Starting phenix.real_space_refine on Sun Oct 12 05:17:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5zbg_6911/10_2025/5zbg_6911.cif Found real_map, /net/cci-nas-00/data/ceres_data/5zbg_6911/10_2025/5zbg_6911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5zbg_6911/10_2025/5zbg_6911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5zbg_6911/10_2025/5zbg_6911.map" model { file = "/net/cci-nas-00/data/ceres_data/5zbg_6911/10_2025/5zbg_6911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5zbg_6911/10_2025/5zbg_6911.cif" } resolution = 4.36 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= 0.021 sd= 0.092 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: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 13824 2.51 5 N 3460 2.21 5 O 3852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21260 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5315 Classifications: {'peptide': 670} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 17, 'TRANS': 652} Chain breaks: 5 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Restraints were copied for chains: B, C, D Time building chain proxies: 5.31, per 1000 atoms: 0.25 Number of scatterers: 21260 At special positions: 0 Unit cell: (127.41, 127.41, 167.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 3852 8.00 N 3460 7.00 C 13824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.12 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5112 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 0 sheets defined 77.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 25 through 37 removed outlier: 3.657A pdb=" N TYR A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 50 removed outlier: 4.379A pdb=" N GLU A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 72 removed outlier: 3.659A pdb=" N ASN A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 83 removed outlier: 3.693A pdb=" N LYS A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 101 Processing helix chain 'A' and resid 102 through 111 removed outlier: 3.548A pdb=" N ASN A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 removed outlier: 4.069A pdb=" N GLU A 140 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP A 141 " --> pdb=" O TYR A 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 137 through 141' Processing helix chain 'A' and resid 150 through 158 Processing helix chain 'A' and resid 160 through 170 removed outlier: 3.520A pdb=" N LYS A 170 " --> pdb=" O MET A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 190 Processing helix chain 'A' and resid 197 through 210 Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 221 through 240 removed outlier: 4.287A pdb=" N THR A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 264 Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.693A pdb=" N VAL A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 removed outlier: 3.921A pdb=" N TYR A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 346 removed outlier: 3.914A pdb=" N CYS A 338 " --> pdb=" O ILE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 358 removed outlier: 3.922A pdb=" N LEU A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 369 through 393 Processing helix chain 'A' and resid 424 through 447 removed outlier: 3.795A pdb=" N LEU A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 455 removed outlier: 4.496A pdb=" N GLN A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 489 removed outlier: 3.563A pdb=" N LEU A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 540 removed outlier: 3.536A pdb=" N ILE A 532 " --> pdb=" O GLY A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.527A pdb=" N LEU A 545 " --> pdb=" O ALA A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 587 removed outlier: 4.733A pdb=" N LYS A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A 587 " --> pdb=" O MET A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 612 Processing helix chain 'A' and resid 618 through 622 Processing helix chain 'A' and resid 628 through 664 removed outlier: 3.503A pdb=" N GLU A 664 " --> pdb=" O SER A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 683 Processing helix chain 'A' and resid 762 through 782 Processing helix chain 'A' and resid 783 through 785 No H-bonds generated for 'chain 'A' and resid 783 through 785' Processing helix chain 'A' and resid 788 through 828 removed outlier: 3.842A pdb=" N LEU A 792 " --> pdb=" O ASN A 788 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 37 removed outlier: 3.657A pdb=" N TYR B 37 " --> pdb=" O ASP B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 50 removed outlier: 4.379A pdb=" N GLU B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 72 removed outlier: 3.659A pdb=" N ASN B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 83 removed outlier: 3.693A pdb=" N LYS B 83 " --> pdb=" O GLU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 101 Processing helix chain 'B' and resid 102 through 111 removed outlier: 3.548A pdb=" N ASN B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 141 removed outlier: 4.069A pdb=" N GLU B 140 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP B 141 " --> pdb=" O TYR B 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 137 through 141' Processing helix chain 'B' and resid 150 through 158 Processing helix chain 'B' and resid 160 through 170 removed outlier: 3.520A pdb=" N LYS B 170 " --> pdb=" O MET B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 190 Processing helix chain 'B' and resid 197 through 210 Processing helix chain 'B' and resid 211 through 218 Processing helix chain 'B' and resid 221 through 240 removed outlier: 4.287A pdb=" N THR B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 264 Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 295 through 304 Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.693A pdb=" N VAL B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 323 removed outlier: 3.921A pdb=" N TYR B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 346 removed outlier: 3.914A pdb=" N CYS B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 358 removed outlier: 3.922A pdb=" N LEU B 351 " --> pdb=" O GLY B 347 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 358 " --> pdb=" O GLY B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 369 through 393 Processing helix chain 'B' and resid 424 through 447 removed outlier: 3.795A pdb=" N LEU B 446 " --> pdb=" O LYS B 442 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 455 removed outlier: 4.496A pdb=" N GLN B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 489 removed outlier: 3.563A pdb=" N LEU B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 540 removed outlier: 3.536A pdb=" N ILE B 532 " --> pdb=" O GLY B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 545 removed outlier: 3.527A pdb=" N LEU B 545 " --> pdb=" O ALA B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 587 removed outlier: 4.733A pdb=" N LYS B 567 " --> pdb=" O LYS B 563 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR B 587 " --> pdb=" O MET B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 612 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 628 through 664 removed outlier: 3.503A pdb=" N GLU B 664 " --> pdb=" O SER B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 683 Processing helix chain 'B' and resid 762 through 782 Processing helix chain 'B' and resid 783 through 785 No H-bonds generated for 'chain 'B' and resid 783 through 785' Processing helix chain 'B' and resid 788 through 828 removed outlier: 3.842A pdb=" N LEU B 792 " --> pdb=" O ASN B 788 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 