Starting phenix.real_space_refine on Sun Aug 24 22:01:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e4t_30987/08_2025/7e4t_30987.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e4t_30987/08_2025/7e4t_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_30987/08_2025/7e4t_30987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e4t_30987/08_2025/7e4t_30987.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e4t_30987/08_2025/7e4t_30987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e4t_30987/08_2025/7e4t_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-2.0-5787/lib/python3.9/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: 3.97, per 1000 atoms: 0.18 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: 1.63 Conformation dependent library (CDL) restraints added in 947.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.59 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: 2.85 Time building geometry restraints manager: 2.11 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: 13632 34.84 - 69.68: 236 69.68 - 104.52: 16 104.52 - 139.36: 8 139.36 - 174.21: 12 Dihedral angle restraints: 13904 sinusoidal: 6040 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 13901 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: 0.04 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: 1.360 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.980 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 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 : 14.086 174.205 8772 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 aren 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 covalent geometry : bond 0.00669 (22776) covalent geometry : angle 0.78570 (30784) SS BOND : bond 0.00035 ( 4) SS BOND : angle 0.34789 ( 8) hydrogen bonds : bond 0.11980 ( 1432) hydrogen bonds : angle 4.63947 ( 4200) metal coordination : bond 0.06300 ( 16) metal coordination : angle 4.89818 ( 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 : 0.648 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: 0.5852 (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: 0.6699 (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: 0.7484 (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: 0.6716 (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: 0.5880 (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: 0.7397 (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: 0.6418 (mmtt) REVERT: D 54 GLU cc_start: 0.6825 (tt0) cc_final: 0.5917 (tm-30) REVERT: D 56 GLU cc_start: 0.5997 (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: 0.7624 (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: 0.6129 time to fit residues: 345.0950 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 : 0.778 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3823 r_free = 0.3823 target = 0.157298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.120123 restraints weight = 25090.260| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.64 r_work: 0.3248 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22796 Z= 0.166 Angle : 0.520 7.310 30804 Z= 0.260 Chirality : 0.037 0.148 3444 Planarity : 0.004 0.034 3784 Dihedral : 14.329 179.501 3569 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.67 % Allowed : 9.88 % Favored : 86.44 % 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 aren not related in a simple way. whole: 2.00 (0.16), residues: 2608 helix: 1.70 (0.11), residues: 1952 sheet: None (None), residues: 0 loop : 0.38 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 754 TYR 0.011 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 B 712 Details of bonding type rmsd covalent geometry : bond 0.00382 (22776) covalent geometry : angle 0.51850 (30784) SS BOND : bond 0.00079 ( 4) SS BOND : angle 0.62175 ( 8) hydrogen bonds : bond 0.04285 ( 1432) hydrogen bonds : angle 3.73598 ( 4200) metal coordination : bond 0.00558 ( 16) metal coordination : angle 2.25597 ( 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 377 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 290 time to evaluate : 0.752 Fit side-chains REVERT: A 42 LYS cc_start: 0.7931 (mtmt) cc_final: 0.7512 (mmtt) REVERT: A 56 GLU cc_start: 0.6439 (mt-10) cc_final: 0.6147 (tm-30) REVERT: A 79 GLU cc_start: 0.7790 (tt0) cc_final: 0.7515 (mp0) REVERT: A 87 GLU cc_start: 0.7677 (tt0) cc_final: 0.7392 (tp30) REVERT: A 170 ARG cc_start: 0.6743 (mtp180) cc_final: 0.6476 (ptp90) REVERT: A 332 LEU cc_start: 0.8152 (tt) cc_final: 0.7608 (mt) REVERT: A 335 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7563 (mpt) REVERT: A 393 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7617 (mp) REVERT: A 520 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7333 (t80) REVERT: A 551 ASN cc_start: 0.8410 (t0) cc_final: 0.7951 (t0) REVERT: B 42 LYS cc_start: 0.7933 (mtmt) cc_final: 0.7517 (mmtt) REVERT: B 56 GLU cc_start: 0.6430 (mt-10) cc_final: 0.6146 (tm-30) REVERT: B 79 GLU cc_start: 0.7782 (tt0) cc_final: 0.7514 (mp0) REVERT: B 87 GLU cc_start: 0.7613 (tt0) cc_final: 0.7292 (tp30) REVERT: B 170 ARG cc_start: 0.6742 (mtp180) cc_final: 0.6464 (ptp90) REVERT: B 332 LEU cc_start: 0.8134 (tt) cc_final: 0.7586 (mt) REVERT: B 393 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7590 (mp) REVERT: B 520 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7345 (t80) REVERT: B 551 ASN cc_start: 0.8441 (t0) cc_final: 0.7980 (t0) REVERT: C 42 LYS cc_start: 0.7976 (mtmt) cc_final: 0.7550 (mmtt) REVERT: C 56 GLU cc_start: 0.6419 (mt-10) cc_final: 0.6131 (tm-30) REVERT: C 79 GLU cc_start: 0.7789 (tt0) cc_final: 0.7574 (mp0) REVERT: C 87 GLU cc_start: 0.7666 (tt0) cc_final: 0.7380 (tp30) REVERT: C 170 ARG cc_start: 0.6702 (mtp180) cc_final: 0.6435 (ptp90) REVERT: C 332 LEU cc_start: 0.8129 (tt) cc_final: 0.7589 (mt) REVERT: C 335 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7705 (mpt) REVERT: C 393 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7575 (mp) REVERT: C 520 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7353 (t80) REVERT: C 551 ASN cc_start: 0.8448 (t0) cc_final: 0.7979 (t0) REVERT: C 570 GLU cc_start: 0.8043 (tp30) cc_final: 0.7816 (mm-30) REVERT: D 42 LYS cc_start: 0.7968 (mtmt) cc_final: 0.7541 (mmtt) REVERT: D 56 GLU cc_start: 0.6442 (mt-10) cc_final: 0.6142 (tm-30) REVERT: D 79 GLU cc_start: 0.7787 (tt0) cc_final: 0.7506 (mp0) REVERT: D 87 GLU cc_start: 0.7661 (tt0) cc_final: 0.7391 (tp30) REVERT: D 170 ARG cc_start: 0.6720 (mtp180) cc_final: 0.6438 (ptp90) REVERT: D 332 LEU cc_start: 0.8139 (tt) cc_final: 0.7592 (mt) REVERT: D 393 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7603 (mp) REVERT: D 520 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7339 (t80) REVERT: D 551 ASN cc_start: 0.8443 (t0) cc_final: 0.7968 (t0) REVERT: D 570 GLU cc_start: 0.8025 (tp30) cc_final: 0.7793 (mm-30) outliers start: 87 outliers final: 40 residues processed: 332 average time/residue: 0.5503 time to fit residues: 208.7934 Evaluate side-chains 288 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 238 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 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 211 LEU Chi-restraints excluded: chain B residue 250 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 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 211 LEU 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 211 LEU 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: 2.9990 chunk 2 optimal weight: 10.0000 chunk 198 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 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: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 626 ASN C 192 HIS D 609 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.157932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.121946 restraints weight = 25122.515| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.58 r_work: 0.3262 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22796 Z= 0.149 Angle : 0.475 6.905 30804 Z= 0.242 Chirality : 0.036 0.149 3444 Planarity : 0.004 0.035 3784 Dihedral : 14.000 171.328 3560 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 4.27 % Allowed : 11.87 % Favored : 83.87 % 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 aren not related in a simple way. whole: 2.39 (0.16), residues: 2608 helix: 2.03 (0.11), residues: 1948 sheet: None (None), residues: 0 loop : 0.37 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 71 TYR 0.010 0.001 TYR B 524 PHE 0.020 0.001 PHE C 341 TRP 0.014 0.001 TRP A 315 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00349 (22776) covalent geometry : angle 0.47417 (30784) SS BOND : bond 0.00037 ( 4) SS BOND : angle 0.43617 ( 8) hydrogen bonds : bond 0.03991 ( 1432) hydrogen bonds : angle 3.55815 ( 4200) metal coordination : bond 0.00477 ( 16) metal coordination : angle 1.57869 ( 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 382 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 281 time to evaluate : 0.572 Fit side-chains REVERT: A 42 LYS cc_start: 0.8079 (mtmt) cc_final: 0.7636 (mmtt) REVERT: A 79 GLU cc_start: 0.7597 (tt0) cc_final: 0.7395 (mp0) REVERT: A 87 GLU cc_start: 0.7722 (tt0) cc_final: 0.7383 (tp30) REVERT: A 115 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8015 (mm) REVERT: A 170 ARG cc_start: 0.7159 (mtp180) cc_final: 0.6658 (ptp90) REVERT: A 332 LEU cc_start: 0.8128 (tt) cc_final: 0.7626 (mt) REVERT: A 335 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7458 (mpt) REVERT: A 393 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7679 (mp) REVERT: A 520 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7314 (t80) REVERT: A 551 ASN cc_start: 0.8425 (t0) cc_final: 0.7922 (t0) REVERT: A 595 GLU cc_start: 0.8146 (mp0) cc_final: 0.7878 (mp0) REVERT: B 42 LYS cc_start: 0.8082 (mtmt) cc_final: 0.7639 (mmtt) REVERT: B 87 GLU cc_start: 0.7747 (tt0) cc_final: 0.7388 (tp30) REVERT: B 115 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8004 (mm) REVERT: B 170 ARG cc_start: 0.7133 (mtp180) cc_final: 0.6649 (ptp90) REVERT: B 332 LEU cc_start: 0.8126 (tt) cc_final: 0.7627 (mt) REVERT: B 335 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7941 (mpt) REVERT: B 393 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7622 (mp) REVERT: B 520 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7346 (t80) REVERT: B 551 ASN cc_start: 0.8416 (t0) cc_final: 0.7915 (t0) REVERT: B 595 GLU cc_start: 0.8152 (mp0) cc_final: 0.7886 (mp0) REVERT: C 42 LYS cc_start: 0.8079 (mtmt) cc_final: 0.7631 (mmtt) REVERT: C 79 GLU cc_start: 0.7690 (tt0) cc_final: 0.7450 (mp0) REVERT: C 87 GLU cc_start: 0.7714 (tt0) cc_final: 0.7381 (tp30) REVERT: C 115 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7999 (mm) REVERT: C 170 ARG cc_start: 0.7140 (mtp180) cc_final: 0.6655 (ptp90) REVERT: C 332 LEU cc_start: 0.8120 (tt) cc_final: 0.7622 (mt) REVERT: C 393 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7594 (mt) REVERT: C 520 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7293 (t80) REVERT: C 551 ASN cc_start: 0.8456 (t0) cc_final: 0.7948 (t0) REVERT: C 595 GLU cc_start: 0.8186 (mp0) cc_final: 0.7913 (mp0) REVERT: D 42 LYS cc_start: 0.8087 (mtmt) cc_final: 0.7636 (mmtt) REVERT: D 79 GLU cc_start: 0.7694 (tt0) cc_final: 0.7429 (mp0) REVERT: D 87 GLU cc_start: 0.7704 (tt0) cc_final: 0.7383 (tp30) REVERT: D 115 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8010 (mm) REVERT: D 170 ARG cc_start: 0.7144 (mtp180) cc_final: 0.6653 (ptp90) REVERT: D 332 LEU cc_start: 0.8139 (tt) cc_final: 0.7647 (mt) REVERT: D 335 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7926 (mpt) REVERT: D 393 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7642 (mt) REVERT: D 520 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7311 (t80) REVERT: D 551 ASN cc_start: 0.8426 (t0) cc_final: 0.7912 (t0) REVERT: D 595 GLU cc_start: 0.8151 (mp0) cc_final: 0.7878 (mp0) outliers start: 101 outliers final: 21 residues processed: 327 average time/residue: 0.5195 time to fit residues: 195.2676 Evaluate side-chains 277 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 241 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 393 LEU Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 617 LEU 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 750 ILE 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 393 LEU Chi-restraints excluded: chain C residue 520 PHE Chi-restraints