: None (None), residues: 0 loop : 0.35 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 754 TYR 0.013 0.001 TYR A 524 PHE 0.020 0.002 PHE C 341 TRP 0.012 0.001 TRP A 315 HIS 0.004 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (22776) covalent geometry : angle 0.51393 / 0.26 (30784) SS BOND : bond 0.00078 / 0.04 ( 4) SS BOND : angle 0.58761 / 0.36 ( 8) hydrogen bonds : bond 0.04209 / 2.82 ( 1432) hydrogen bonds : angle 3.75819 / 2.74 ( 4200) metal coordination : bond 0.00609 / 0.58 ( 16) metal coordination : angle 1.95954 / 1.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 290 time to evaluate : 0.805 Fit side-chains REVERT: A 42 LYS cc_start: 0.7959 (mtmt) cc_final: 0.7560 (mmtt) REVERT: A 56 GLU cc_start: 0.6436 (mt-10) cc_final: 0.6133 (tm-30) REVERT: A 79 GLU cc_start: 0.7786 (tt0) cc_final: 0.7498 (mp0) REVERT: A 87 GLU cc_start: 0.7662 (tt0) cc_final: 0.7351 (tp30) REVERT: A 170 ARG cc_start: 0.6677 (mtp180) cc_final: 0.6454 (ptp90) REVERT: A 332 LEU cc_start: 0.8140 (tt) cc_final: 0.7596 (mt) REVERT: A 335 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7503 (mpt) REVERT: A 393 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7611 (mp) REVERT: A 520 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7341 (t80) REVERT: A 551 ASN cc_start: 0.8416 (t0) cc_final: 0.7956 (t0) REVERT: B 42 LYS cc_start: 0.7957 (mtmt) cc_final: 0.7562 (mmtt) REVERT: B 56 GLU cc_start: 0.6433 (mt-10) cc_final: 0.6128 (tm-30) REVERT: B 79 GLU cc_start: 0.7772 (tt0) cc_final: 0.7494 (mp0) REVERT: B 87 GLU cc_start: 0.7604 (tt0) cc_final: 0.7287 (tp30) REVERT: B 170 ARG cc_start: 0.6673 (mtp180) cc_final: 0.6449 (ptp90) REVERT: B 332 LEU cc_start: 0.8125 (tt) cc_final: 0.7581 (mt) REVERT: B 335 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7624 (mpt) REVERT: B 393 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7582 (mp) REVERT: B 520 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7347 (t80) REVERT: B 551 ASN cc_start: 0.8435 (t0) cc_final: 0.7962 (t0) REVERT: C 42 LYS cc_start: 0.7956 (mtmt) cc_final: 0.7532 (mmtt) REVERT: C 56 GLU cc_start: 0.6422 (mt-10) cc_final: 0.6118 (tm-30) REVERT: C 79 GLU cc_start: 0.7772 (tt0) cc_final: 0.7501 (mp0) REVERT: C 87 GLU cc_start: 0.7612 (tt0) cc_final: 0.7334 (tp30) REVERT: C 170 ARG cc_start: 0.6665 (mtp180) cc_final: 0.6426 (ptp90) REVERT: C 332 LEU cc_start: 0.8115 (tt) cc_final: 0.7576 (mt) REVERT: C 335 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7619 (mpt) REVERT: C 393 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7546 (mp) REVERT: C 520 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7312 (t80) REVERT: C 551 ASN cc_start: 0.8450 (t0) cc_final: 0.7966 (t0) REVERT: C 570 GLU cc_start: 0.8046 (tp30) cc_final: 0.7818 (mm-30) REVERT: D 42 LYS cc_start: 0.7950 (mtmt) cc_final: 0.7528 (mmtt) REVERT: D 56 GLU cc_start: 0.6442 (mt-10) cc_final: 0.6124 (tm-30) REVERT: D 79 GLU cc_start: 0.7783 (tt0) cc_final: 0.7495 (mp0) REVERT: D 87 GLU cc_start: 0.7632 (tt0) cc_final: 0.7327 (tp30) REVERT: D 170 ARG cc_start: 0.6676 (mtp180) cc_final: 0.6414 (ptp90) REVERT: D 332 LEU cc_start: 0.8117 (tt) cc_final: 0.7588 (mt) REVERT: D 393 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7573 (mp) REVERT: D 520 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7339 (t80) REVERT: D 551 ASN cc_start: 0.8429 (t0) cc_final: 0.7940 (t0) outliers start: 86 outliers final: 36 residues processed: 328 average time/residue: 0.5874 time to fit residues: 221.0202 Evaluate side-chains 290 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 243 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 633 ASP Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 520 PHE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 520 PHE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 520 PHE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain D residue 750 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 226 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 230 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 626 ASN D 609 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.157197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.121303 restraints weight = 25163.053| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.56 r_work: 0.3256 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22796 Z= 0.166 Angle : 0.494 7.082 30804 Z= 0.251 Chirality : 0.037 0.150 3444 Planarity : 0.004 0.035 3784 Dihedral : 13.767 170.243 3256 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.56 % Allowed : 12.04 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.16), residues: 2608 helix: 1.98 (0.11), residues: 1944 sheet: None (None), residues: 0 loop : 0.30 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 71 TYR 0.012 0.001 TYR A 539 PHE 0.022 0.002 PHE C 341 TRP 0.016 0.001 TRP D 315 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (22776) covalent geometry : angle 0.49349 / 0.25 (30784) SS BOND : bond 0.00055 / 0.03 ( 4) SS BOND : angle 0.46594 / 0.29 ( 8) hydrogen bonds : bond 0.04096 / 2.75 ( 1432) hydrogen bonds : angle 3.59056 / 2.62 ( 4200) metal coordination : bond 0.00561 / 0.52 ( 16) metal coordination : angle 1.56292 / 1.