828 " --> pdb=" O LEU B 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 37 removed outlier: 3.657A pdb=" N TYR C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 50 removed outlier: 4.379A pdb=" N GLU C 48 " --> pdb=" O ARG C 44 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 72 removed outlier: 3.659A pdb=" N ASN C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 83 removed outlier: 3.693A pdb=" N LYS C 83 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 101 Processing helix chain 'C' and resid 102 through 111 removed outlier: 3.548A pdb=" N ASN C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 141 removed outlier: 4.069A pdb=" N GLU C 140 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP C 141 " --> pdb=" O TYR C 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 137 through 141' Processing helix chain 'C' and resid 150 through 158 Processing helix chain 'C' and resid 160 through 170 removed outlier: 3.520A pdb=" N LYS C 170 " --> pdb=" O MET C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 190 Processing helix chain 'C' and resid 197 through 210 Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 221 through 240 removed outlier: 4.287A pdb=" N THR C 225 " --> pdb=" O ASP C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 264 Processing helix chain 'C' and resid 267 through 276 Processing helix chain 'C' and resid 295 through 304 Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.693A pdb=" N VAL C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 323 removed outlier: 3.921A pdb=" N TYR C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 346 removed outlier: 3.914A pdb=" N CYS C 338 " --> pdb=" O ILE C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 358 removed outlier: 3.922A pdb=" N LEU C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 358 " --> pdb=" O GLY C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 367 Processing helix chain 'C' and resid 369 through 393 Processing helix chain 'C' and resid 424 through 447 removed outlier: 3.795A pdb=" N LEU C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU C 447 " --> pdb=" O GLU C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 455 removed outlier: 4.496A pdb=" N GLN C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 489 removed outlier: 3.563A pdb=" N LEU C 460 " --> pdb=" O LEU C 456 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 540 removed outlier: 3.536A pdb=" N ILE C 532 " --> pdb=" O GLY C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 545 removed outlier: 3.527A pdb=" N LEU C 545 " --> pdb=" O ALA C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 587 removed outlier: 4.733A pdb=" N LYS C 567 " --> pdb=" O LYS C 563 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE C 568 " --> pdb=" O ASP C 564 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY C 582 " --> pdb=" O ALA C 578 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR C 587 " --> pdb=" O MET C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 618 through 622 Processing helix chain 'C' and resid 628 through 664 removed outlier: 3.503A pdb=" N GLU C 664 " --> pdb=" O SER C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 683 Processing helix chain 'C' and resid 762 through 782 Processing helix chain 'C' and resid 783 through 785 No H-bonds generated for 'chain 'C' and resid 783 through 785' Processing helix chain 'C' and resid 788 through 828 removed outlier: 3.842A pdb=" N LEU C 792 " --> pdb=" O ASN C 788 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 828 " --> pdb=" O LEU C 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 37 removed outlier: 3.657A pdb=" N TYR D 37 " --> pdb=" O ASP D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 50 removed outlier: 4.379A pdb=" N GLU D 48 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.659A pdb=" N ASN D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 83 removed outlier: 3.693A pdb=" N LYS D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 101 Processing helix chain 'D' and resid 102 through 111 removed outlier: 3.548A pdb=" N ASN D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 141 removed outlier: 4.069A pdb=" N GLU D 140 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP D 141 " --> pdb=" O TYR D 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 137 through 141' Processing helix chain 'D' and resid 150 through 158 Processing helix chain 'D' and resid 160 through 170 removed outlier: 3.520A pdb=" N LYS D 170 " --> pdb=" O MET D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 190 Processing helix chain 'D' and resid 197 through 210 Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 221 through 240 removed outlier: 4.287A pdb=" N THR D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 264 Processing helix chain 'D' and resid 267 through 276 Processing helix chain 'D' and resid 295 through 304 Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.693A pdb=" N VAL D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 323 removed outlier: 3.921A pdb=" N TYR D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 346 removed outlier: 3.914A pdb=" N CYS D 338 " --> pdb=" O ILE D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 358 removed outlier: 3.922A pdb=" N LEU D 351 " --> pdb=" O GLY D 347 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA D 358 " --> pdb=" O GLY D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 367 Processing helix chain 'D' and resid 369 through 393 Processing helix chain 'D' and resid 424 through 447 removed outlier: 3.795A pdb=" N LEU D 446 " --> pdb=" O LYS D 442 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU D 447 " --> pdb=" O GLU D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 455 removed outlier: 4.496A pdb=" N GLN D 455 " --> pdb=" O GLU D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 489 removed outlier: 3.563A pdb=" N LEU D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D 489 " --> pdb=" O ALA D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 540 removed outlier: 3.536A pdb=" N ILE D 532 " --> pdb=" O GLY D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 545 removed outlier: 3.527A pdb=" N LEU D 545 " --> pdb=" O ALA D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 587 removed outlier: 4.733A pdb=" N LYS D 567 " --> pdb=" O LYS D 563 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE D 568 " --> pdb=" O ASP D 564 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY D 582 " --> pdb=" O ALA D 578 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR D 587 " --> pdb=" O MET D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 612 Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 628 through 664 removed outlier: 3.503A pdb=" N GLU D 664 " --> pdb=" O SER D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 683 Processing helix chain 'D' and resid 762 through 782 Processing helix chain 'D' and resid 783 through 785 No H-bonds generated for 'chain 'D' and resid 783 through 785' Processing helix chain 'D' and resid 788 through 828 removed outlier: 3.842A pdb=" N LEU D 792 " --> pdb=" O ASN D 788 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 828 " --> pdb=" O LEU D 824 " (cutoff:3.500A) 1428 hydrogen bonds defined for protein. 