excluded: chain C residue 617 LEU 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 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 750 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 233 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 256 optimal weight: 0.8980 chunk 171 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 146 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 211 optimal weight: 0.0770 chunk 59 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.158061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121887 restraints weight = 24442.875| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.59 r_work: 0.3270 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2427 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 : 0.447 6.810 30804 Z= 0.228 Chirality : 0.034 0.142 3444 Planarity : 0.003 0.036 3784 Dihedral : 13.535 162.361 3552 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.89 % Allowed : 13.30 % 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 aren not related in a simple way. whole: 2.71 (0.16), residues: 2608 helix: 2.28 (0.11), residues: 1948 sheet: None (None), residues: 0 loop : 0.41 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 71 TYR 0.010 0.001 TYR D 200 PHE 0.019 0.001 PHE C 341 TRP 0.011 0.001 TRP A 315 HIS 0.004 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00225 (22776) covalent geometry : angle 0.44685 (30784) SS BOND : bond 0.00019 ( 4) SS BOND : angle 0.20190 ( 8) hydrogen bonds : bond 0.03552 ( 1432) hydrogen bonds : angle 3.47534 ( 4200) metal coordination : bond 0.00317 ( 16) metal coordination : angle 1.16438 ( 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 383 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 291 time to evaluate : 0.788 Fit side-chains REVERT: A 42 LYS cc_start: 0.8074 (mtmt) cc_final: 0.7588 (mmtt) REVERT: A 54 GLU cc_start: 0.7257 (mp0) cc_final: 0.6287 (tm-30) REVERT: A 87 GLU cc_start: 0.7716 (tt0) cc_final: 0.7387 (tp30) REVERT: A 170 ARG cc_start: 0.7123 (mtp180) cc_final: 0.6645 (ptp90) REVERT: A 332 LEU cc_start: 0.8082 (tt) cc_final: 0.7621 (mt) REVERT: A 335 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7755 (mpt) REVERT: A 393 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7666 (mp) REVERT: A 471 MET cc_start: 0.8919 (ttt) cc_final: 0.8668 (ttt) REVERT: A 551 ASN cc_start: 0.8375 (t0) cc_final: 0.7886 (t0) REVERT: A 595 GLU cc_start: 0.8190 (mp0) cc_final: 0.7905 (mp0) REVERT: B 42 LYS cc_start: 0.8069 (mtmt) cc_final: 0.7592 (mmtt) REVERT: B 54 GLU cc_start: 0.7299 (mp0) cc_final: 0.6333 (tm-30) REVERT: B 71 ARG cc_start: 0.6629 (mtm110) cc_final: 0.5904 (mtp180) REVERT: B 79 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: B 87 GLU cc_start: 0.7714 (tt0) cc_final: 0.7385 (tp30) REVERT: B 115 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8067 (mm) REVERT: B 170 ARG cc_start: 0.7108 (mtp180) cc_final: 0.6640 (ptp90) REVERT: B 332 LEU cc_start: 0.8086 (tt) cc_final: 0.7621 (mt) REVERT: B 335 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7923 (mpt) REVERT: B 393 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7640 (mp) REVERT: B 471 MET cc_start: 0.8916 (ttt) cc_final: 0.8680 (ttt) REVERT: B 551 ASN cc_start: 0.8367 (t0) cc_final: 0.7878 (t0) REVERT: B 595 GLU cc_start: 0.8193 (mp0) cc_final: 0.7920 (mp0) REVERT: C 42 LYS cc_start: 0.8038 (mtmt) cc_final: 0.7561 (mmtt) REVERT: C 54 GLU cc_start: 0.7273 (mp0) cc_final: 0.6296 (tm-30) REVERT: C 87 GLU cc_start: 0.7681 (tt0) cc_final: 0.7410 (tp30) REVERT: C 170 ARG cc_start: 0.7097 (mtp180) cc_final: 0.6620 (ptp90) REVERT: C 332 LEU cc_start: 0.8082 (tt) cc_final: 0.7623 (mt) REVERT: C 393 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7638 (mp) REVERT: C 471 MET cc_start: 0.8891 (ttt) cc_final: 0.8669 (ttt) REVERT: C 551 ASN cc_start: 0.8397 (t0) cc_final: 0.7903 (t0) REVERT: C 595 GLU cc_start: 0.8172 (mp0) cc_final: 0.7894 (mp0) REVERT: D 42 LYS cc_start: 0.8052 (mtmt) cc_final: 0.7565 (mmtt) REVERT: D 54 GLU cc_start: 0.7271 (mp0) cc_final: 0.6295 (tm-30) REVERT: D 87 GLU cc_start: 0.7678 (tt0) cc_final: 0.7399 (tp30) REVERT: D 170 ARG cc_start: 0.7099 (mtp180) cc_final: 0.6616 (ptp90) REVERT: D 332 LEU cc_start: 0.8085 (tt) cc_final: 0.7628 (mt) REVERT: D 335 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7983 (mpt) REVERT: D 393 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7652 (mp) REVERT: D 471 MET cc_start: 0.8900 (ttt) cc_final: 0.8678 (ttt) REVERT: D 551 ASN cc_start: 0.8391 (t0) cc_final: 0.7869 (t0) REVERT: D 595 GLU cc_start: 0.8160 (mp0) cc_final: 0.7873 (mp0) outliers start: 92 outliers final: 34 residues processed: 346 average time/residue: 0.5506 time to fit residues: 217.5869 Evaluate side-chains 300 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 257 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 96 VAL 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 393 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 715 GLU 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 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 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 750 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 393 LEU 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 75 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 211 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 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: 8.9990 chunk 170 optimal weight: 9.9990 chunk 72 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 156 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.155059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.118727 restraints weight = 24476.527| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.58 r_work: 0.3233 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22796 Z= 0.208 Angle : 0.541 11.225 30804 Z= 0.270 Chirality : 0.038 0.155 3444 Planarity : 0.004 0.038 3784 Dihedral : 13.786 164.870 3552 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.10 % Allowed : 14.27 % Favored : 81.63 % 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 aren not related in a simple way. whole: 2.43 (0.16), residues: 2608 helix: 2.07 (0.11), residues: 1944 sheet: None (None), residues: 0 loop : 0.33 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 71 TYR 0.011 0.001 TYR C 539 PHE 0.021 0.002 PHE C 341 TRP 0.017 0.001 TRP C 315 HIS 0.003 0.001 HIS C 473 Details of bonding type rmsd covalent geometry : bond 0.00507 (22776) covalent geometry : angle 0.54041 (30784) SS BOND : bond 0.00095 ( 4) SS BOND : angle 0.51076 ( 8) hydrogen bonds : bond 0.04169 ( 1432) hydrogen bonds : angle 3.59165 ( 4200) metal coordination : bond 0.00489 ( 16) metal coordination : angle 1.39325 ( 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 352 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 255 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8089 (mtmt) cc_final: 0.7497 (mmtt) REVERT: A 71 ARG cc_start: 0.6705 (mtm110) cc_final: 0.5750 (mtp85) REVERT: A 87 GLU cc_start: 0.7783 (tt0) cc_final: 0.7348 (tp30) REVERT: A 170 ARG cc_start: 0.7440 (mtp180) cc_final: 0.6737 (ptp90) REVERT: A 332 LEU cc_start: 0.8073 (tt) cc_final: 0.7639 (mt) REVERT: A 335 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7547 (mpt) REVERT: A 393 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7686 (mp) REVERT: A 471 MET cc_start: 0.8971 (ttt) cc_final: 0.8697 (ttt) REVERT: A 520 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7294 (t80) REVERT: A 551 ASN cc_start: 0.8483 (t0) cc_final: 0.7932 (t0) REVERT: A 595 GLU cc_start: 0.8274 (mp0) cc_final: 0.7903 (mp0) REVERT: B 42 LYS cc_start: 0.8136 (mtmt) cc_final: 0.7532 (mmtt) REVERT: B 71 ARG cc_start: 0.6663 (mtm110) cc_final: 0.5802 (mtp85) REVERT: B 87 GLU cc_start: 0.7771 (tt0) cc_final: 0.7321 (tp30) REVERT: B 115 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8087 (mm) REVERT: B 170 ARG cc_start: 0.7437 (mtp180) cc_final: 0.6739 (ptp90) REVERT: B 332 LEU cc_start: 0.8060 (tt) cc_final: 0.7623 (mt) REVERT: B 335 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7963 (mpt) REVERT: B 393 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7640 (mp) REVERT: B 520 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7293 (t80) REVERT: B 551 ASN cc_start: 0.8469 (t0) cc_final: 0.7919 (t0) REVERT: B 595 GLU cc_start: 0.8290 (mp0) cc_final: 0.7961 (mp0) REVERT: C 42 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7529 (mmtt) REVERT: C 71 ARG cc_start: 0.6722 (mtm110) cc_final: 0.5768 (mtp85) REVERT: C 87 GLU cc_start: 0.7793 (tt0) cc_final: 0.7374 (tp30) REVERT: C 170 ARG cc_start: 0.7413 (mtp180) cc_final: 0.6712 (ptp90) REVERT: C 332 LEU cc_start: 0.8065 (tt) cc_final: 0.7632 (mt) REVERT: C 520 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7340 (t80) REVERT: C 551 ASN cc_start: 0.8465 (t0) cc_final: 0.7911 (t0) REVERT: C 595 GLU cc_start: 0.8294 (mp0) cc_final: 0.7952 (mp0) REVERT: D 42 LYS cc_start: 0.8097 (mtmt) cc_final: 0.7509 (mmtt) REVERT: D 71 ARG cc_start: 0.6713 (mtm110) cc_final: 0.5789 (mtp85) REVERT: D 87 GLU cc_start: 0.7779 (tt0) cc_final: 0.7371 (tp30) REVERT: D 170 ARG cc_start: 0.7431 (mtp180) cc_final: 0.6724 (ptp90) REVERT: D 332 LEU cc_start: 0.8068 (tt) cc_final: 0.7635 (mt) REVERT: D 335 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7955 (mpt) REVERT: D 520 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7333 (t80) REVERT: D 551 ASN cc_start: 0.8471 (t0) cc_final: 0.7919 (t0) REVERT: D 595 GLU cc_start: 0.8280 (mp0) cc_final: 0.7908 (mp0) REVERT: D 619 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8164 (tpt) REVERT: D 623 MET cc_start: 0.8704 (mtp) cc_final: 0.8488 (mtm) outliers start: 97 outliers final: 40 residues processed: 308 average time/residue: 0.6406 time to fit residues: 224.0908 Evaluate side-chains 296 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 245 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 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 656 THR Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 717 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 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 518 LEU Chi-restraints excluded: chain B residue 520 PHE 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 B residue 750 ILE Chi-restraints excluded: chain C residue 114 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 520 PHE Chi-restraints excluded: chain C residue 617 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 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 520 PHE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 619 MET Chi-restraints excluded: chain D residue 715 GLU Chi-restraints excluded: chain D residue 717 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: 0.8980 chunk 183 optimal weight: 0.9980 chunk 257 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 157 optimal weight: 0.9990 chunk 166 optimal weight: 8.9990 chunk 112 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN B 326 HIS C 80 ASN C 192 HIS ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.156961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.120887 restraints weight = 24482.672| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.58 r_work: 0.3267 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2786 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= 0.105 Angle : 0.455 9.355 30804 Z= 0.230 Chirality : 0.035 0.143 3444 Planarity : 0.003 0.037 3784 Dihedral : 13.261 166.380 3548 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.59 % Allowed : 15.16 % Favored : 81.25 % 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 aren not related in a simple way. whole: 2.68 (0.16), residues: 2608 helix: 2.27 (0.11), residues: 1944 sheet: None (None), residues: 0 loop : 0.35 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 323 TYR 0.009 0.001 TYR A 200 PHE 0.020 0.001 PHE C 341 TRP 0.010 0.001 TRP D 315 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00236 (22776) covalent geometry : angle 0.45435 (30784) SS BOND : bond 0.00018 ( 4) SS BOND : angle 0.18558 ( 8) hydrogen bonds : bond 0.03544 ( 1432) hydrogen bonds : angle 3.49322 ( 4200) metal coordination : bond 0.00237 ( 16) metal coordination : angle 1.03864 ( 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 352 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 267 time to evaluate : 0.962 Fit side-chains REVERT: A 42 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7544 (mmtt) REVERT: A 71 ARG cc_start: 0.6632 (mtm110) cc_final: 0.5827 (mtp85) REVERT: A 87 GLU cc_start: 0.7736 (tt0) cc_final: 0.7341 (tp30) REVERT: A 170 ARG cc_start: 0.7433 (mtp180) cc_final: 0.6719 (ptp90) REVERT: A 332 LEU cc_start: 0.8055 (tt) cc_final: 0.7686 (mt) REVERT: A 471 MET cc_start: 0.8906 (ttt) cc_final: 0.8595 (ttp) REVERT: A 510 LEU cc_start: 0.8494 (tp) cc_final: 0.8262 (mm) REVERT: A 551 ASN cc_start: 0.8400 (t0) cc_final: 0.7845 (t0) REVERT: A 595 GLU cc_start: 0.8263 (mp0) cc_final: 0.7912 (mp0) REVERT: B 42 LYS cc_start: 0.8103 (mtmt) cc_final: 0.7529 (mmtt) REVERT: B 71 ARG cc_start: 0.6687 (mtm110) cc_final: 0.5814 (mtp85) REVERT: B 87 GLU cc_start: 0.7734 (tt0) cc_final: 0.7307 (tp30) REVERT: B 115 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8113 (mm) REVERT: B 170 ARG cc_start: 0.7418 (mtp180) cc_final: 0.6710 (ptp90) REVERT: B 332 LEU cc_start: 0.8050 (tt) cc_final: 0.7674 (mt) REVERT: B 528 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8823 (tp) REVERT: B 551 ASN cc_start: 0.8398 (t0) cc_final: 0.7847 (t0) REVERT: B 595 GLU cc_start: 0.8244 (mp0) cc_final: 0.7922 (mp0) REVERT: C 42 LYS cc_start: 0.8107 (mtmt) cc_final: 0.7527 (mmtt) REVERT: C 71 ARG cc_start: 0.6634 (mtm110) cc_final: 0.5824 (mtp85) REVERT: C 87 GLU cc_start: 0.7717 (tt0) cc_final: 0.7342 (tp30) REVERT: C 170 ARG cc_start: 0.7416 (mtp180) cc_final: 0.6713 (ptp90) REVERT: C 332 LEU cc_start: 0.8042 (tt) cc_final: 0.7676 (mt) REVERT: C 335 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7870 (mpt) REVERT: C 393 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7673 (mp) REVERT: C 551 ASN cc_start: 0.8426 (t0) cc_final: 0.7869 (t0) REVERT: C 595 GLU cc_start: 0.8250 (mp0) cc_final: 0.7911 (mp0) REVERT: C 624 MET cc_start: 0.8366 (mtt) cc_final: 0.8141 (mtt) REVERT: D 42 LYS cc_start: 0.8112 (mtmt) cc_final: 0.7528 (mmtt) REVERT: D 71 ARG cc_start: 0.6635 (mtm110) cc_final: 0.5825 (mtp85) REVERT: D 87 GLU cc_start: 0.7715 (tt0) cc_final: 0.7340 (tp30) REVERT: D 170 ARG cc_start: 0.7414 (mtp180) cc_final: 0.6698 (ptp90) REVERT: D 332 LEU cc_start: 0.8033 (tt) cc_final: 0.7665 (mt) REVERT: D 393 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7679 (mt) REVERT: D 528 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8840 (tp) REVERT: D 551 ASN cc_start: 0.8417 (t0) cc_final: 0.7880 (t0) REVERT: D 595 GLU cc_start: 0.8235 (mp0) cc_final: 0.7842 (mp0) outliers start: 85 outliers final: 39 residues processed: 316 average time/residue: 0.6668 time to fit residues: 241.0808 Evaluate side-chains 289 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 244 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 353 ARG Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 656 THR 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 96 VAL 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 353 ARG Chi-restraints excluded: chain B residue 515 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 653 GLU 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 B residue 750 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 353 ARG Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 617 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 96 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 353 ARG Chi-restraints excluded: chain D residue 393 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 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: 8.9990 chunk 95 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 210 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN C 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.154055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117830 restraints weight = 24621.802| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.59 r_work: 0.3218 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22796 Z= 0.167 Angle : 0.497 6.743 30804 Z= 0.253 Chirality : 0.037 0.150 3444 Planarity : 0.004 0.038 3784 Dihedral : 13.253 168.540 3544 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.80 % Allowed : 15.62 % Favored : 80.57 % 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 aren not related in a simple way. whole: 2.54 (0.16), residues: 2608 helix: 2.17 (0.11), residues: 1944 sheet: None (None), residues: 0 loop : 0.31 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 71 TYR 0.008 0.001 TYR A 539 PHE 0.021 0.001 PHE A 341 TRP 0.022 0.001 TRP A 327 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00405 (22776) covalent geometry : angle 0.49650 (30784) SS BOND : bond 0.00070 ( 4) SS BOND : angle 0.39555 ( 8) hydrogen bonds : bond 0.03884 ( 1432) hydrogen bonds : angle 3.54717 ( 4200) metal coordination : bond 0.00344 ( 16) metal coordination : angle 1.12483 ( 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 336 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 246 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8227 (mtmt) cc_final: 0.7581 (mmtt) REVERT: A 71 ARG cc_start: 0.6806 (mtm110) cc_final: 0.5936 (mtp85) REVERT: A 87 GLU cc_start: 0.7718 (tt0) cc_final: 0.7328 (tp30) REVERT: A 170 ARG cc_start: 0.7503 (mtp180) cc_final: 0.6695 (ptp90) REVERT: A 332 LEU cc_start: 0.8119 (tt) cc_final: 0.7785 (mt) REVERT: A 393 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7710 (mp) REVERT: A 551 ASN cc_start: 0.8441 (t0) cc_final: 0.7884 (t0) REVERT: A 595 GLU cc_start: 0.8317 (mp0) cc_final: 0.7979 (mp0) REVERT: A 623 MET cc_start: 0.8661 (mtp) cc_final: 0.8453 (mtm) REVERT: A 624 MET cc_start: 0.8464 (mtt) cc_final: 0.8168 (mtt) REVERT: B 42 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7582 (mmtt) REVERT: B 71 ARG cc_start: 0.6792 (mtm110) cc_final: 0.5936 (mtp85) REVERT: B 87 GLU cc_start: 0.7716 (tt0) cc_final: 0.7323 (tp30) REVERT: B 115 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8173 (mm) REVERT: B 170 ARG cc_start: 0.7513 (mtp180) cc_final: 0.6697 (ptp90) REVERT: B 332 LEU cc_start: 0.8059 (tt) cc_final: 0.7713 (mt) REVERT: B 393 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7695 (mp) REVERT: B 551 ASN cc_start: 0.8417 (t0) cc_final: 0.7854 (t0) REVERT: B 595 GLU