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 278 time to evaluate : 0.821 Fit side-chains REVERT: A 42 LYS cc_start: 0.8052 (mtmt) cc_final: 0.7617 (mmtt) REVERT: A 79 GLU cc_start: 0.7724 (tt0) cc_final: 0.7453 (mp0) REVERT: A 87 GLU cc_start: 0.7718 (tt0) cc_final: 0.7371 (tp30) REVERT: A 115 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8036 (mm) REVERT: A 170 ARG cc_start: 0.7130 (mtp180) cc_final: 0.6616 (ptp90) REVERT: A 332 LEU cc_start: 0.8139 (tt) cc_final: 0.7648 (mt) REVERT: A 335 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7483 (mpt) REVERT: A 393 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7701 (mp) REVERT: A 520 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7306 (t80) REVERT: A 551 ASN cc_start: 0.8434 (t0) cc_final: 0.7924 (t0) REVERT: A 595 GLU cc_start: 0.8169 (mp0) cc_final: 0.7870 (mp0) REVERT: B 42 LYS cc_start: 0.8064 (mtmt) cc_final: 0.7619 (mmtt) REVERT: B 79 GLU cc_start: 0.7714 (tt0) cc_final: 0.7450 (mp0) REVERT: B 87 GLU cc_start: 0.7754 (tt0) cc_final: 0.7393 (tp30) REVERT: B 115 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8023 (mm) REVERT: B 170 ARG cc_start: 0.7132 (mtp180) cc_final: 0.6616 (ptp90) REVERT: B 332 LEU cc_start: 0.8110 (tt) cc_final: 0.7615 (mt) REVERT: B 393 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7686 (mp) REVERT: B 520 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7348 (t80) REVERT: B 551 ASN cc_start: 0.8405 (t0) cc_final: 0.7894 (t0) REVERT: B 595 GLU cc_start: 0.8165 (mp0) cc_final: 0.7887 (mp0) REVERT: C 42 LYS cc_start: 0.8059 (mtmt) cc_final: 0.7618 (mmtt) REVERT: C 79 GLU cc_start: 0.7706 (tt0) cc_final: 0.7452 (mp0) REVERT: C 87 GLU cc_start: 0.7706 (tt0) cc_final: 0.7375 (tp30) REVERT: C 115 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8018 (mm) REVERT: C 170 ARG cc_start: 0.7117 (mtp180) cc_final: 0.6605 (ptp90) REVERT: C 332 LEU cc_start: 0.8122 (tt) cc_final: 0.7628 (mt) REVERT: C 393 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7607 (mp) REVERT: C 520 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7298 (t80) REVERT: C 551 ASN cc_start: 0.8456 (t0) cc_final: 0.7945 (t0) REVERT: C 595 GLU cc_start: 0.8184 (mp0) cc_final: 0.7907 (mp0) REVERT: D 42 LYS cc_start: 0.8060 (mtmt) cc_final: 0.7610 (mmtt) REVERT: D 79 GLU cc_start: 0.7735 (tt0) cc_final: 0.7452 (mp0) REVERT: D 87 GLU cc_start: 0.7704 (tt0) cc_final: 0.7367 (tp30) REVERT: D 115 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8034 (mm) REVERT: D 170 ARG cc_start: 0.7127 (mtp180) cc_final: 0.6615 (ptp90) REVERT: D 332 LEU cc_start: 0.8138 (tt) cc_final: 0.7648 (mt) REVERT: D 335 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7866 (mpt) REVERT: D 393 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7654 (mp) REVERT: D 520 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7292 (t80) REVERT: D 551 ASN cc_start: 0.8436 (t0) cc_final: 0.7920 (t0) REVERT: D 595 GLU cc_start: 0.8169 (mp0) cc_final: 0.7886 (mp0) outliers start: 108 outliers final: 31 residues processed: 329 average time/residue: 0.5681 time to fit residues: 214.6550 Evaluate side-chains 287 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 242 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 520 PHE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 520 PHE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 520 PHE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 750 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 233 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 256 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 chunk 211 optimal weight: 0.0010 chunk 59 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.154022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117474 restraints weight = 24600.566| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.59 r_work: 0.3214 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22796 Z= 0.180 Angle : 0.511 6.993 30804 Z= 0.258 Chirality : 0.037 0.150 3444 Planarity : 0.004 0.036 3784 Dihedral : 13.638 161.856 3256 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.81 % Allowed : 12.37 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.16), residues: 2608 helix: 2.03 (0.11), residues: 1944 sheet: None (None), residues: 0 loop : 0.32 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 71 TYR 0.011 0.001 TYR A 539 PHE 0.023 0.002 PHE D 341 TRP 0.016 0.001 TRP B 315 HIS 0.003 0.001 HIS D 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (22776) covalent geometry : angle 0.51017 / 0.26 (30784) SS BOND : bond 0.00044 / 0.02 ( 4) SS BOND : angle 0.44613 / 0.28 ( 8) hydrogen bonds : bond 0.04079 / 2.74 ( 1432) hydrogen bonds : angle 3.59125 / 2.62 ( 4200) metal coordination : bond 0.00536 / 0.51 ( 16) metal coordination : angle 1.43775 / 1.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 259 time to evaluate : 0.817 Fit side-chains REVERT: A 42 LYS cc_start: 0.8126 (mtmt) cc_final: 0.7587 (mmtt) REVERT: A 54 GLU cc_start: 0.7307 (mp0) cc_final: 0.6169 (tm-30) REVERT: A 79 GLU cc_start: 0.7663 (tt0) cc_final: 0.7440 (mp0) REVERT: A 87 GLU cc_start: 0.7820 (tt0) cc_final: 0.7383 (tp30) REVERT: A 115 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8052 (mm) REVERT: A 170 ARG cc_start: 0.7387 (mtp180) cc_final: 0.6761 (ptp90) REVERT: A 332 LEU cc_start: 0.8168 (tt) cc_final: 0.7701 (mt) REVERT: A 335 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7592 (mpt) REVERT: A 393 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7704 (mp) REVERT: A 471 MET cc_start: 0.9011 (ttt) cc_final: 0.8709 (ttt) REVERT: A 520 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7285 (t80) REVERT: A 551 ASN cc_start: 0.8439 (t0) cc_final: 0.7903 (t0) REVERT: A 595 GLU cc_start: 0.8244 (mp0) cc_final: 0.7930 (mp0) REVERT: B 42 LYS cc_start: 0.8118 (mtmt) cc_final: 0.7580 (mmtt) REVERT: B 79 GLU cc_start: 0.7685 (tt0) cc_final: 0.7449 (mp0) REVERT: B 87 GLU cc_start: 0.7820 (tt0) cc_final: 0.7407 (tp30) REVERT: B 115 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8048 (mm) REVERT: B 170 ARG cc_start: 0.7384 (mtp180) cc_final: 0.6768 (ptp90) REVERT: B 332 LEU cc_start: 0.8103 (tt) cc_final: 0.7657 (mt) REVERT: B 335 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7996 (mpt) REVERT: B 393 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7650 (mp) REVERT: B 520 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7294 (t80) REVERT: B 551 ASN cc_start: 0.8432 (t0) cc_final: 0.7898 (t0) REVERT: B 595 GLU cc_start: 0.8269 (mp0) cc_final: 0.7963 (mp0) REVERT: C 42 LYS cc_start: 0.8123 (mtmt) cc_final: 0.7579 (mmtt) REVERT: C 54 GLU cc_start: 0.7329 (mp0) cc_final: 0.6193 (tm-30) REVERT: C 79 GLU cc_start: 0.7670 (tt0) cc_final: 0.7446 (mp0) REVERT: C 87 GLU cc_start: 0.7759 (tt0) cc_final: 0.7381 (tp30) REVERT: C 115 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8069 (mm) REVERT: C 170 ARG cc_start: 0.7393 (mtp180) cc_final: 0.6775 (ptp90) REVERT: C 332 LEU cc_start: 0.8103 (tt) cc_final: 0.7661 (mt) REVERT: C 471 MET cc_start: 0.8980 (ttt) cc_final: 0.8717 (ttt) REVERT: C 520 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7285 (t80) REVERT: C 551 ASN cc_start: 0.8423 (t0) cc_final: 0.7890 (t0) REVERT: C 595 GLU cc_start: 0.8249 (mp0) cc_final: 0.7923 (mp0) REVERT: D 42 LYS cc_start: 0.8139 (mtmt) cc_final: 0.7600 (mmtt) REVERT: D 79 GLU cc_start: 0.7652 (tt0) cc_final: 0.7436 (mp0) REVERT: D 87 GLU cc_start: 0.7782 (tt0) cc_final: 0.7391 (tp30) REVERT: D 115 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8054 (mm) REVERT: D 170 ARG cc_start: 0.7390 (mtp180) cc_final: 0.6766 (ptp90) REVERT: D 332 LEU cc_start: 0.8110 (tt) cc_final: 0.7670 (mt) REVERT: D 335 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7949 (mpt) REVERT: D 393 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7692 (mp) REVERT: D 471 MET cc_start: 0.9002 (ttt) cc_final: 0.8740 (ttt) REVERT: D 520 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7267 (t80) REVERT: D 551 ASN cc_start: 0.8448 (t0) cc_final: 0.7914 (t0) REVERT: D 595 GLU cc_start: 0.8257 (mp0) cc_final: 0.7926 (mp0) outliers start: 114 outliers final: 42 residues processed: 323 average time/residue: 0.6384 time to fit residues: 235.9113 Evaluate side-chains 293 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 237 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 520 PHE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain C residue 520 PHE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 715 GLU Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 520 PHE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 715 GLU Chi-restraints excluded: chain D residue 750 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 232 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 54 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.152587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116089 restraints weight = 24493.077| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.59 r_work: 0.3191 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 22796 Z= 0.215 Angle : 0.536 11.375 30804 Z= 0.271 Chirality : 0.038 0.152 3444 Planarity : 0.004 0.036 3784 Dihedral : 13.699 179.836 3246 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.80 % Allowed : 14.32 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.16), residues: 2608 helix: 1.94 (0.11), residues: 1944 sheet: None (None), residues: 0 loop : 0.23 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 71 TYR 0.010 0.001 TYR D 539 PHE 0.024 0.002 PHE D 341 TRP 0.017 0.001 TRP B 315 HIS 0.003 0.001 HIS B 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.21 (22776) covalent geometry : angle 0.53570 / 0.27 (30784) SS BOND : bond 0.00082 / 0.04 ( 4) SS BOND : angle 0.56143 / 0.34 ( 8) hydrogen bonds : bond 0.04261 / 2.85 ( 1432) hydrogen bonds : angle 3.62624 / 2.65 ( 4200) metal coordination : bond 0.00478 / 0.45 ( 16) metal coordination : angle 1.39711 / 1.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 249 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8266 (mtmt) cc_final: 0.7624 (mmtt) REVERT: A 79 GLU cc_start: 0.7722 (tt0) cc_final: 0.7480 (mp0) REVERT: A 87 GLU cc_start: 0.7790 (tt0) cc_final: 0.7374 (tp30) REVERT: A 115 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8089 (mm) REVERT: A 170 ARG cc_start: 0.7589 (mtp180) cc_final: 0.6748 (ptp90) REVERT: A 332 LEU cc_start: 0.8145 (tt) cc_final: 0.7801 (mt) REVERT: A 335 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7637 (mpt) REVERT: A 520 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7281 (t80) REVERT: A 551 ASN cc_start: 0.8554 (t0) cc_final: 0.7960 (t0) REVERT: A 595 GLU cc_start: 0.8324 (mp0) cc_final: 0.7990 (mp0) REVERT: B 42 LYS cc_start: 0.8265 (mtmt) cc_final: 0.7624 (mmtt) REVERT: B 87 GLU cc_start: 0.7784 (tt0) cc_final: 0.7357 (tp30) REVERT: B 115 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8119 (mm) REVERT: B 170 ARG cc_start: 0.7582 (mtp180) cc_final: 0.6748 (ptp90) REVERT: B 332 LEU cc_start: 0.8156 (tt) cc_final: 0.7804 (mt) REVERT: B 520 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7297 (t80) REVERT: B 551 ASN cc_start: 0.8554 (t0) cc_final: 0.7959 (t0) REVERT: B 595 GLU cc_start: 0.8315 (mp0) cc_final: 0.7966 (mp0) REVERT: C 42 LYS cc_start: 0.8271 (mtmt) cc_final: 0.7630 (mmtt) REVERT: C 87 