4248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.73 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6704 1.35 - 1.47: 5280 1.47 - 1.59: 9508 1.59 - 1.71: 0 1.71 - 1.84: 204 Bond restraints: 21696 Sorted by residual: bond pdb=" CA SER C 683 " pdb=" C SER C 683 " ideal model delta sigma weight residual 1.522 1.563 -0.041 1.72e-02 3.38e+03 5.64e+00 bond pdb=" CA SER D 683 " pdb=" C SER D 683 " ideal model delta sigma weight residual 1.522 1.563 -0.041 1.72e-02 3.38e+03 5.64e+00 bond pdb=" CA SER A 683 " pdb=" C SER A 683 " ideal model delta sigma weight residual 1.522 1.563 -0.041 1.72e-02 3.38e+03 5.64e+00 bond pdb=" CA SER B 683 " pdb=" C SER B 683 " ideal model delta sigma weight residual 1.522 1.563 -0.041 1.72e-02 3.38e+03 5.64e+00 bond pdb=" C ALA B 310 " pdb=" N HIS B 311 " ideal model delta sigma weight residual 1.340 1.225 0.115 5.87e-02 2.90e+02 3.86e+00 ... (remaining 21691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 28500 1.71 - 3.43: 668 3.43 - 5.14: 144 5.14 - 6.86: 16 6.86 - 8.57: 12 Bond angle restraints: 29340 Sorted by residual: angle pdb=" CA TRP C 681 " pdb=" CB TRP C 681 " pdb=" CG TRP C 681 " ideal model delta sigma weight residual 113.60 122.17 -8.57 1.90e+00 2.77e-01 2.03e+01 angle pdb=" CA TRP D 681 " pdb=" CB TRP D 681 " pdb=" CG TRP D 681 " ideal model delta sigma weight residual 113.60 122.17 -8.57 1.90e+00 2.77e-01 2.03e+01 angle pdb=" CA TRP B 681 " pdb=" CB TRP B 681 " pdb=" CG TRP B 681 " ideal model delta sigma weight residual 113.60 122.17 -8.57 1.90e+00 2.77e-01 2.03e+01 angle pdb=" CA TRP A 681 " pdb=" CB TRP A 681 " pdb=" CG TRP A 681 " ideal model delta sigma weight residual 113.60 122.17 -8.57 1.90e+00 2.77e-01 2.03e+01 angle pdb=" C LEU A 680 " pdb=" N TRP A 681 " pdb=" CA TRP A 681 " ideal model delta sigma weight residual 122.65 116.33 6.32 1.66e+00 3.63e-01 1.45e+01 ... (remaining 29335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 11764 17.39 - 34.79: 892 34.79 - 52.18: 244 52.18 - 69.57: 40 69.57 - 86.97: 16 Dihedral angle restraints: 12956 sinusoidal: 5076 harmonic: 7880 Sorted by residual: dihedral pdb=" CA PHE A 145 " pdb=" C PHE A 145 " pdb=" N SER A 146 " pdb=" CA SER A 146 " ideal model delta harmonic sigma weight residual 180.00 160.45 19.55 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA PHE D 145 " pdb=" C PHE D 145 " pdb=" N SER D 146 " pdb=" CA SER D 146 " ideal model delta harmonic sigma weight residual 180.00 160.45 19.55 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA PHE C 145 " pdb=" C PHE C 145 " pdb=" N SER C 146 " pdb=" CA SER C 146 " ideal model delta harmonic sigma weight residual 180.00 160.45 19.55 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 12953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2352 0.039 - 0.078: 828 0.078 - 0.117: 136 0.117 - 0.157: 16 0.157 - 0.196: 8 Chirality restraints: 3340 Sorted by residual: chirality pdb=" CA TRP B 681 " pdb=" N TRP B 681 " pdb=" C TRP B 681 " pdb=" CB TRP B 681 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" CA TRP C 681 " pdb=" N TRP C 681 " pdb=" C TRP C 681 " pdb=" CB TRP C 681 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" CA TRP A 681 " pdb=" N TRP A 681 " pdb=" C TRP A 681 " pdb=" CB TRP A 681 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.58e-01 ... (remaining 3337 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 627 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.01e+00 pdb=" C ASP D 627 " 0.030 2.00e-02 2.50e+03 pdb=" O ASP D 627 " -0.011 2.00e-02 2.50e+03 pdb=" N HIS D 628 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 627 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.01e+00 pdb=" C ASP C 627 " 0.030 2.00e-02 2.50e+03 pdb=" O ASP C 627 " -0.011 2.00e-02 2.50e+03 pdb=" N HIS C 628 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 627 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.01e+00 pdb=" C ASP A 627 " -0.030 2.00e-02 2.50e+03 pdb=" O ASP A 627 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS A 628 " 0.010 2.00e-02 2.50e+03 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4984 2.79 - 3.31: 20804 3.31 - 3.84: 34092 3.84 - 4.37: 36554 4.37 - 4.90: 62656 Nonbonded interactions: 159090 Sorted by model distance: nonbonded pdb=" N PHE A 599 " pdb=" OE2 GLU A 604 " model vdw 2.258 3.120 nonbonded pdb=" N PHE D 599 " pdb=" OE2 GLU D 604 " model vdw 2.258 3.120 nonbonded pdb=" N PHE B 599 " pdb=" OE2 GLU B 604 " model vdw 2.258 3.120 nonbonded pdb=" N PHE C 599 " pdb=" OE2 GLU C 604 " model vdw 2.258 3.120 nonbonded pdb=" NZ LYS A 594 " pdb=" O SER A 621 " model vdw 2.279 3.120 ... (remaining 159085 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: 0.06 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.800 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 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 : 0.005 0.115 21696 Z= 0.216 Angle : 0.697 8.569 29340 Z= 0.378 Chirality : 0.039 0.196 3340 Planarity : 0.004 0.039 3668 Dihedral : 13.892 86.965 7844 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.99 % Favored : 92.71 % Rotamer: Outliers : 4.79 % Allowed : 11.52 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.22 (0.14), residues: 2632 helix: -0.55 (0.10), residues: 1968 sheet: None (None), residues: 0 loop : -4.18 (0.17), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 540 TYR 0.016 0.002 TYR D 136 PHE 0.014 0.002 PHE B 577 TRP 0.022 0.002 TRP B 681 HIS 0.004 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00491 (21696) covalent geometry : angle 0.69720 (29340) hydrogen bonds : bond 0.11969 ( 1428) hydrogen bonds : angle 5.01540 ( 4248) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 564 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ILE cc_start: 0.9838 (OUTLIER) cc_final: 0.9520 (pt) REVERT: A 144 ARG cc_start: 0.9332 (OUTLIER) cc_final: 0.9084 (ptp-170) REVERT: A 154 LEU cc_start: 0.9833 (tp) cc_final: 0.9578 (tt) REVERT: A 158 CYS cc_start: 0.9284 (m) cc_final: 0.8569 (t) REVERT: A 160 LYS cc_start: 0.9294 (mmtt) cc_final: 0.8280 (mmtp) REVERT: A 188 MET cc_start: 0.9635 (ttp) cc_final: 0.9341 (tmm) REVERT: A 228 GLU cc_start: 0.9628 (tt0) cc_final: 0.9253 (tm-30) REVERT: A 232 GLU cc_start: 0.9488 (tt0) cc_final: 0.9204 (tp30) REVERT: A 252 MET cc_start: 0.9668 (ttp) cc_final: 0.8946 (ppp) REVERT: A 264 LEU cc_start: 0.9756 (tp) cc_final: 0.9519 (tt) REVERT: A 301 ILE cc_start: 0.9618 (pt) cc_final: 0.9400 (mm) REVERT: A 427 MET cc_start: 0.9042 (mtp) cc_final: 0.8605 (mmt) REVERT: A 432 TRP cc_start: 0.9355 (t-100) cc_final: 0.8764 (t-100) REVERT: A 437 MET cc_start: 0.9467 (ttp) cc_final: 0.9248 (tpp) REVERT: A 440 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8909 (tp30) REVERT: A 564 ASP cc_start: 0.8936 (m-30) cc_final: 0.8425 (t70) REVERT: A 568 PHE cc_start: 0.9529 (m-80) cc_final: 0.9033 (m-10) REVERT: A 604 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7154 (tm-30) REVERT: A 609 LEU cc_start: 0.9657 (OUTLIER) cc_final: 0.9338 (tt) REVERT: A 632 GLU cc_start: 0.9284 (tt0) cc_final: 0.8760 (tp30) REVERT: A 650 LEU cc_start: 0.9710 (mm) cc_final: 0.9290 (tt) REVERT: A 654 LEU cc_start: 0.9861 (OUTLIER) cc_final: 0.9585 (mp) REVERT: A 657 MET cc_start: 0.9465 (mmm) cc_final: 0.9154 (tmm) REVERT: A 658 ILE cc_start: 0.9696 (mt) cc_final: 0.9357 (mt) REVERT: A 672 GLU cc_start: 0.9633 (mt-10) cc_final: 0.9321 (mm-30) REVERT: A 779 GLN cc_start: 0.9701 (tt0) cc_final: 0.9156 (tm-30) REVERT: A 781 ASP cc_start: 0.9488 (m-30) cc_final: 0.9263 (t0) REVERT: A 782 LYS cc_start: 0.9417 (ttpt) cc_final: 0.9200 (tppt) REVERT: A 783 GLU cc_start: 0.9572 (mt-10) cc_final: 0.9127 (mp0) REVERT: B 40 ILE cc_start: 0.9837 (OUTLIER) cc_final: 0.9520 (pt) REVERT: B 144 ARG cc_start: 0.9333 (OUTLIER) cc_final: 0.9084 (ptp-170) REVERT: B 154 LEU cc_start: 0.9833 (tp) cc_final: 0.9578 (tt) REVERT: B 158 CYS cc_start: 0.9283 (m) cc_final: 0.8568 (t) REVERT: B 160 LYS cc_start: 0.9293 (mmtt) cc_final: 0.8277 (mmtp) REVERT: B 188 MET cc_start: 0.9634 (ttp) cc_final: 0.9342 (tmm) REVERT: B 228 GLU cc_start: 0.9628 (tt0) cc_final: 0.9253 (tm-30) REVERT: B 232 GLU cc_start: 0.9489 (tt0) cc_final: 0.9205 (tp30) REVERT: B 252 MET cc_start: 0.9669 (ttp) cc_final: 0.8946 (ppp) REVERT: B 264 LEU cc_start: 0.9756 (tp) cc_final: 0.9519 (tt) REVERT: B 301 ILE cc_start: 0.9617 (pt) cc_final: 0.9399 (mm) REVERT: B 427 MET cc_start: 0.9042 (mtp) cc_final: 0.8605 (mmt) REVERT: B 432 TRP cc_start: 0.9356 (t-100) cc_final: 0.8764 (t-100) REVERT: B 437 MET cc_start: 0.9466 (ttp) cc_final: 0.9248 (tpp) REVERT: B 440 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8909 (tp30) REVERT: B 564 ASP cc_start: 0.8936 (m-30) cc_final: 0.8425 (t70) REVERT: B 568 PHE cc_start: 0.9530 (m-80) cc_final: 0.9033 (m-10) REVERT: B 604 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7146 (tm-30) REVERT: B 609 LEU cc_start: 0.9657 (OUTLIER) cc_final: 0.9339 (tt) REVERT: B 632 GLU cc_start: 0.9284 (tt0) cc_final: 0.8758 (tp30) REVERT: B 650 LEU cc_start: 0.9711 (mm) cc_final: 0.9291 (tt) REVERT: B 654 LEU cc_start: 0.9861 (OUTLIER) cc_final: 0.9585 (mp) REVERT: B 657 MET cc_start: 0.9467 (mmm) cc_final: 0.9154 (tmm) REVERT: B 658 ILE cc_start: 0.9696 (mt) cc_final: 0.9359 (mt) REVERT: B 672 GLU cc_start: 0.9632 (mt-10) cc_final: 0.9320 (mm-30) REVERT: B 779 GLN cc_start: 0.9700 (tt0) cc_final: 0.9157 (tm-30) REVERT: B 781 ASP cc_start: 0.9487 (m-30) cc_final: 0.9264 (t0) REVERT: B 782 LYS cc_start: 0.9418 (ttpt) cc_final: 0.9199 (tppt) REVERT: B 783 GLU cc_start: 0.9573 (mt-10) cc_final: 0.9128 (mp0) REVERT: C 40 ILE cc_start: 0.9837 (OUTLIER) cc_final: 0.9519 (pt) REVERT: C 144 ARG cc_start: 0.9333 (OUTLIER) cc_final: 0.9083 (ptp-170) REVERT: C 154 LEU cc_start: 0.9832 (tp) cc_final: 0.9577 (tt) REVERT: C 158 CYS cc_start: 0.9285 (m) cc_final: 0.8570 (t) REVERT: C 160 LYS cc_start: 0.9294 (mmtt) cc_final: 0.8279 (mmtp) REVERT: C 188 MET cc_start: 0.9635 (ttp) cc_final: 0.9342 (tmm) REVERT: C 228 GLU cc_start: 0.9628 (tt0) cc_final: 0.9252 (tm-30) REVERT: C 232 GLU cc_start: 0.9488 (tt0) cc_final: 0.9204 (tp30) REVERT: C 252 MET cc_start: 0.9669 (ttp) cc_final: 0.8945 (ppp) REVERT: C 264 LEU cc_start: 0.9755 (tp) cc_final: 0.9520 (tt) REVERT: C 301 ILE cc_start: 0.9618 (pt) cc_final: 0.9400 (mm) REVERT: C 427 MET cc_start: 0.9042 (mtp) cc_final: 0.8605 (mmt) REVERT: C 432 TRP cc_start: 0.9357 (t-100) cc_final: 0.8764 (t-100) REVERT: C 437 MET cc_start: 0.9467 (ttp) cc_final: 0.9248 (tpp) REVERT: C 440 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8908 (tp30) REVERT: C 564 ASP cc_start: 0.8935 (m-30) cc_final: 0.8425 (t70) REVERT: C 568 PHE cc_start: 0.9530 (m-80) cc_final: 0.9035 (m-10) REVERT: C 604 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7150 (tm-30) REVERT: C 609 LEU cc_start: 0.9657 (OUTLIER) cc_final: 0.9338 (tt) REVERT: C 632 GLU cc_start: 0.9284 (tt0) cc_final: 0.8759 (tp30) REVERT: C 650 LEU cc_start: 0.9710 (mm) cc_final: 0.9291 (tt) REVERT: C 654 LEU cc_start: 0.9861 (OUTLIER) cc_final: 0.9584 (mp) REVERT: C 657 MET cc_start: 0.9467 (mmm) cc_final: 0.9155 (tmm) REVERT: C 658 ILE cc_start: 0.9696 (mt) cc_final: 0.9358 (mt) REVERT: C 672 GLU cc_start: 0.9632 (mt-10) cc_final: 0.9320 (mm-30) REVERT: C 779 GLN cc_start: 0.9700 (tt0) cc_final: 0.9156 (tm-30) REVERT: C 781 ASP cc_start: 0.9489 (m-30) cc_final: 0.9264 (t0) REVERT: C 782 LYS cc_start: 0.9418 (ttpt) cc_final: 0.9200 (tppt) REVERT: C 783 GLU cc_start: 0.9574 (mt-10) cc_final: 0.9127 (mp0) REVERT: D 40 ILE cc_start: 0.9838 (OUTLIER) cc_final: 0.9519 (pt) REVERT: D 144 ARG cc_start: 0.9332 (OUTLIER) cc_final: 0.9083 (ptp-170) REVERT: D 154 LEU cc_start: 0.9832 (tp) cc_final: 0.9577 (tt) REVERT: D 158 CYS cc_start: 0.9285 (m) cc_final: 0.8567 (t) REVERT: D 160 LYS cc_start: 0.9294 (mmtt) cc_final: 0.8277 (mmtp) REVERT: D 188 MET cc_start: 0.9634 (ttp) cc_final: 0.9341 (tmm) REVERT: D 228 GLU cc_start: 0.9627 (tt0) cc_final: 0.9252 (tm-30) REVERT: D 232 GLU cc_start: 0.9488 (tt0) cc_final: 0.9206 (tp30) REVERT: D 252 MET cc_start: 0.9669 (ttp) cc_final: 0.8946 (ppp) REVERT: D 264 LEU cc_start: 0.9755 (tp) cc_final: 0.9519 (tt) REVERT: D 301 ILE cc_start: 0.9618 (pt) cc_final: 0.9400 (mm) REVERT: D 427 MET cc_start: 0.9043 (mtp) cc_final: 0.8606 (mmt) REVERT: D 432 TRP cc_start: 0.9356 (t-100) cc_final: 0.8765 (t-100) REVERT: D 437 MET cc_start: 0.9466 (ttp) cc_final: 0.9248 (tpp) REVERT: D 440 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8909 (tp30) REVERT: D 564 ASP cc_start: 0.8936 (m-30) cc_final: 0.8425 (t70) REVERT: D 568 PHE cc_start: 0.9530 (m-80) cc_final: 0.9031 (m-10) REVERT: D 604 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7148 (tm-30) REVERT: D 609 LEU cc_start: 0.9657 (OUTLIER) cc_final: 0.9338 (tt) REVERT: D 632 GLU cc_start: 0.9284 (tt0) cc_final: 0.8759 (tp30) REVERT: D 650 LEU cc_start: 0.9710 (mm) cc_final: 0.9290 (tt) REVERT: D 654 LEU cc_start: 0.9861 (OUTLIER) cc_final: 0.9584 (mp) REVERT: D 657 MET cc_start: 0.9465 (mmm) cc_final: 0.9155 (tmm) REVERT: D 658 ILE cc_start: 0.9696 (mt) cc_final: 0.9357 (mt) REVERT: D 672 GLU cc_start: 0.9632 (mt-10) cc_final: 0.9319 (mm-30) REVERT: D 779 GLN cc_start: 0.9700 (tt0) cc_final: 0.9157 (tm-30) REVERT: D 781 ASP cc_start: 0.9488 (m-30) cc_final: 0.9263 (t0) REVERT: D 782 LYS cc_start: 0.9417 (ttpt) cc_final: 0.9200 (tppt) REVERT: D 783 GLU cc_start: 0.9573 (mt-10) cc_final: 0.9127 (mp0) outliers start: 108 outliers final: 28 residues processed: 656 average time/residue: 0.1407 time to fit residues: 147.4101 Evaluate side-chains 433 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 385 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN B 276 ASN C 276 ASN D 276 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.051163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.040850 restraints weight = 124513.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.042194 restraints weight = 73130.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.043133 restraints weight = 50300.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.043838 restraints weight = 38289.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.044342 restraints weight = 31208.558| |-----------------------------------------------------------------------------| r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21696 Z= 0.200 Angle : 0.678 7.928 29340 Z= 0.350 Chirality : 0.040 0.177 3340 Planarity : 0.004 0.043 3668 Dihedral : 4.569 20.010 2872 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.02 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.12 (0.16), residues: 2632 helix: 1.20 (0.11), residues: 1984 sheet: None (None), residues: 0 loop : -3.59 (0.19), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 266 TYR 0.017 0.002 TYR C 138 PHE 0.012 0.001 PHE A 577 TRP 0.014 0.002 TRP D 356 HIS 0.007 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00411 (21696) covalent geometry : angle 0.67835 (29340) hydrogen bonds : bond 0.04400 ( 1428) hydrogen bonds : angle 4.12630 ( 4248) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 CYS cc_start: 0.8575 (m) cc_final: 0.8340 (m) REVERT: A 160 LYS cc_start: 0.9309 (mmtt) cc_final: 0.8928 (mmtp) REVERT: A 166 MET cc_start: 0.9386 (mmp) cc_final: 0.9103 (mmp) REVERT: A 188 MET cc_start: 0.9539 (ttp) cc_final: 0.9139 (tmm) REVERT: A 252 MET cc_start: 0.9391 (ttp) cc_final: 0.8593 (ppp) REVERT: A 256 ASP cc_start: 0.9230 (m-30) cc_final: 0.8563 (m-30) REVERT: A 264 LEU cc_start: 0.9714 (tp) cc_final: 0.9512 (tt) REVERT: A 427 MET cc_start: 0.8987 (mtp) cc_final: 0.8766 (ptp) REVERT: A 440 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8754 (tp30) REVERT: A 464 MET cc_start: 0.9337 (ppp) cc_final: 0.9039 (ppp) REVERT: A 