cc_start: 0.8320 (mp0) cc_final: 0.8001 (mp0) REVERT: B 623 MET cc_start: 0.8663 (mtp) cc_final: 0.8452 (mtm) REVERT: B 624 MET cc_start: 0.8476 (mtt) cc_final: 0.8178 (mtt) REVERT: C 42 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7588 (mmtt) REVERT: C 71 ARG cc_start: 0.6792 (mtm110) cc_final: 0.5913 (mtp85) REVERT: C 87 GLU cc_start: 0.7680 (tt0) cc_final: 0.7321 (tp30) REVERT: C 170 ARG cc_start: 0.7545 (mtp180) cc_final: 0.6697 (ptp90) REVERT: C 332 LEU cc_start: 0.8080 (tt) cc_final: 0.7722 (mt) REVERT: C 393 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7658 (mt) REVERT: C 551 ASN cc_start: 0.8438 (t0) cc_final: 0.7871 (t0) REVERT: C 595 GLU cc_start: 0.8309 (mp0) cc_final: 0.7976 (mp0) REVERT: C 624 MET cc_start: 0.8517 (mtt) cc_final: 0.8154 (mtt) REVERT: D 42 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7581 (mmtt) REVERT: D 71 ARG cc_start: 0.6810 (mtm110) cc_final: 0.5933 (mtp85) REVERT: D 87 GLU cc_start: 0.7683 (tt0) cc_final: 0.7321 (tp30) REVERT: D 170 ARG cc_start: 0.7544 (mtp180) cc_final: 0.6692 (ptp90) REVERT: D 332 LEU cc_start: 0.8101 (tt) cc_final: 0.7768 (mt) REVERT: D 393 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7693 (mp) REVERT: D 551 ASN cc_start: 0.8444 (t0) cc_final: 0.7878 (t0) REVERT: D 595 GLU cc_start: 0.8287 (mp0) cc_final: 0.7915 (mp0) REVERT: D 623 MET cc_start: 0.8561 (mtm) cc_final: 0.8361 (mtp) outliers start: 90 outliers final: 48 residues processed: 304 average time/residue: 0.6368 time to fit residues: 219.8189 Evaluate side-chains 294 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 241 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 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 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 653 GLU Chi-restraints excluded: chain A residue 656 THR 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 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 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 653 GLU 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 114 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 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 617 LEU Chi-restraints excluded: chain C residue 653 GLU 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 250 LEU Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 353 ARG 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 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: 0.7980 chunk 69 optimal weight: 7.9990 chunk 172 optimal weight: 6.9990 chunk 250 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3787 r_free = 0.3787 target = 0.155191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119147 restraints weight = 24505.971| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.58 r_work: 0.3235 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22796 Z= 0.124 Angle : 0.459 6.780 30804 Z= 0.234 Chirality : 0.036 0.144 3444 Planarity : 0.003 0.037 3784 Dihedral : 12.937 170.258 3544 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.76 % Allowed : 15.41 % Favored : 80.83 % 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 aren not related in a simple way. whole: 2.61 (0.16), residues: 2608 helix: 2.24 (0.11), residues: 1944 sheet: None (None), residues: 0 loop : 0.27 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 323 TYR 0.009 0.001 TYR B 524 PHE 0.021 0.001 PHE B 341 TRP 0.013 0.001 TRP C 315 HIS 0.005 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00290 (22776) covalent geometry : angle 0.45890 (30784) SS BOND : bond 0.00042 ( 4) SS BOND : angle 0.29201 ( 8) hydrogen bonds : bond 0.03628 ( 1432) hydrogen bonds : angle 3.49893 ( 4200) metal coordination : bond 0.00256 ( 16) metal coordination : angle 0.98626 ( 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 341 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 252 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8227 (mtmt) cc_final: 0.7561 (mmtt) REVERT: A 71 ARG cc_start: 0.6821 (mtm110) cc_final: 0.6041 (mtp180) REVERT: A 87 GLU cc_start: 0.7709 (tt0) cc_final: 0.7311 (tp30) REVERT: A 170 ARG cc_start: 0.7545 (mtp180) cc_final: 0.6763 (ptp90) REVERT: A 327 TRP cc_start: 0.7343 (p-90) cc_final: 0.7093 (p-90) REVERT: A 332 LEU cc_start: 0.8133 (tt) cc_final: 0.7808 (mt) REVERT: A 393 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7708 (mp) REVERT: A 510 LEU cc_start: 0.8473 (tp) cc_final: 0.8239 (mp) REVERT: A 551 ASN cc_start: 0.8412 (t0) cc_final: 0.7866 (t0) REVERT: A 595 GLU cc_start: 0.8320 (mp0) cc_final: 0.8000 (mp0) REVERT: A 623 MET cc_start: 0.8664 (mtp) cc_final: 0.8422 (mtm) REVERT: A 624 MET cc_start: 0.8459 (mtt) cc_final: 0.8148 (mtt) REVERT: B 42 LYS cc_start: 0.8242 (mtmt) cc_final: 0.7574 (mmtt) REVERT: B 71 ARG cc_start: 0.6865 (mtm110) cc_final: 0.6043 (mtp180) REVERT: B 87 GLU cc_start: 0.7702 (tt0) cc_final: 0.7311 (tp30) REVERT: B 115 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8151 (mm) REVERT: B 170 ARG cc_start: 0.7517 (mtp180) cc_final: 0.6757 (ptp90) REVERT: B 332 LEU cc_start: 0.8034 (tt) cc_final: 0.7682 (mt) REVERT: B 393 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7703 (mp) REVERT: B 551 ASN cc_start: 0.8381 (t0) cc_final: 0.7828 (t0) REVERT: B 595 GLU cc_start: 0.8301 (mp0) cc_final: 0.7958 (mp0) REVERT: B 624 MET cc_start: 0.8450 (mtt) cc_final: 0.8186 (mtt) REVERT: C 42 LYS cc_start: 0.8242 (mtmt) cc_final: 0.7572 (mmtt) REVERT: C 71 ARG cc_start: 0.6776 (mtm110) cc_final: 0.5995 (mtp180) REVERT: C 87 GLU cc_start: 0.7686 (tt0) cc_final: 0.7331 (tp30) REVERT: C 170 ARG cc_start: 0.7524 (mtp180) cc_final: 0.6766 (ptp90) REVERT: C 332 LEU cc_start: 0.8068 (tt) cc_final: 0.7728 (mt) REVERT: C 393 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7671 (mp) REVERT: C 551 ASN cc_start: 0.8414 (t0) cc_final: 0.7859 (t0) REVERT: C 595 GLU cc_start: 0.8313 (mp0) cc_final: 0.7970 (mp0) REVERT: C 624 MET cc_start: 0.8518 (mtt) cc_final: 0.8214 (mtt) REVERT: D 42 LYS cc_start: 0.8235 (mtmt) cc_final: 0.7567 (mmtt) REVERT: D 71 ARG cc_start: 0.6796 (mtm110) cc_final: 0.6012 (mtp180) REVERT: D 87 GLU cc_start: 0.7668 (tt0) cc_final: 0.7309 (tp30) REVERT: D 170 ARG cc_start: 0.7511 (mtp180) cc_final: 0.6740 (ptp90) REVERT: D 332 