GLU cc_start: 0.7759 (tt0) cc_final: 0.7362 (tp30) REVERT: C 115 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8124 (mm) REVERT: C 170 ARG cc_start: 0.7603 (mtp180) cc_final: 0.6733 (ptp90) REVERT: C 332 LEU cc_start: 0.8158 (tt) cc_final: 0.7808 (mt) REVERT: C 393 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7667 (mp) REVERT: C 520 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7294 (t80) REVERT: C 551 ASN cc_start: 0.8577 (t0) cc_final: 0.7976 (t0) REVERT: C 595 GLU cc_start: 0.8299 (mp0) cc_final: 0.7933 (mp0) REVERT: D 42 LYS cc_start: 0.8267 (mtmt) cc_final: 0.7625 (mmtt) REVERT: D 79 GLU cc_start: 0.7689 (tt0) cc_final: 0.7470 (mp0) REVERT: D 87 GLU cc_start: 0.7775 (tt0) cc_final: 0.7368 (tp30) REVERT: D 115 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8089 (mm) REVERT: D 170 ARG cc_start: 0.7571 (mtp180) cc_final: 0.6731 (ptp90) REVERT: D 332 LEU cc_start: 0.8155 (tt) cc_final: 0.7817 (mt) REVERT: D 335 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.8019 (mpt) REVERT: D 520 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7275 (t80) REVERT: D 551 ASN cc_start: 0.8569 (t0) cc_final: 0.7970 (t0) REVERT: D 595 GLU cc_start: 0.8298 (mp0) cc_final: 0.7942 (mp0) outliers start: 90 outliers final: 45 residues processed: 302 average time/residue: 0.6310 time to fit residues: 218.4600 Evaluate side-chains 293 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 237 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 520 PHE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain C residue 520 PHE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 715 GLU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 520 PHE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 715 GLU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 750 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 132 optimal weight: 10.0000 chunk 208 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 157 optimal weight: 0.5980 chunk 166 optimal weight: 8.9990 chunk 112 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.154371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118247 restraints weight = 24612.726| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.58 r_work: 0.3225 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22796 Z= 0.136 Angle : 0.471 6.839 30804 Z= 0.240 Chirality : 0.036 0.146 3444 Planarity : 0.003 0.036 3784 Dihedral : 12.678 153.955 3240 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.01 % Allowed : 14.70 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.16), residues: 2608 helix: 2.11 (0.11), residues: 1944 sheet: None (None), residues: 0 loop : 0.20 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 323 TYR 0.009 0.001 TYR A 200 PHE 0.022 0.001 PHE D 341 TRP 0.014 0.001 TRP D 315 HIS 0.002 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (22776) covalent geometry : angle 0.47057 / 0.24 (30784) SS BOND : bond 0.00021 / 0.01 ( 4) SS BOND : angle 0.31689 / 0.20 ( 8) hydrogen bonds : bond 0.03785 / 2.53 ( 1432) hydrogen bonds : angle 3.54551 / 2.59 ( 4200) metal coordination : bond 0.00307 / 0.28 ( 16) metal coordination : angle 1.17458 / 0.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 264 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8275 (mtmt) cc_final: 0.7620 (mmtt) REVERT: A 79 GLU cc_start: 0.7653 (tt0) cc_final: 0.7447 (mp0) REVERT: A 87 GLU cc_start: 0.7761 (tt0) cc_final: 0.7336 (tp30) REVERT: A 115 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8164 (mm) REVERT: A 170 ARG cc_start: 0.7611 (mtp180) cc_final: 0.6690 (ptp90) REVERT: A 332 LEU cc_start: 0.8124 (tt) cc_final: 0.7795 (mt) REVERT: A 335 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7544 (mpt) REVERT: A 393 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7747 (mp) REVERT: A 520 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7417 (t80) REVERT: A 551 ASN cc_start: 0.8499 (t0) cc_final: 0.7892 (t0) REVERT: A 595 GLU cc_start: 0.8320 (mp0) cc_final: 0.7965 (mp0) REVERT: B 42 LYS cc_start: 0.8275 (mtmt) cc_final: 0.7619 (mmtt) REVERT: B 71 ARG cc_start: 0.6640 (mtm110) cc_final: 0.5825 (mtp85) REVERT: B 79 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6576 (tp30) REVERT: B 87 GLU cc_start: 0.7746 (tt0) cc_final: 0.7331 (tp30) REVERT: B 115 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8139 (mm) REVERT: B 170 ARG cc_start: 0.7606 (mtp180) cc_final: 0.6694 (ptp90) REVERT: B 332 LEU cc_start: 0.8122 (tt) cc_final: 0.7790 (mt) REVERT: B 551 ASN cc_start: 0.8499 (t0) cc_final: 0.7893 (t0) REVERT: B 595 GLU cc_start: 0.8320 (mp0) cc_final: 0.7985 (mp0) REVERT: B 623 MET cc_start: 0.8711 (mtp) cc_final: 0.8497 (mtm) REVERT: B 624 MET cc_start: 0.8500 (mtt) cc_final: 0.8214 (mtt) REVERT: C 42 LYS cc_start: 0.8285 (mtmt) cc_final: 0.7625 (mmtt) REVERT: C 71 ARG cc_start: 0.6624 (mtm110) cc_final: 0.5825 (mtp85) REVERT: C 79 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6605 (tp30) REVERT: C 87 GLU cc_start: 0.7732 (tt0) cc_final: 0.7330 (tp30) REVERT: C 115 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8165 (mm) REVERT: C 170 ARG cc_start: 0.7608 (mtp180) cc_final: 0.6686 (ptp90) REVERT: C 332 LEU cc_start: 0.8138 (tt) cc_final: 0.7804 (mt) REVERT: C 393 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7720 (mp) REVERT: C 520 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7326 (t80) REVERT: C 551 ASN cc_start: 0.8506 (t0) cc_final: 0.7891 (t0) REVERT: C 595 GLU cc_start: 0.8330 (mp0) cc_final: 0.7987 (mp0) REVERT: D 42 LYS cc_start: 0.8284 (mtmt) cc_final: 0.7627 (mmtt) REVERT: D 87 GLU cc_start: 0.7773 (tt0) cc_final: 0.7367 (tp30) REVERT: D 115 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8163 (mm) REVERT: D 170 ARG cc_start: 0.7612 (mtp180) cc_final: 0.6695 (ptp90) REVERT: D 332 LEU cc_start: 0.8146 (tt) cc_final: 0.7803 (mt) REVERT: D 520 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7350 (t80) REVERT: D 551 ASN cc_start: 0.8520 (t0) cc_final: 0.7906 (t0) REVERT: D 595 GLU cc_start: 0.8316 (mp0) cc_final: 0.7958 (mp0) REVERT: D 623 MET cc_start: 0.8756 (mtp) cc_final: 0.8513 (mtm) outliers start: 95 outliers final: 36 residues processed: 318 average time/residue: 0.5996 time to fit residues: 220.0406 Evaluate side-chains 294 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 246 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 520 PHE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 715 GLU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 520 PHE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 715 GLU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 750 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 139 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 210 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 731 ASN C 731 ASN D 731 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.154282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118044 restraints weight = 24499.587| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.57 r_work: 0.3210 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22796 Z= 0.180 Angle : 0.508 6.859 30804 Z= 0.257 Chirality : 0.037 0.154 3444 Planarity : 0.004 0.037 3784 Dihedral : 12.440 154.999 3240 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.93 % Allowed : 15.54 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.16), residues: 2608 helix: 2.05 (0.11), residues: 1944 sheet: None (None), residues: 0 loop : 0.15 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 323 TYR 0.008 0.001 TYR C 586 PHE 0.026 0.002 PHE D 359 TRP 0.016 0.001 TRP D 315 HIS 0.002 0.001 HIS C 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 (22776) covalent geometry : angle 0.50746 / 0.26 (30784) SS BOND : bond 0.00082 / 0.04 ( 4) SS BOND : angle 0.44952 / 0.28 ( 8) hydrogen bonds : bond 0.04029 / 2.69 ( 1432) hydrogen bonds : angle 3.58212 / 2.62 ( 4200) metal coordination : bond 0.00340 / 0.31 ( 16) metal coordination : angle 1.15991 / 0.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 239 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8219 (mtmt) cc_final: 0.7631 (mmtt) REVERT: A 79 GLU cc_start: 0.7618 (tt0) cc_final: 0.7381 (mp0) REVERT: A 87 GLU cc_start: 0.7745 (tt0) cc_final: 0.7312 (tp30) REVERT: A 115 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8167 (mm) REVERT: A 170 ARG cc_start: 0.7649 (mtp180) cc_final: 0.6884 (ptp-170) REVERT: A 332 LEU cc_start: 0.8131 (tt) cc_final: 0.7791 (mt) REVERT: A 335 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7591 (mpt) REVERT: A 510 LEU cc_start: 0.8267 (tp) cc_final: 0.7974 (mp) REVERT: A 520 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7446 (t80) REVERT: A 551 ASN cc_start: 0.8533 (t0) cc_final: 0.7912 (t0) REVERT: A 595 GLU cc_start: 0.8344 (mp0) cc_final: 0.8027 (mp0) REVERT: B 42 LYS cc_start: 0.8217 (mtmt) cc_final: 0.7557 (mmtt) REVERT: B 71 ARG cc_start: 0.6825 (mtm110) cc_final: 0.5964 (mtp85) REVERT: B 79 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6568 (tp30) REVERT: B 87 GLU cc_start: 0.7731 (tt0) cc_final: 0.7319 (tp30) REVERT: B 115 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8159 (mm) REVERT: B 170 ARG cc_start: 0.7662 (mtp180) cc_final: 0.6905 (ptp-170) REVERT: B 332 LEU cc_start: 0.8131 (tt) cc_final: 0.7780 (mt) REVERT: B 393 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7717 (mt) REVERT: B 551 ASN cc_start: 0.8528 (t0) cc_final: 0.7889 (t0) REVERT: B 595 GLU cc_start: 0.8362 (mp0) cc_final: 0.8008 (mp0) REVERT: B 624 MET cc_start: 0.8636 (mtt) cc_final: 0.8252 (mtt) REVERT: C 42 LYS cc_start: 0.8221 (mtmt) cc_final: 0.7561 (mmtt) REVERT: C 71 ARG cc_start: 0.6824 (mtm110) cc_final: 0.5959 (mtp85) REVERT: C 79 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6612 (tp30) REVERT: C 87 GLU cc_start: 0.7698 (tt0) cc_final: 0.7316 (tp30) REVERT: C 115 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8173 (mm) REVERT: C 170 ARG cc_start: 0.7651 (mtp180) cc_final: 0.6896 (ptp-170) REVERT: C 332 LEU cc_start: 0.8162 (tt) cc_final: 0.7807 (mt) REVERT: C 393 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7736 (mt) REVERT: C 520 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7397 (t80) REVERT: C 551 ASN cc_start: 0.8528 (t0) cc_final: 0.7891 (t0) REVERT: C 595 GLU cc_start: 0.8353 (mp0) cc_final: 0.7999 (mp0) REVERT: D 42 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7564 (mmtt) REVERT: D 71 ARG cc_start: 0.6768 (mtm110) cc_final: 0.5966 (mtp85) REVERT: D 79 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6401 (tp30) REVERT: D 87 GLU cc_start: 0.7741 (tt0) cc_final: 0.7329 (tp30) REVERT: D 115 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8146 (mm) REVERT: D 170 ARG cc_start: 0.7651 (mtp180) cc_final: 0.6895 (ptp-170) REVERT: D 332 LEU cc_start: 0.8129 (tt) cc_final: 0.7784 (mt) REVERT: D 393 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7722 (mp) REVERT: D 520 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7411 (t80) REVERT: D 551 ASN cc_start: 0.8531 (t0) cc_final: 0.7905 (t0) REVERT: D 595 GLU cc_start: 0.8339 (mp0) cc_final: 0.8007 (mp0) REVERT: D 623 MET cc_start: 0.8762 (mtp) cc_final: 0.8536 (mtm) outliers start: 93 outliers final: 42 residues processed: 300 average time/residue: 0.6091 time to fit residues: 210.6796 Evaluate side-chains 294 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 520 PHE Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 653 GLU Chi-restraints excluded: chain C residue 715 GLU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 520 PHE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 653 GLU Chi-restraints excluded: chain D residue 715 GLU Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 146 optimal weight: 20.0000 chunk 58 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 250 optimal weight: 0.6980 chunk 6 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 731 ASN B 731 ASN C 731 ASN D 731 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.154956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.119021 restraints weight = 24473.325| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.58 r_work: 0.3238 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22796 Z= 0.120 Angle : 0.459 6.811 30804 Z= 0.234 Chirality : 0.035 0.146 3444 Planarity : 0.003 0.037 3784 Dihedral : 11.797 152.915 3240 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.51 % Allowed : 16.05 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.16), residues: 2608 helix: 2.23 (0.11), residues: 1944 sheet: None (None), residues: 0 loop : 0.18 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 323 TYR 0.009 0.001 TYR A 200 PHE 0.028 0.001 PHE D 341 TRP 0.013 0.001 TRP D 315 HIS 0.002 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (22776) covalent geometry : angle 0.45855 / 0.23 (30784) SS BOND : bond 0.00013 / 0.01 ( 4) SS BOND : angle 0.23162 / 0.16 ( 8) hydrogen bonds : bond 0.03632 / 2.42 ( 1432) hydrogen bonds : angle 3.51027 / 2.56 ( 4200) metal coordination : bond 0.00184 / 0.15 ( 16) metal coordination : angle 0.98553 / 0.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 266 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8178 (mtmt) cc_final: 0.7587 (mmtt) REVERT: A 71 ARG cc_start: 0.6860 (mtm110) cc_final: 0.6628 (mtm-85) REVERT: A 79 GLU cc_start: 0.7577 (tt0) cc_final: 0.7329 (mp0) REVERT: A 87 GLU cc_start: 0.7682 (tt0) cc_final: 0.7262 (tp30) REVERT: A 115 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8144 (mm) REVERT: A 170 ARG cc_start: 0.7711 (mtp180) cc_final: 0.6902 (ptp-170) REVERT: A 332 LEU cc_start: 0.8121 (tt) cc_final: 0.7771 (mt) REVERT: A 393 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7756 (mp) REVERT: A 551 ASN cc_start: 0.8477 (t0) cc_final: 0.7871 (t0) REVERT: B 42 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7558 (mmtt) REVERT: B 71 ARG cc_start: 0.6735 (mtm110) cc_final: 0.6004 (mtp180) REVERT: B 87 GLU cc_start: 0.7671 (tt0) cc_final: 0.7255 (tp30) REVERT: B 115 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8134 (mm) REVERT: B 170 ARG cc_start: 0.7714 (mtp180) cc_final: 0.6907 (ptp-170) REVERT: B 332 LEU cc_start: 0.8122 (tt) cc_final: 0.7772 (mt) REVERT: B 393 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7743 (mp) REVERT: B 551 ASN cc_start: 0.8472 (t0) cc_final: 0.7865 (t0) REVERT: B 595 GLU cc_start: 0.8344 (mp0) cc_final: 0.8013 (mp0) REVERT: B 624 MET cc_start: 0.8538 (mtt) cc_final: 0.8230 (mtt) REVERT: C 42 LYS cc_start: 0.8157 (mtmt) cc_final: 0.7560 (mmtt) REVERT: C 71 ARG cc_start: 0.6722 (mtm110) cc_final: 0.5991 (mtp180) REVERT: C 87 GLU cc_start: 0.7651 (tt0) cc_final: 0.7263 (tp30) REVERT: C 115 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8144 (mm) REVERT: C 170 ARG cc_start: 0.7703 (mtp180) cc_final: 0.6898 (ptp-170) REVERT: C 332 LEU cc_start: 0.8164 (tt) cc_final: 0.7830 (mt) REVERT: C 393 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7749 (mt) REVERT: C 528 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8840 (tp) REVERT: C 551 ASN cc_start: 0.8482 (t0) cc_final: 0.7872 (t0) REVERT: C 595 GLU cc_start: 0.8354 (mp0) cc_final: 0.8019 (mp0) REVERT: D 42 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7555 (mmtt) REVERT: D 71 ARG cc_start: 0.6688 (mtm110) cc_final: 0.5922 (mtp85) REVERT: D 79 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6298 (tp30) REVERT: D 87 GLU cc_start: 0.7681 (tt0) cc_final: 0.7266 (tp30) REVERT: D 115 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8142 (mm) REVERT: D 170 ARG cc_start: 0.7700 (mtp180) cc_final: 0.6898 (ptp-170) REVERT: D 332 LEU cc_start: 0.8118 (tt) cc_final: 0.7793 (mt) REVERT: D 341 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.7837 (p90) REVERT: D 393 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7717 (mp) REVERT: D 551 ASN cc_start: 0.8479 (t0) cc_final: 0.7867 (t0) REVERT: D 595 GLU cc_start: 0.8347 (mp0) cc_final: 0.8009 (mp0) outliers start: 83 outliers final: 44 residues processed: 323 average time/residue: 0.5197 time to fit residues: 195.1320 Evaluate side-chains 300 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 245 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 715 GLU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 715 GLU Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 114 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 151 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 145 optimal weight: 0.0970 chunk 216 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 chunk 71 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 