LEU cc_start: 0.8111 (tt) cc_final: 0.7787 (mt) REVERT: D 393 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7696 (mp) REVERT: D 528 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8830 (tp) REVERT: D 551 ASN cc_start: 0.8414 (t0) cc_final: 0.7861 (t0) REVERT: D 595 GLU cc_start: 0.8309 (mp0) cc_final: 0.7962 (mp0) outliers start: 89 outliers final: 46 residues processed: 309 average time/residue: 0.6279 time to fit residues: 220.9756 Evaluate side-chains 292 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 240 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 211 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 653 GLU Chi-restraints excluded: chain A residue 656 THR 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 115 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 211 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 653 GLU 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 114 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 211 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 617 LEU Chi-restraints excluded: chain C residue 653 GLU 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 346 ILE 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 653 GLU 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: 4.9990 chunk 13 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3769 r_free = 0.3769 target = 0.153634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.117579 restraints weight = 24490.186| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.58 r_work: 0.3213 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22796 Z= 0.169 Angle : 0.510 7.866 30804 Z= 0.259 Chirality : 0.037 0.146 3444 Planarity : 0.004 0.041 3784 Dihedral : 12.888 171.579 3544 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.08 % Allowed : 15.96 % Favored : 80.95 % 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 aren not related in a simple way. whole: 2.48 (0.16), residues: 2608 helix: 2.14 (0.11), residues: 1944 sheet: None (None), residues: 0 loop : 0.24 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 323 TYR 0.008 0.001 TYR C 586 PHE 0.022 0.001 PHE D 341 TRP 0.021 0.001 TRP C 327 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00409 (22776) covalent geometry : angle 0.51011 (30784) SS BOND : bond 0.00079 ( 4) SS BOND : angle 0.46148 ( 8) hydrogen bonds : bond 0.03894 ( 1432) hydrogen bonds : angle 3.56839 ( 4200) metal coordination : bond 0.00335 ( 16) metal coordination : angle 1.09496 ( 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 321 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 248 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8237 (mtmt) cc_final: 0.7523 (mmtt) REVERT: A 71 ARG cc_start: 0.6826 (mtm110) cc_final: 0.6049 (mtp180) REVERT: A 87 GLU cc_start: 0.7705 (tt0) cc_final: 0.7310 (tp30) REVERT: A 170 ARG cc_start: 0.7706 (mtp180) cc_final: 0.6832 (ptp90) REVERT: A 327 TRP cc_start: 0.7392 (p-90) cc_final: 0.7110 (p-90) REVERT: A 332 LEU cc_start: 0.8094 (tt) cc_final: 0.7774 (mt) REVERT: A 393 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7718 (mp) REVERT: A 551 ASN cc_start: 0.8529 (t0) cc_final: 0.7943 (t0) REVERT: A 595 GLU cc_start: 0.8347 (mp0) cc_final: 0.8007 (mp0) REVERT: A 623 MET cc_start: 0.8661 (mtp) cc_final: 0.8410 (mtm) REVERT: A 624 MET cc_start: 0.8535 (mtt) cc_final: 0.8138 (mtt) REVERT: B 42 LYS cc_start: 0.8141 (mtmt) cc_final: 0.7482 (mmtt) REVERT: B 71 ARG cc_start: 0.6829 (mtm110) cc_final: 0.6055 (mtp180) REVERT: B 87 GLU cc_start: 0.7688 (tt0) cc_final: 0.7316 (tp30) REVERT: B 115 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8156 (mm) REVERT: B 170 ARG cc_start: 0.7666 (mtp180) cc_final: 0.6799 (ptp90) REVERT: B 332 LEU cc_start: 0.8044 (tt) cc_final: 0.7692 (mt) REVERT: B 393 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7699 (mt) REVERT: B 551 ASN cc_start: 0.8516 (t0) cc_final: 0.7928 (t0) REVERT: B 595 GLU cc_start: 0.8350 (mp0) cc_final: 0.7996 (mp0) REVERT: B 624 MET cc_start: 0.8536 (mtt) cc_final: 0.8205 (mtt) REVERT: C 42 LYS cc_start: 0.8189 (mtmt) cc_final: 0.7539 (mmtt) REVERT: C 71 ARG cc_start: 0.6839 (mtm110) cc_final: 0.6047 (mtp180) REVERT: C 87 GLU cc_start: 0.7666 (tt0) cc_final: 0.7318 (tp30) REVERT: C 170 ARG cc_start: 0.7662 (mtp180) cc_final: 0.6818 (ptp90) REVERT: C 332 LEU cc_start: 0.8111 (tt) cc_final: 0.7773 (mt) REVERT: C 393 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7733 (mp) REVERT: C 551 ASN cc_start: 0.8537 (t0) cc_final: 0.7946 (t0) REVERT: C 595 GLU cc_start: 0.8349 (mp0) cc_final: 0.8015 (mp0) REVERT: C 624 MET cc_start: 0.8548 (mtt) cc_final: 0.8252 (mtt) REVERT: D 42 LYS cc_start: 0.8141 (mtmt) cc_final: 0.7475 (mmtt) REVERT: D 71 ARG cc_start: 0.6816 (mtm110) cc_final: 0.6039 (mtp180) REVERT: D 87 GLU cc_start: 0.7686 (tt0) cc_final: 0.7314 (tp30) REVERT: D 170 ARG cc_start: 0.7666 (mtp180) cc_final: 0.6799 (ptp90) REVERT: D 327 TRP cc_start: 0.7375 (p-90) cc_final: 0.7148 (p-90) REVERT: D 332 LEU cc_start: 0.8108 (tt) cc_final: 0.7797 (mt) REVERT: D 393 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7727 (mt) REVERT: D 551 ASN cc_start: 0.8538 (t0) cc_final: 0.7945 (t0) REVERT: D 595 GLU cc_start: 0.8315 (mp0) cc_final: 0.7987 (mp0) outliers start: 73 outliers final: 46 residues processed: 296 average time/residue: 0.6503 time to fit residues: 218.4536 Evaluate side-chains 284 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 233 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 250 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 653 GLU Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 79 GLU 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 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 653 GLU 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 114 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 617 LEU Chi-restraints excluded: chain C residue 653 GLU 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 250 LEU Chi-restraints excluded: chain D residue 346 ILE 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 653 GLU 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: 4.9990 chunk 246 optimal weight: 1.9990 chunk 234 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3793 r_free = 0.3793 target = 0.155875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119941 restraints weight = 24571.850| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.58 r_work: 0.3246 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22796 Z= 0.113 Angle : 0.469 6.933 30804 Z= 0.238 Chirality : 0.036 0.143 3444 Planarity : 0.003 0.038 3784 Dihedral : 12.246 172.828 3544 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.62 % Allowed : 16.47 % Favored : 80.91 % 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 aren not related in a simple way. whole: 2.65 (0.16), residues: 2608 helix: 2.27 (0.11), residues: 1944 sheet: None (None), residues: 0 loop : 0.28 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 323 TYR 0.008 0.001 TYR C 586 PHE 0.021 0.001 PHE D 341 TRP 0.014 0.001 TRP D 327 HIS 0.005 0.001 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00259 (22776) covalent geometry : angle 0.46875 (30784) SS BOND : bond 0.00012 ( 4) SS BOND : angle 0.24049 ( 8) hydrogen bonds : bond 0.03537 ( 1432) hydrogen bonds : angle 3.52721 ( 4200) metal coordination : bond 0.00191 ( 16) metal coordination : angle 0.93259 ( 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 321 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 259 time to evaluate : 0.784 Fit side-chains REVERT: A 42 LYS cc_start: 0.8256 (mtmt) cc_final: 0.7560 (mmtt) REVERT: A 71 ARG cc_start: 0.6909 (mtm110) cc_final: 0.6120 (mtp180) REVERT: A 87 GLU cc_start: 0.7633 (tt0) cc_final: 0.7244 (tp30) REVERT: A 170 ARG cc_start: 0.7698 (mtp180) cc_final: 0.6902 (ptp-170) REVERT: A 327 TRP cc_start: 0.7424 (p-90) cc_final: 0.7141 (p-90) REVERT: A 393 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7716 (mp) REVERT: A 551 ASN cc_start: 0.8404 (t0) cc_final: 0.7853 (t0) REVERT: A 595 GLU cc_start: 0.8315 (mp0) cc_final: 0.8005 (mp0) REVERT: A 624 MET cc_start: 0.8520 (mtt) cc_final: 0.8262 (mtt) REVERT: B 42 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7470 (mmtt) REVERT: B 71 ARG cc_start: 0.6924 (mtm110) cc_final: 0.6125 (mtp180) REVERT: B 87 GLU cc_start: 0.7656 (tt0) cc_final: 0.7297 (tp30) REVERT: B 115 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8148 (mm) REVERT: B 170 ARG cc_start: 0.7674 (mtp180) cc_final: 0.6900 (ptp-170) REVERT: B 393 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7702 (mt) REVERT: B 551 ASN cc_start: 0.8389 (t0) cc_final: 0.7832 (t0) REVERT: B 595 GLU cc_start: 0.8279 (mp0) cc_final: 0.7960 (mp0) REVERT: B 624 MET cc_start: 0.8456 (mtt) cc_final: 0.8158 (mtt) REVERT: C 42 LYS cc_start: 0.8141 (mtmt) cc_final: 0.7481 (mmtt) REVERT: C 71 ARG cc_start: 0.6891 (mtm110) cc_final: 0.6096 (mtp180) REVERT: C 87 GLU cc_start: 0.7592 (tt0) cc_final: 0.7255 (tp30) REVERT: C 170 ARG cc_start: 0.7692 (mtp180) cc_final: 0.6912 (ptp-170) REVERT: C 393 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7712 (mp) REVERT: C 551 ASN cc_start: 0.8414 (t0) cc_final: 0.7860 (t0) REVERT: C 595 GLU cc_start: 0.8293 (mp0) cc_final: 0.7966 (mp0) REVERT: C 624 MET cc_start: 0.8493 (mtt) cc_final: 0.8243 (mtt) REVERT: C 745 GLU cc_start: 0.5791 (mt-10) cc_final: 0.5306 (mp0) REVERT: D 42 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7478 (mmtt) REVERT: D 71 ARG cc_start: 0.6892 (mtm110) cc_final: 0.6100 (mtp180) REVERT: D 87 GLU cc_start: 0.7578 (tt0) cc_final: 0.7249 (tp30) REVERT: D 170 ARG cc_start: 0.7684 (mtp180) cc_final: 0.6899 (ptp-170) REVERT: D 327 TRP cc_start: 0.7333 (p-90) cc_final: 0.7088 (p-90) REVERT: D 393 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7711 (mt) REVERT: D 528 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8828 (tp) REVERT: D 551 ASN cc_start: 0.8417 (t0) cc_final: 0.7859 (t0) REVERT: D 595 GLU cc_start: 0.8291 (mp0) cc_final: 0.7956 (mp0) outliers start: 62 outliers final: 43 residues processed: 303 average time/residue: 0.6762 time to fit residues: 232.3163 Evaluate side-chains 289 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 240 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 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 653 GLU Chi-restraints excluded: chain A residue 656 THR 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 115 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 211 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 656 THR Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 211 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 617 LEU Chi-restraints excluded: chain C residue 653 GLU 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 346 ILE 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 653 GLU 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: 1.9990 chunk 103 optimal weight: 10.0000 chunk 216 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 236 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 731 ASN B 163 GLN B 731 ASN C 163 GLN D 163 GLN D 731 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.155106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.119449 restraints weight = 24448.251| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.55 r_work: 0.3240 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22796 Z= 0.142 Angle : 0.503 8.984 30804 Z= 0.253 Chirality : 0.037 0.154 3444 Planarity : 0.004 0.039 3784 Dihedral : 11.846 173.592 3544 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.87 % Allowed : 16.72 % Favored : 80.41 % 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 aren not related in a simple way. whole: 2.57 (0.16), residues: 2608 helix: 2.20 (0.11), residues: 1944 sheet: None (None), residues: 0 loop : 0.26 (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 D 586 PHE 0.022 0.001 PHE B 341 TRP 0.018 0.001 TRP C 327 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00338 (22776) covalent geometry : angle 0.50228 (30784) SS BOND : bond 0.00045 ( 4) SS BOND : angle 0.38001 ( 8) hydrogen bonds : bond 0.03739 ( 1432) hydrogen bonds : angle 3.55930 ( 4200) metal coordination : bond 0.00254 ( 16) metal coordination : angle 0.99069 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7288.43 seconds wall clock time: 124 minutes 55.01 seconds (7495.01 seconds total)