731 ASN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN C 731 ASN ** D 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 731 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.156418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.120795 restraints weight = 24409.125| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.58 r_work: 0.3262 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22796 Z= 0.099 Angle : 0.455 6.864 30804 Z= 0.232 Chirality : 0.035 0.141 3444 Planarity : 0.003 0.037 3784 Dihedral : 11.129 150.584 3240 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.17 % Allowed : 16.55 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.16), residues: 2608 helix: 2.37 (0.11), residues: 1948 sheet: None (None), residues: 0 loop : 0.20 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 323 TYR 0.010 0.001 TYR A 200 PHE 0.028 0.001 PHE D 341 TRP 0.029 0.001 TRP A 327 HIS 0.002 0.000 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (22776) covalent geometry : angle 0.45484 / 0.23 (30784) SS BOND : bond 0.00005 / 0.00 ( 4) SS BOND : angle 0.21336 / 0.15 ( 8) hydrogen bonds : bond 0.03441 / 2.29 ( 1432) hydrogen bonds : angle 3.49325 / 2.55 ( 4200) metal coordination : bond 0.00142 / 0.11 ( 16) metal coordination : angle 0.91129 / 0.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 265 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7591 (mmtt) REVERT: A 79 GLU cc_start: 0.7599 (tt0) cc_final: 0.7390 (mp0) REVERT: A 87 GLU cc_start: 0.7606 (tt0) cc_final: 0.7224 (tp30) REVERT: A 170 ARG cc_start: 0.7693 (mtp180) cc_final: 0.6887 (ptp-170) REVERT: A 332 LEU cc_start: 0.8110 (tt) cc_final: 0.7809 (mt) REVERT: A 393 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7756 (mp) REVERT: A 551 ASN cc_start: 0.8372 (t0) cc_final: 0.7804 (t0) REVERT: A 595 GLU cc_start: 0.8344 (mp0) cc_final: 0.7964 (mp0) REVERT: A 623 MET cc_start: 0.8689 (mtp) cc_final: 0.8439 (mtm) REVERT: A 745 GLU cc_start: 0.5922 (mt-10) cc_final: 0.5523 (mp0) REVERT: B 42 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7535 (mmtt) REVERT: B 71 ARG cc_start: 0.6806 (mtm110) cc_final: 0.6073 (mtp180) REVERT: B 87 GLU cc_start: 0.7603 (tt0) cc_final: 0.7229 (tp30) REVERT: B 115 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8083 (mm) REVERT: B 170 ARG cc_start: 0.7701 (mtp180) cc_final: 0.6886 (ptp-170) REVERT: B 332 LEU cc_start: 0.8112 (tt) cc_final: 0.7803 (mt) REVERT: B 393 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7749 (mt) REVERT: B 528 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8850 (tp) REVERT: B 551 ASN cc_start: 0.8364 (t0) cc_final: 0.7813 (t0) REVERT: B 745 GLU cc_start: 0.5907 (mt-10) cc_final: 0.5417 (mp0) REVERT: C 42 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7532 (mmtt) REVERT: C 71 ARG cc_start: 0.6799 (mtm110) cc_final: 0.6064 (mtp180) REVERT: C 87 GLU cc_start: 0.7592 (tt0) cc_final: 0.7234 (tp30) REVERT: C 170 ARG cc_start: 0.7681 (mtp180) cc_final: 0.6895 (ptp-170) REVERT: C 332 LEU cc_start: 0.8077 (tt) cc_final: 0.7756 (mt) REVERT: C 341 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.7671 (p90) REVERT: C 393 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7726 (mp) REVERT: C 528 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8860 (tp) REVERT: C 551 ASN cc_start: 0.8383 (t0) cc_final: 0.7821 (t0) REVERT: C 595 GLU cc_start: 0.8323 (mp0) cc_final: 0.8000 (mp0) REVERT: C 745 GLU cc_start: 0.5917 (mt-10) cc_final: 0.5433 (mp0) REVERT: D 42 LYS cc_start: 0.8108 (mtmt) cc_final: 0.7515 (mmtt) REVERT: D 71 ARG cc_start: 0.6816 (mtm110) cc_final: 0.6110 (mtp180) REVERT: D 87 GLU cc_start: 0.7596 (tt0) cc_final: 0.7235 (tp30) REVERT: D 170 ARG cc_start: 0.7680 (mtp180) cc_final: 0.6887 (ptp-170) REVERT: D 332 LEU cc_start: 0.8128 (tt) cc_final: 0.7818 (mt) REVERT: D 341 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.7864 (p90) REVERT: D 393 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7766 (mt) REVERT: D 528 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8840 (tp) REVERT: D 551 ASN cc_start: 0.8375 (t0) cc_final: 0.7810 (t0) REVERT: D 595 GLU cc_start: 0.8340 (mp0) cc_final: 0.8011 (mp0) REVERT: D 745 GLU cc_start: 0.5908 (mt-10) cc_final: 0.5428 (mp0) outliers start: 75 outliers final: 43 residues processed: 323 average time/residue: 0.5659 time to fit residues: 211.4211 Evaluate side-chains 304 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 251 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 715 GLU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 715 GLU Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 62 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 79 optimal weight: 0.0970 chunk 0 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN A 731 ASN B 82 ASN B 731 ASN B 748 GLN C 82 ASN C 163 GLN C 192 HIS C 731 ASN C 748 GLN D 82 ASN D 731 ASN D 748 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.156853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.121178 restraints weight = 24601.309| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.59 r_work: 0.3262 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22796 Z= 0.102 Angle : 0.459 6.862 30804 Z= 0.234 Chirality : 0.035 0.140 3444 Planarity : 0.003 0.038 3784 Dihedral : 10.350 150.085 3240 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.87 % Allowed : 16.98 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.16), residues: 2608 helix: 2.41 (0.11), residues: 1948 sheet: None (None), residues: 0 loop : 0.23 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 323 TYR 0.009 0.001 TYR A 200 PHE 0.029 0.001 PHE D 341 TRP 0.042 0.001 TRP A 327 HIS 0.002 0.000 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (22776) covalent geometry : angle 0.45896 / 0.23 (30784) SS BOND : bond 0.00015 / 0.01 ( 4) SS BOND : angle 0.19755 / 0.13 ( 8) hydrogen bonds : bond 0.03428 / 2.28 ( 1432) hydrogen bonds : angle 3.48407 / 2.54 ( 4200) metal coordination : bond 0.00125 / 0.09 ( 16) metal coordination : angle 0.81625 / 0.61 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 259 time to evaluate : 0.865 Fit side-chains REVERT: A 42 LYS cc_start: 0.8115 (mtmt) cc_final: 0.7522 (mmtt) REVERT: A 71 ARG cc_start: 0.6797 (mtm110) cc_final: 0.6560 (mtm110) REVERT: A 75 LEU cc_start: 0.7998 (mp) cc_final: 0.7726 (mt) REVERT: A 79 GLU cc_start: 0.7432 (tt0) cc_final: 0.7214 (mp0) REVERT: A 87 GLU cc_start: 0.7606 (tt0) cc_final: 0.7245 (tp30) REVERT: A 170 ARG cc_start: 0.7712 (mtp180) cc_final: 0.6882 (ptp-170) REVERT: A 341 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.7673 (p90) REVERT: A 393 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7755 (mp) REVERT: A 551 ASN cc_start: 0.8362 (t0) cc_final: 0.7840 (t0) REVERT: A 595 GLU cc_start: 0.8309 (mp0) cc_final: 0.7927 (mp0) REVERT: A 623 MET cc_start: 0.8746 (mtp) cc_final: 0.8530 (mtm) REVERT: A 745 GLU cc_start: 0.5916 (mt-10) cc_final: 0.5437 (mp0) REVERT: B 42 LYS cc_start: 0.8120 (mtmt) cc_final: 0.7469 (mmtt) REVERT: B 71 ARG cc_start: 0.6882 (mtm110) cc_final: 0.6161 (mtp180) REVERT: B 87 GLU cc_start: 0.7611 (tt0) cc_final: 0.7241 (tp30) REVERT: B 170 ARG cc_start: 0.7692 (mtp180) cc_final: 0.6876 (ptp-170) REVERT: B 341 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.7662 (p90) REVERT: B 393 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7778 (mp) REVERT: B 528 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8845 (tp) REVERT: B 551 ASN cc_start: 0.8349 (t0) cc_final: 0.7807 (t0) REVERT: B 595 GLU cc_start: 0.8323 (mp0) cc_final: 0.7945 (mp0) REVERT: B 745 GLU cc_start: 0.5882 (mt-10) cc_final: 0.5401 (mp0) REVERT: C 42 LYS cc_start: 0.8145 (mtmt) cc_final: 0.7485 (mmtt) REVERT: C 71 ARG cc_start: 0.6861 (mtm110) cc_final: 0.6150 (mtp180) REVERT: C 87 GLU cc_start: 0.7603 (tt0) cc_final: 0.7250 (tp30) REVERT: C 170 ARG cc_start: 0.7690 (mtp180) cc_final: 0.6870 (ptp-170) REVERT: C 332 LEU cc_start: 0.8114 (tt) cc_final: 0.7799 (mt) REVERT: C 341 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.7654 (p90) REVERT: C 393 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7723 (mt) REVERT: C 528 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8854 (tp) REVERT: C 551 ASN cc_start: 0.8373 (t0) cc_final: 0.7839 (t0) REVERT: C 745 GLU cc_start: 0.5878 (mt-10) cc_final: 0.5406 (mp0) REVERT: D 42 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7472 (mmtt) REVERT: D 71 ARG cc_start: 0.6859 (mtm110) cc_final: 0.6134 (mtp180) REVERT: D 87 GLU cc_start: 0.7597 (tt0) cc_final: 0.7245 (tp30) REVERT: D 170 ARG cc_start: 0.7696 (mtp180) cc_final: 0.6874 (ptp-170) REVERT: D 341 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7897 (p90) REVERT: D 393 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7768 (mp) REVERT: D 528 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8851 (tp) REVERT: D 551 ASN cc_start: 0.8380 (t0) cc_final: 0.7843 (t0) REVERT: D 619 MET cc_start: 0.8278 (ttt) cc_final: 0.8067 (ttp) REVERT: D 745 GLU cc_start: 0.5866 (mt-10) cc_final: 0.5398 (mp0) outliers start: 68 outliers final: 38 residues processed: 307 average time/residue: 0.6055 time to fit residues: 214.4550 Evaluate side-chains 300 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 251 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 715 GLU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 715 GLU Chi-restraints excluded: chain D residue 717 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 214 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 216 optimal weight: 0.1980 chunk 143 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN A 731 ASN A 748 GLN B 82 ASN B 163 GLN B 731 ASN C 82 ASN C 192 HIS C 731 ASN D 82 ASN D 163 GLN D 731 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.155749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.120349 restraints weight = 24514.589| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.54 r_work: 0.3248 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22796 Z= 0.122 Angle : 0.477 6.893 30804 Z= 0.242 Chirality : 0.036 0.143 3444 Planarity : 0.003 0.038 3784 Dihedral : 10.050 152.059 3240 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.21 % Allowed : 16.85 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.16), residues: 2608 helix: 2.34 (0.11), residues: 1948 sheet: None (None), residues: 0 loop : 0.21 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 323 TYR 0.008 0.001 TYR A 586 PHE 0.029 0.001 PHE D 341 TRP 0.055 0.002 TRP A 327 HIS 0.002 0.000 HIS B 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (22776) covalent geometry : angle 0.47635 / 0.24 (30784) SS BOND : bond 0.00020 / 0.01 ( 4) SS BOND : angle 0.24048 / 0.16 ( 8) hydrogen bonds : bond 0.03570 / 2.38 ( 1432) hydrogen bonds : angle 3.50693 / 2.56 ( 4200) metal coordination : bond 0.00190 / 0.16 ( 16) metal coordination : angle 0.87265 / 0.66 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7431.43 seconds wall clock time: 127 minutes 25.86 seconds (7645.86 seconds total)