529 LEU cc_start: 0.9705 (mt) cc_final: 0.9489 (mt) REVERT: A 564 ASP cc_start: 0.8924 (m-30) cc_final: 0.8445 (t70) REVERT: A 568 PHE cc_start: 0.9313 (m-80) cc_final: 0.8546 (m-80) REVERT: A 569 MET cc_start: 0.9163 (ttm) cc_final: 0.8724 (mtp) REVERT: A 650 LEU cc_start: 0.9676 (mm) cc_final: 0.9210 (tt) REVERT: A 654 LEU cc_start: 0.9819 (mp) cc_final: 0.9427 (mp) REVERT: A 657 MET cc_start: 0.9331 (mmm) cc_final: 0.8806 (tmm) REVERT: A 658 ILE cc_start: 0.9538 (mt) cc_final: 0.9175 (mt) REVERT: A 779 GLN cc_start: 0.9620 (tt0) cc_final: 0.9409 (tm-30) REVERT: A 781 ASP cc_start: 0.9521 (m-30) cc_final: 0.9288 (t0) REVERT: B 158 CYS cc_start: 0.8578 (m) cc_final: 0.8342 (m) REVERT: B 160 LYS cc_start: 0.9311 (mmtt) cc_final: 0.8931 (mmtp) REVERT: B 166 MET cc_start: 0.9392 (mmp) cc_final: 0.9107 (mmp) REVERT: B 188 MET cc_start: 0.9539 (ttp) cc_final: 0.9140 (tmm) REVERT: B 252 MET cc_start: 0.9394 (ttp) cc_final: 0.8600 (ppp) REVERT: B 256 ASP cc_start: 0.9235 (m-30) cc_final: 0.8568 (m-30) REVERT: B 264 LEU cc_start: 0.9721 (tp) cc_final: 0.9521 (tt) REVERT: B 427 MET cc_start: 0.8989 (mtp) cc_final: 0.8768 (ptp) REVERT: B 440 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8754 (tp30) REVERT: B 464 MET cc_start: 0.9336 (ppp) cc_final: 0.9039 (ppp) REVERT: B 529 LEU cc_start: 0.9703 (mt) cc_final: 0.9489 (mt) REVERT: B 564 ASP cc_start: 0.8921 (m-30) cc_final: 0.8441 (t70) REVERT: B 568 PHE cc_start: 0.9314 (m-80) cc_final: 0.8548 (m-80) REVERT: B 569 MET cc_start: 0.9162 (ttm) cc_final: 0.8725 (mtp) REVERT: B 650 LEU cc_start: 0.9678 (mm) cc_final: 0.9211 (tt) REVERT: B 654 LEU cc_start: 0.9818 (mp) cc_final: 0.9425 (mp) REVERT: B 657 MET cc_start: 0.9331 (mmm) cc_final: 0.8807 (tmm) REVERT: B 658 ILE cc_start: 0.9539 (mt) cc_final: 0.9176 (mt) REVERT: B 779 GLN cc_start: 0.9622 (tt0) cc_final: 0.9411 (tm-30) REVERT: B 781 ASP cc_start: 0.9521 (m-30) cc_final: 0.9290 (t0) REVERT: C 158 CYS cc_start: 0.8579 (m) cc_final: 0.8342 (m) REVERT: C 160 LYS cc_start: 0.9312 (mmtt) cc_final: 0.8933 (mmtp) REVERT: C 166 MET cc_start: 0.9389 (mmp) cc_final: 0.9104 (mmp) REVERT: C 188 MET cc_start: 0.9540 (ttp) cc_final: 0.9142 (tmm) REVERT: C 252 MET cc_start: 0.9392 (ttp) cc_final: 0.8593 (ppp) REVERT: C 256 ASP cc_start: 0.9233 (m-30) cc_final: 0.8559 (m-30) REVERT: C 264 LEU cc_start: 0.9718 (tp) cc_final: 0.9517 (tt) REVERT: C 427 MET cc_start: 0.8986 (mtp) cc_final: 0.8766 (ptp) REVERT: C 440 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8755 (tp30) REVERT: C 464 MET cc_start: 0.9341 (ppp) cc_final: 0.9042 (ppp) REVERT: C 529 LEU cc_start: 0.9707 (mt) cc_final: 0.9492 (mt) REVERT: C 564 ASP cc_start: 0.8920 (m-30) cc_final: 0.8441 (t70) REVERT: C 568 PHE cc_start: 0.9313 (m-80) cc_final: 0.8549 (m-80) REVERT: C 569 MET cc_start: 0.9164 (ttm) cc_final: 0.8724 (mtp) REVERT: C 650 LEU cc_start: 0.9676 (mm) cc_final: 0.9208 (tt) REVERT: C 654 LEU cc_start: 0.9819 (mp) cc_final: 0.9428 (mp) REVERT: C 657 MET cc_start: 0.9335 (mmm) cc_final: 0.8810 (tmm) REVERT: C 658 ILE cc_start: 0.9539 (mt) cc_final: 0.9175 (mt) REVERT: C 779 GLN cc_start: 0.9624 (tt0) cc_final: 0.9414 (tm-30) REVERT: C 781 ASP cc_start: 0.9520 (m-30) cc_final: 0.9291 (t0) REVERT: D 158 CYS cc_start: 0.8587 (m) cc_final: 0.8349 (m) REVERT: D 160 LYS cc_start: 0.9318 (mmtt) cc_final: 0.8938 (mmtp) REVERT: D 166 MET cc_start: 0.9406 (mmp) cc_final: 0.9130 (mmp) REVERT: D 188 MET cc_start: 0.9542 (ttp) cc_final: 0.9141 (tmm) REVERT: D 252 MET cc_start: 0.9392 (ttp) cc_final: 0.8595 (ppp) REVERT: D 256 ASP cc_start: 0.9234 (m-30) cc_final: 0.8563 (m-30) REVERT: D 264 LEU cc_start: 0.9714 (tp) cc_final: 0.9513 (tt) REVERT: D 427 MET cc_start: 0.8985 (mtp) cc_final: 0.8765 (ptp) REVERT: D 440 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8756 (tp30) REVERT: D 464 MET cc_start: 0.9341 (ppp) cc_final: 0.9043 (ppp) REVERT: D 529 LEU cc_start: 0.9706 (mt) cc_final: 0.9491 (mt) REVERT: D 564 ASP cc_start: 0.8921 (m-30) cc_final: 0.8441 (t70) REVERT: D 568 PHE cc_start: 0.9314 (m-80) cc_final: 0.8549 (m-80) REVERT: D 569 MET cc_start: 0.9169 (ttm) cc_final: 0.8726 (mtp) REVERT: D 650 LEU cc_start: 0.9676 (mm) cc_final: 0.9208 (tt) REVERT: D 654 LEU cc_start: 0.9819 (mp) cc_final: 0.9427 (mp) REVERT: D 657 MET cc_start: 0.9331 (mmm) cc_final: 0.8806 (tmm) REVERT: D 658 ILE cc_start: 0.9537 (mt) cc_final: 0.9173 (mt) REVERT: D 779 GLN cc_start: 0.9623 (tt0) cc_final: 0.9407 (tm-30) REVERT: D 781 ASP cc_start: 0.9522 (m-30) cc_final: 0.9291 (t0) REVERT: D 802 LEU cc_start: 0.9897 (tp) cc_final: 0.9681 (mt) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.1388 time to fit residues: 88.4429 Evaluate side-chains 320 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 181 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 227 optimal weight: 0.7980 chunk 88 optimal weight: 7.9990 chunk 191 optimal weight: 20.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.052982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.042074 restraints weight = 118785.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.043430 restraints weight = 71270.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.044387 restraints weight = 49803.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.045125 restraints weight = 38110.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.045661 restraints weight = 31225.234| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21696 Z= 0.120 Angle : 0.573 7.113 29340 Z= 0.296 Chirality : 0.037 0.160 3340 Planarity : 0.004 0.042 3668 Dihedral : 4.208 18.736 2872 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.18 % Allowed : 2.26 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.97 (0.17), residues: 2632 helix: 1.82 (0.12), residues: 1988 sheet: None (None), residues: 0 loop : -3.34 (0.20), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 803 TYR 0.021 0.002 TYR A 642 PHE 0.012 0.001 PHE B 576 TRP 0.016 0.001 TRP D 681 HIS 0.007 0.001 HIS C 311 Details of bonding type rmsd covalent geometry : bond 0.00251 (21696) covalent geometry : angle 0.57324 (29340) hydrogen bonds : bond 0.03989 ( 1428) hydrogen bonds : angle 3.68000 ( 4248) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 434 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9237 (mmp) cc_final: 0.9023 (mmm) REVERT: A 68 LEU cc_start: 0.9714 (tp) cc_final: 0.9507 (tt) REVERT: A 158 CYS cc_start: 0.8420 (m) cc_final: 0.8094 (m) REVERT: A 160 LYS cc_start: 0.9237 (mmtt) cc_final: 0.8571 (mmtp) REVERT: A 188 MET cc_start: 0.9538 (ttp) cc_final: 0.9134 (tmm) REVERT: A 252 MET cc_start: 0.9372 (ttp) cc_final: 0.8814 (ppp) REVERT: A 301 ILE cc_start: 0.9587 (pt) cc_final: 0.9382 (mm) REVERT: A 314 CYS cc_start: 0.9417 (t) cc_final: 0.9039 (t) REVERT: A 427 MET cc_start: 0.8894 (mtp) cc_final: 0.8572 (ptp) REVERT: A 437 MET cc_start: 0.9513 (ttt) cc_final: 0.9241 (tpp) REVERT: A 440 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8580 (tp30) REVERT: A 441 CYS cc_start: 0.9147 (t) cc_final: 0.8847 (p) REVERT: A 464 MET cc_start: 0.9345 (ppp) cc_final: 0.9051 (ppp) REVERT: A 545 LEU cc_start: 0.9705 (tp) cc_final: 0.9475 (tp) REVERT: A 564 ASP cc_start: 0.8843 (m-30) cc_final: 0.8427 (t70) REVERT: A 568 PHE cc_start: 0.9165 (m-80) cc_final: 0.8958 (m-10) REVERT: A 580 MET cc_start: 0.9554 (tmm) cc_final: 0.9292 (tmm) REVERT: A 650 LEU cc_start: 0.9641 (mm) cc_final: 0.9185 (tt) REVERT: A 653 MET cc_start: 0.9586 (tpp) cc_final: 0.9284 (tpp) REVERT: A 657 MET cc_start: 0.9272 (mmm) cc_final: 0.8945 (mmp) REVERT: A 672 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8984 (mm-30) REVERT: A 781 ASP cc_start: 0.9478 (m-30) cc_final: 0.9264 (t0) REVERT: A 783 GLU cc_start: 0.9399 (mt-10) cc_final: 0.8948 (tm-30) REVERT: B 61 MET cc_start: 0.9252 (mmp) cc_final: 0.9029 (mmm) REVERT: B 68 LEU cc_start: 0.9714 (tp) cc_final: 0.9509 (tt) REVERT: B 158 CYS cc_start: 0.8411 (m) cc_final: 0.8085 (m) REVERT: B 160 LYS cc_start: 0.9228 (mmtt) cc_final: 0.8559 (mmtp) REVERT: B 188 MET cc_start: 0.9549 (ttp) cc_final: 0.9142 (tmm) REVERT: B 252 MET cc_start: 0.9373 (ttp) cc_final: 0.8813 (ppp) REVERT: B 301 ILE cc_start: 0.9586 (pt) cc_final: 0.9380 (mm) REVERT: B 314 CYS cc_start: 0.9421 (t) cc_final: 0.9039 (t) REVERT: B 427 MET cc_start: 0.8893 (mtp) cc_final: 0.8571 (ptp) REVERT: B 437 MET cc_start: 0.9516 (ttt) cc_final: 0.9244 (tpp) REVERT: B 440 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8579 (tp30) REVERT: B 441 CYS cc_start: 0.9150 (t) cc_final: 0.8849 (p) REVERT: B 464 MET cc_start: 0.9347 (ppp) cc_final: 0.9053 (ppp) REVERT: B 545 LEU cc_start: 0.9706 (tp) cc_final: 0.9478 (tp) REVERT: B 564 ASP cc_start: 0.8842 (m-30) cc_final: 0.8407 (t70) REVERT: B 568 PHE cc_start: 0.9167 (m-80) cc_final: 0.8930 (m-80) REVERT: B 580 MET cc_start: 0.9554 (tmm) cc_final: 0.9293 (tmm) REVERT: B 650 LEU cc_start: 0.9641 (mm) cc_final: 0.9163 (tt) REVERT: B 653 MET cc_start: 0.9590 (tpp) cc_final: 0.9231 (tpp) REVERT: B 654 LEU cc_start: 0.9784 (mp) cc_final: 0.9571 (mp) REVERT: B 657 MET cc_start: 0.9281 (mmm) cc_final: 0.8946 (mmp) REVERT: B 672 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8982 (mm-30) REVERT: B 781 ASP cc_start: 0.9477 (m-30) cc_final: 0.9263 (t0) REVERT: B 783 GLU cc_start: 0.9399 (mt-10) cc_final: 0.8948 (tm-30) REVERT: C 61 MET cc_start: 0.9253 (mmp) cc_final: 0.9031 (mmm) REVERT: C 68 LEU cc_start: 0.9712 (tp) cc_final: 0.9505 (tt) REVERT: C 158 CYS cc_start: 0.8410 (m) cc_final: 0.8080 (m) REVERT: C 160 LYS cc_start: 0.9236 (mmtt) cc_final: 0.8567 (mmtp) REVERT: C 188 MET cc_start: 0.9548 (ttp) cc_final: 0.9143 (tmm) REVERT: C 252 MET cc_start: 0.9369 (ttp) cc_final: 0.8810 (ppp) REVERT: C 301 ILE cc_start: 0.9585 (pt) cc_final: 0.9379 (mm) REVERT: C 314 CYS cc_start: 0.9424 (t) cc_final: 0.9040 (t) REVERT: C 427 MET cc_start: 0.8891 (mtp) cc_final: 0.8570 (ptp) REVERT: C 437 MET cc_start: 0.9518 (ttt) cc_final: 0.9247 (tpp) REVERT: C 440 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8585 (tp30) REVERT: C 441 CYS cc_start: 0.9155 (t) cc_final: 0.8855 (p) REVERT: C 464 MET cc_start: 0.9351 (ppp) cc_final: 0.9055 (ppp) REVERT: C 545 LEU cc_start: 0.9707 (tp) cc_final: 0.9478 (tp) REVERT: C 564 ASP cc_start: 0.8843 (m-30) cc_final: 0.8408 (t70) REVERT: C 568 PHE cc_start: 0.9167 (m-80) cc_final: 0.8939 (m-80) REVERT: C 580 MET cc_start: 0.9551 (tmm) cc_final: 0.9291 (tmm) REVERT: C 650 LEU cc_start: 0.9639 (mm) cc_final: 0.9166 (tt) REVERT: C 653 MET cc_start: 0.9593 (tpp) cc_final: 0.9281 (tpp) REVERT: C 654 LEU cc_start: 0.9785 (mp) cc_final: 0.9574 (mp) REVERT: C 657 MET cc_start: 0.9281 (mmm) cc_final: 0.8951 (mmp) REVERT: C 672 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8985 (mm-30) REVERT: C 781 ASP cc_start: 0.9479 (m-30) cc_final: 0.9265 (t0) REVERT: C 783 GLU cc_start: 0.9402 (mt-10) cc_final: 0.8948 (tm-30) REVERT: D 61 MET cc_start: 0.9253 (mmp) cc_final: 0.9034 (mmm) REVERT: D 68 LEU cc_start: 0.9713 (tp) cc_final: 0.9506 (tt) REVERT: D 160 LYS cc_start: 0.9238 (mmtt) cc_final: 0.8816 (mmtp) REVERT: D 188 MET cc_start: 0.9542 (ttp) cc_final: 0.9135 (tmm) REVERT: D 252 MET cc_start: 0.9372 (ttp) cc_final: 0.8815 (ppp) REVERT: D 301 ILE cc_start: 0.9587 (pt) cc_final: 0.9381 (mm) REVERT: D 314 CYS cc_start: 0.9431 (t) cc_final: 0.9056 (t) REVERT: D 427 MET cc_start: 0.8891 (mtp) cc_final: 0.8569 (ptp) REVERT: D 437 MET cc_start: 0.9517 (ttt) cc_final: 0.9246 (tpp) REVERT: D 440 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8585 (tp30) REVERT: D 441 CYS cc_start: 0.9151 (t) cc_final: 0.8852 (p) REVERT: D 464 MET cc_start: 0.9351 (ppp) cc_final: 0.9055 (ppp) REVERT: D 545 LEU cc_start: 0.9707 (tp) cc_final: 0.9478 (tp) REVERT: D 564 ASP cc_start: 0.8839 (m-30) cc_final: 0.8405 (t70) REVERT: D 568 PHE cc_start: 0.9166 (m-80) cc_final: 0.8935 (m-80) REVERT: D 580 MET cc_start: 0.9550 (tmm) cc_final: 0.9288 (tmm) REVERT: D 650 LEU cc_start: 0.9636 (mm) cc_final: 0.9164 (tt) REVERT: D 653 MET cc_start: 0.9592 (tpp) cc_final: 0.9279 (tpp) REVERT: D 654 LEU cc_start: 0.9784 (mp) cc_final: 0.9574 (mp) REVERT: D 657 MET cc_start: 0.9274 (mmm) cc_final: 0.8943 (mmp) REVERT: D 672 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8981 (mm-30) REVERT: D 781 ASP cc_start: 0.9483 (m-30) cc_final: 0.9269 (t0) REVERT: D 783 GLU cc_start: 0.9400 (mt-10) cc_final: 0.8951 (tm-30) outliers start: 4 outliers final: 0 residues processed: 438 average time/residue: 0.1353 time to fit residues: 97.1635 Evaluate side-chains 295 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 21 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 38 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 176 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.050663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.040422 restraints weight = 126479.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.041720 restraints weight = 74849.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.042630 restraints weight = 52015.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.043353 restraints weight = 39720.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.043862 restraints weight = 32359.298| |-----------------------------------------------------------------------------| r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 21696 Z= 0.224 Angle : 0.664 8.851 29340 Z= 0.345 Chirality : 0.038 0.182 3340 Planarity : 0.004 0.046 3668 Dihedral : 4.568 21.386 2872 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.10 (0.17), residues: 2632 helix: 1.88 (0.12), residues: 1988 sheet: None (None), residues: 0 loop : -3.18 (0.20), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 266 TYR 0.018 0.002 TYR A 662 PHE 0.011 0.001 PHE C 576 TRP 0.027 0.002 TRP B 681 HIS 0.009 0.002 HIS D 311 Details of bonding type rmsd covalent geometry : bond 0.00464 (21696) covalent geometry : angle 0.66363 (29340) hydrogen bonds : bond 0.04197 ( 1428) hydrogen bonds : angle 4.06477 ( 4248) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9336 (mmp) cc_final: 0.9117 (mmm) REVERT: A 158 CYS cc_start: 0.8679 (m) cc_final: 0.8389 (m) REVERT: A 160 LYS cc_start: 0.9366 (mmtt) cc_final: 0.8924 (mmtp) REVERT: A 188 MET cc_start: 0.9553 (ttp) cc_final: 0.9138 (tmm) REVERT: A 252 MET cc_start: 0.9353 (ttp) cc_final: 0.9017 (ttm) REVERT: A 256 ASP cc_start: 0.9208 (m-30) cc_final: 0.9002 (m-30) REVERT: A 427 MET cc_start: 0.8889 (mtp) cc_final: 0.8582 (ptp) REVERT: A 437 MET cc_start: 0.9535 (ttt) cc_final: 0.9277 (tpp) REVERT: A 440 GLU cc_start: 0.9339 (mm-30) cc_final: 0.8694 (tp30) REVERT: A 441 CYS cc_start: 0.9272 (t) cc_final: 0.8958 (p) REVERT: A 464 MET cc_start: 0.9306 (ppp) cc_final: 0.9032 (ppp) REVERT: A 545 LEU cc_start: 0.9700 (tp) cc_final: 0.9494 (tp) REVERT: A 564 ASP cc_start: 0.9043 (m-30) cc_final: 0.8513 (t70) REVERT: A 569 MET cc_start: 0.9291 (ttm) cc_final: 0.8707 (mtp) REVERT: A 580 MET cc_start: 0.9538 (tmm) cc_final: 0.9335 (tmm) REVERT: A 650 LEU cc_start: 0.9581 (mm) cc_final: 0.9298 (pp) REVERT: A 668 ASP cc_start: 0.8664 (m-30) cc_final: 0.8162 (m-30) REVERT: A 672 GLU cc_start: 0.9271 (mm-30) cc_final: 0.9056 (mm-30) REVERT: A 781 ASP cc_start: 0.9514 (m-30) cc_final: 0.9243 (t0) REVERT: B 61 MET cc_start: 0.9333 (mmp) cc_final: 0.9128 (mmm) REVERT: B 158 CYS cc_start: 0.8684 (m) cc_final: 0.8392 (m) REVERT: B 160 LYS cc_start: 0.9367 (mmtt) cc_final: 0.8924 (mmtp) REVERT: B 188 MET cc_start: 0.9550 (ttp) cc_final: 0.9135 (tmm) REVERT: B 252 MET cc_start: 0.9354 (ttp) cc_final: 0.9019 (ttm) REVERT: B 256 ASP cc_start: 0.9208 (m-30) cc_final: 0.9003 (m-30) REVERT: B 427 MET cc_start: 0.8892 (mtp) cc_final: 0.8586 (ptp) REVERT: B 437 MET cc_start: 0.9536 (ttt) cc_final: 0.9279 (tpp) REVERT: B 440 GLU cc_start: 0.9338 (mm-30) cc_final: 0.8692 (tp30) REVERT: B 441 CYS cc_start: 0.9274 (t) cc_final: 0.8959 (p) REVERT: B 464 MET cc_start: 0.9309 (ppp) cc_final: 0.9033 (ppp) REVERT: B 545 LEU cc_start: 0.9701 (tp) cc_final: 0.9493 (tp) REVERT: B 564 ASP cc_start: 0.9032 (m-30) cc_final: 0.8342 (t70) REVERT: B 568 PHE cc_start: 0.9147 (m-80) cc_final: 0.8509 (m-80) REVERT: B 569 MET cc_start: 0.9303 (ttm) cc_final: 0.8724 (mtp) REVERT: B 580 MET cc_start: 0.9537 (tmm) cc_final: 0.9332 (tmm) REVERT: B 650 LEU cc_start: 0.9577 (mm) cc_final: 0.9283 (pp) REVERT: B 654 LEU cc_start: 0.9822 (mp) cc_final: 0.9599 (mp) REVERT: B 657 MET cc_start: 0.9232 (mmm) cc_final: 0.8769 (tmm) REVERT: B 668 ASP cc_start: 0.8667 (m-30) cc_final: 0.8166 (m-30) REVERT: B 672 GLU cc_start: 0.9274 (mm-30) cc_final: 0.9059 (mm-30) REVERT: B 781 ASP cc_start: 0.9515 (m-30) cc_final: 0.9246 (t0) REVERT: C 61 MET cc_start: 0.9330 (mmp) cc_final: 0.9125 (mmm) REVERT: C 158 CYS cc_start: 0.8678 (m) cc_final: 0.8386 (m) REVERT: C 160 LYS cc_start: 0.9369 (mmtt) cc_final: 0.8926 (mmtp) REVERT: C 188 MET cc_start: 0.9556 (ttp) cc_final: 0.9142 (tmm) REVERT: C 252 MET cc_start: 0.9355 (ttp) cc_final: 0.9020 (ttm) REVERT: C 256 ASP cc_start: 0.9209 (m-30) cc_final: 0.9003 (m-30) REVERT: C 427 MET cc_start: 0.8893 (mtp) cc_final: 0.8586 (ptp) REVERT: C 437 MET cc_start: 0.9536 (ttt) cc_final: 0.9279 (tpp) REVERT: C 440 GLU cc_start: 0.9340 (mm-30) cc_final: 0.8694 (tp30) REVERT: C 441 CYS cc_start: 0.9273 (t) cc_final: 0.8960 (p) REVERT: C 464 MET cc_start: 0.9312 (ppp) cc_final: 0.9034 (ppp) REVERT: C 545 LEU cc_start: 0.9701 (tp) cc_final: 0.9493 (tp) REVERT: C 564 ASP cc_start: 0.9032 (m-30) cc_final: 0.8339 (t70) REVERT: C 568 PHE cc_start: 0.9145 (m-80) cc_final: 0.8506 (m-80) REVERT: C 569 MET cc_start: 0.9300 (ttm) cc_final: 0.8720 (mtp) REVERT: C 580 MET cc_start: 0.9537 (tmm) cc_final: 0.9333 (tmm) REVERT: C 650 LEU cc_start: 0.9604 (mm) cc_final: 0.9300 (pp) REVERT: C 654 LEU cc_start: 0.9824 (mp) cc_final: 0.9602 (mp) REVERT: C 657 MET cc_start: 0.9239 (mmm) cc_final: 0.8769 (tmm) REVERT: C 668 ASP cc_start: 0.8665 (m-30) cc_final: 0.8167 (m-30) REVERT: C 672 GLU cc_start: 0.9272 (mm-30) cc_final: 0.9057 (mm-30) REVERT: C 781 ASP cc_start: 0.9513 (m-30) cc_final: 0.9247 (t0) REVERT: D 61 MET cc_start: 0.9334 (mmp) cc_final: 0.9125 (mmm) REVERT: D 158 CYS cc_start: 0.8669 (m) cc_final: 0.8397 (m) REVERT: D 160 LYS cc_start: 0.9374 (mmtt) cc_final: 0.8972 (mmtp) REVERT: D 188 MET cc_start: 0.9554 (ttp) cc_final: 0.9137 (tmm) REVERT: D 252 MET cc_start: 0.9353 (ttp) cc_final: 0.9014 (ttm) REVERT: D 256 ASP cc_start: 0.9207 (m-30) cc_final: 0.9000 (m-30) REVERT: D 427 MET cc_start: 0.8890 (mtp) cc_final: 0.8583 (ptp) REVERT: D 437 MET cc_start: 0.9535 (ttt) cc_final: 0.9279 (tpp) REVERT: D 440 GLU cc_start: 0.9340 (mm-30) cc_final: 0.8697 (tp30) REVERT: D 441 CYS cc_start: 0.9268 (t) cc_final: 0.8956 (p) REVERT: D 464 MET cc_start: 0.9308 (ppp) cc_final: 0.9032 (ppp) REVERT: D 545 LEU cc_start: 0.9698 (tp) cc_final: 0.9491 (tp) REVERT: D 564 ASP cc_start: 0.9000 (m-30) cc_final: 0.8338 (t70) REVERT: D 568 PHE cc_start: 0.9148 (m-80) cc_final: 0.8510 (m-80) REVERT: D 569 MET cc_start: 0.9307 (ttm) cc_final: 0.8724 (mtp) REVERT: D 580 MET cc_start: 0.9539 (tmm) cc_final: 0.9334 (tmm) REVERT: D 650 LEU cc_start: 0.9602 (mm) cc_final: 0.9298 (pp) REVERT: D 654 LEU cc_start: 0.9824 (mp) cc_final: 0.9600 (mp) REVERT: D 657 MET cc_start: 0.9235 (mmm) cc_final: 0.8767 (tmm) REVERT: D 668 ASP cc_start: 0.8665 (m-30) cc_final: 0.8166 (m-30) REVERT: D 672 GLU cc_start: 0.9272 (mm-30) cc_final: 0.9054 (mm-30) REVERT: D 781 ASP cc_start: 0.9518 (m-30) cc_final: 0.9247 (t0) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.1371 time to fit residues: 79.5439 Evaluate side-chains 280 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 138 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 226 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 142 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.051149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.040877 restraints weight = 125572.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.042183 restraints weight = 74862.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.043124 restraints weight = 52091.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.043805 restraints weight = 39788.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.044328 restraints weight = 32588.377| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21696 Z= 0.160 Angle : 0.615 7.632 29340 Z= 0.316 Chirality : 0.037 0.176 3340 Planarity : 0.004 0.048 3668 Dihedral : 4.328 21.279 2872 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.49 (0.17), residues: 2632 helix: 2.16 (0.12), residues: 1992 sheet: None (None), residues: 0 loop : -3.05 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.018 0.002 TYR A 662 PHE 0.006 0.001 PHE D 468 TRP 0.027 0.002 TRP A 681 HIS 0.006 0.001 HIS D 311 Details of bonding type rmsd covalent geometry : bond 0.00336 (21696) covalent geometry : angle 0.61510 (29340) hydrogen bonds : bond 0.03891 ( 1428) hydrogen bonds : angle 3.80507 ( 4248) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 CYS cc_start: 0.8612 (m) cc_final: 0.8243 (m) REVERT: A 160 LYS cc_start: 0.9344 (mmtt) cc_final: 0.8653 (mmtp) REVERT: A 188 MET cc_start: 0.9540 (ttp) cc_final: 0.9108 (mmm) REVERT: A 252 MET cc_start: 0.9335 (ttp) cc_final: 0.9002 (ttm) REVERT: A 256 ASP cc_start: 0.9197 (m-30) cc_final: 0.8955 (m-30) REVERT: A 427 MET cc_start: 0.8901 (mtp) cc_final: 0.8603 (ptp) REVERT: A 437 MET cc_start: 0.9513 (ttt) cc_final: 0.9220 (tpp) REVERT: A 440 GLU cc_start: 0.9344 (mm-30) cc_final: 0.8709 (tp30) REVERT: A 464 MET cc_start: 0.9387 (ppp) cc_final: 0.9050 (ppp) REVERT: A 545 LEU cc_start: 0.9700 (tp) cc_final: 0.9456 (tp) REVERT: A 564 ASP cc_start: 0.8923 (m-30) cc_final: 0.8304 (t70) REVERT: A 568 PHE cc_start: 0.9211 (m-10) cc_final: 0.8403 (m-10) REVERT: A 569 MET cc_start: 0.9176 (ttm) cc_final: 0.8614 (mtp) REVERT: A 574 MET cc_start: 0.9539 (ttt) cc_final: 0.9282 (tmm) REVERT: A 580 MET cc_start: 0.9567 (tmm) cc_final: 0.9359 (tmm) REVERT: A 650 LEU cc_start: 0.9556 (mm) cc_final: 0.9145 (tt) REVERT: A 654 LEU cc_start: 0.9767 (mp) cc_final: 0.9548 (mp) REVERT: A 657 MET cc_start: 0.9189 (mmp) cc_final: 0.8546 (tmm) REVERT: A 668 ASP cc_start: 0.8594 (m-30) cc_final: 0.8082 (m-30) REVERT: A 672 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8963 (mm-30) REVERT: A 779 GLN cc_start: 0.9510 (tm-30) cc_final: 0.9094 (tm-30) REVERT: B 158 CYS cc_start: 0.8616 (m) cc_final: 0.8244 (m) REVERT: B 160 LYS cc_start: 0.9345 (mmtt) cc_final: 0.8651 (mmtp) REVERT: B 188 MET cc_start: 0.9538 (ttp) cc_final: 0.9103 (mmm) REVERT: B 252 MET cc_start: 0.9336 (ttp) cc_final: 0.9000 (ttm) REVERT: B 256 ASP cc_start: 0.9195 (m-30) cc_final: 0.8952 (m-30) REVERT: B 427 MET cc_start: 0.8905 (mtp) cc_final: 0.8604 (ptp) REVERT: B 437 MET cc_start: 0.9516 (ttt) cc_final: 0.9225 (tpp) REVERT: B 440 GLU cc_start: 0.9339 (mm-30) cc_final: 0.8702 (tp30) REVERT: B 464 MET cc_start: 0.9392 (ppp) cc_final: 0.9054 (ppp) REVERT: B 545 LEU cc_start: 0.9698 (tp) cc_final: 0.9454 (tp) REVERT: B 564 ASP cc_start: 0.9002 (m-30) cc_final: 0.8448 (t70) REVERT: B 569 MET cc_start: 0.9188 (ttm) cc_final: 0.8623 (mtp) REVERT: B 574 MET cc_start: 0.9539 (ttt) cc_final: 0.9281 (tmm) REVERT: B 580 MET cc_start: 0.9567 (tmm) cc_final: 0.9359 (tmm) REVERT: B 650 LEU cc_start: 0.9567 (mm) cc_final: 0.9253 (pp) REVERT: B 653 MET cc_start: 0.9229 (tpp) cc_final: 0.8912 (tpp) REVERT: B 657 MET cc_start: 0.9082 (mmm) cc_final: 0.8864 (mmp) REVERT: B 668 ASP cc_start: 0.8594 (m-30) cc_final: 0.8081 (m-30) REVERT: B 672 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8966 (mm-30) REVERT: B 779 GLN cc_start: 0.9510 (tm-30) cc_final: 0.9094 (tm-30) REVERT: C 158 CYS cc_start: 0.8613 (m) cc_final: 0.8241 (m) REVERT: C 160 LYS cc_start: 0.9347 (mmtt) cc_final: 0.8655 (mmtp) REVERT: C 188 MET cc_start: 0.9550 (ttp) cc_final: 0.9111 (mmm) REVERT: C 252 MET cc_start: 0.9335 (ttp) cc_final: 0.9001 (ttm) REVERT: C 256 ASP cc_start: 0.9196 (m-30) cc_final: 0.8952 (m-30) REVERT: C 427 MET cc_start: 0.8902 (mtp) cc_final: 0.8603 (ptp) REVERT: C 437 MET cc_start: 0.9517 (ttt) cc_final: 0.9226 (tpp) REVERT: C 440 GLU cc_start: 0.9339 (mm-30) cc_final: 0.8701 (tp30) REVERT: C 464 MET cc_start: 0.9393 (ppp) cc_final: 0.9052 (ppp) REVERT: C 545 LEU cc_start: 0.9700 (tp) cc_final: 0.9456 (tp) REVERT: C 564 ASP cc_start: 0.9002 (m-30) cc_final: 0.8271 (t70) REVERT: C 568 PHE cc_start: 0.9110 (m-80) cc_final: 0.8493 (m-80) REVERT: C 569 MET cc_start: 0.9187 (ttm) cc_final: 0.8620 (mtp) REVERT: C 574 MET cc_start: 0.9537 (ttt) cc_final: 0.9279 (tmm) REVERT: C 580 MET cc_start: 0.9563 (tmm) cc_final: 0.9357 (tmm) REVERT: C 650 LEU cc_start: 0.9568 (mm) cc_final: 0.9255 (pp) REVERT: C 654 LEU cc_start: 0.9790 (mp) cc_final: 0.9586 (mp) REVERT: C 657 MET cc_start: 0.9085 (mmm) cc_final: 0.8727 (tmm) REVERT: C 668 ASP cc_start: 0.8595 (m-30) cc_final: 0.8085 (m-30) REVERT: C 672 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8966 (mm-30) REVERT: C 779 GLN cc_start: 0.9511 (tm-30) cc_final: 0.9096 (tm-30) REVERT: D 158 CYS cc_start: 0.8652 (m) cc_final: 0.8269 (m) REVERT: D 160 LYS cc_start: 0.9371 (mmtt) cc_final: 0.8699 (mmtp) REVERT: D 188 MET cc_start: 0.9541 (ttp) cc_final: 0.9106 (mmm) REVERT: D 252 MET cc_start: 0.9336 (ttp) cc_final: 0.9000 (ttm) REVERT: D 256 ASP cc_start: 0.9195 (m-30) cc_final: 0.8950 (m-30) REVERT: D 427 MET cc_start: 0.8899 (mtp) cc_final: 0.8603 (ptp) REVERT: D 437 MET cc_start: 0.9517 (ttt) cc_final: 0.9225 (tpp) REVERT: D 440 GLU cc_start: 0.9345 (mm-30) cc_final: 0.8711 (tp30) REVERT: D 464 MET cc_start: 0.9388 (ppp) cc_final: 0.9051 (ppp) REVERT: D 545 LEU cc_start: 0.9698 (tp) cc_final: 0.9451 (tp) REVERT: D 564 ASP cc_start: 0.8969 (m-30) cc_final: 0.8440 (t70) REVERT: D 569 MET cc_start: 0.9191 (ttm) cc_final: 0.8622 (mtp) REVERT: D 574 MET cc_start: 0.9541 (ttt) cc_final: 0.9282 (tmm) REVERT: D 580 MET cc_start: 0.9565 (tmm) cc_final: 0.9355 (tmm) REVERT: D 650 LEU cc_start: 0.9567 (mm) cc_final: 0.9253 (pp) REVERT: D 653 MET cc_start: 0.9236 (tpp) cc_final: 0.8966 (tpp) REVERT: D 657 MET cc_start: 0.9076 (mmm) cc_final: 0.8860 (mmp) REVERT: D 668 ASP cc_start: 0.8593 (m-30) cc_final: 0.8081 (m-30) REVERT: D 672 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8966 (mm-30) REVERT: D 779 GLN cc_start: 0.9508 (tm-30) cc_final: 0.9099 (tm-30) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.1244 time to fit residues: 71.4012 Evaluate side-chains 267 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 209 optimal weight: 0.8980 chunk 41 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 0.0570 chunk 95 optimal weight: 8.9990 overall best weight: 3.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 GLN B 315 GLN B 797 GLN C 315 GLN C 797 GLN ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 GLN D 797 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.051803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.041567 restraints weight = 126229.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.042861 restraints weight = 74711.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.043761 restraints weight = 51766.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.044453 restraints weight = 39835.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.044956 restraints weight = 32582.147| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21696 Z= 0.166 Angle : 0.613 7.740 29340 Z= 0.324 Chirality : 0.038 0.173 3340 Planarity : 0.004 0.048 3668 Dihedral : 4.330 21.030 2872 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.51 (0.17), residues: 2632 helix: 2.20 (0.12), residues: 1988 sheet: None (None), residues: 0 loop : -3.10 (0.20), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 773 TYR 0.017 0.002 TYR B 662 PHE 0.008 0.001 PHE C 31 TRP 0.027 0.002 TRP D 681 HIS 0.006 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00346 (21696) covalent geometry : angle 0.61315 (29340) hydrogen bonds : bond 0.03904 ( 1428) hydrogen bonds : angle 3.86353 ( 4248) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 CYS cc_start: 0.8587 (m) cc_final: 0.8199 (m) REVERT: A 160 LYS cc_start: 0.9384 (mmtt) cc_final: 0.8681 (mmtp) REVERT: A 188 MET cc_start: 0.9524 (ttp) cc_final: 0.9107 (mmm) REVERT: A 252 MET cc_start: 0.9323 (ttp) cc_final: 0.8962 (mmp) REVERT: A 427 MET cc_start: 0.8735 (mtp) cc_final: 0.8508 (ptp) REVERT: A 437 MET cc_start: 0.9517 (ttt) cc_final: 0.9214 (tpp) REVERT: A 440 GLU cc_start: 0.9344 (mm-30) cc_final: 0.8637 (tp30) REVERT: A 464 MET cc_start: 0.9402 (ppp) cc_final: 0.9035 (ppp) REVERT: A 545 LEU cc_start: 0.9711 (tp) cc_final: 0.9469 (tp) REVERT: A 564 ASP cc_start: 0.8852 (m-30) cc_final: 0.8214 (t70) REVERT: A 568 PHE cc_start: 0.9152 (m-10) cc_final: 0.8555 (m-10) REVERT: A 569 MET cc_start: 0.9178 (ttm) cc_final: 0.8598 (mtp) REVERT: A 574 MET cc_start: 0.9606 (ttt) cc_final: 0.9313 (tmm) REVERT: A 580 MET cc_start: 0.9576 (tmm) cc_final: 0.9326 (tmm) REVERT: A 628 HIS cc_start: 0.7237 (m170) cc_final: 0.6762 (m90) REVERT: A 650 LEU cc_start: 0.9520 (mm) cc_final: 0.9141 (pp) REVERT: A 657 MET cc_start: 0.8951 (mmp) cc_final: 0.8570 (tmm) REVERT: A 668 ASP cc_start: 0.8563 (m-30) cc_final: 0.8058 (m-30) REVERT: A 672 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8955 (mm-30) REVERT: A 779 GLN cc_start: 0.9534 (tm-30) cc_final: 0.9316 (tm-30) REVERT: B 158 CYS cc_start: 0.8587 (m) cc_final: 0.8200 (m) REVERT: B 160 LYS cc_start: 0.9383 (mmtt) cc_final: 0.8681 (mmtp) REVERT: B 188 MET cc_start: 0.9527 (ttp) cc_final: 0.9109 (mmm) REVERT: B 252 MET cc_start: 0.9321 (ttp) cc_final: 0.8961 (mmp) REVERT: B 427 MET cc_start: 0.8736 (mtp) cc_final: 0.8507 (ptp) REVERT: B 437 MET cc_start: 0.9519 (ttt) cc_final: 0.9220 (tpp) REVERT: B 440 GLU cc_start: 0.9344 (mm-30) cc_final: 0.8637 (tp30) REVERT: B 464 MET cc_start: 0.9404 (ppp) cc_final: 0.9036 (ppp) REVERT: B 545 LEU cc_start: 0.9707 (tp) cc_final: 0.9465 (tp) REVERT: B 564 ASP cc_start: 0.8903 (m-30) cc_final: 0.8220 (t70) REVERT: B 568 PHE cc_start: 0.9015 (m-80) cc_final: 0.8508 (m-10) REVERT: B 569 MET cc_start: 0.9216 (ttm) cc_final: 0.8649 (mtp) REVERT: B 574 MET cc_start: 0.9604 (ttt) cc_final: 0.9296 (tmm) REVERT: B 580 MET cc_start: 0.9570 (tmm) cc_final: 0.9321 (tmm) REVERT: B 628 HIS cc_start: 0.7234 (m170) cc_final: 0.6759 (m90) REVERT: B 650 LEU cc_start: 0.9518 (mm) cc_final: 0.9150 (pp) REVERT: B 657 MET cc_start: 0.9104 (mmm) cc_final: 0.8732 (tmm) REVERT: B 668 ASP cc_start: 0.8561 (m-30) cc_final: 0.8062 (m-30) REVERT: B 672 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8959 (mm-30) REVERT: B 779 GLN cc_start: 0.9534 (tm-30) cc_final: 0.9316 (tm-30) REVERT: C 158 CYS cc_start: 0.8587 (m) cc_final: 0.8198 (m) REVERT: C 160 LYS cc_start: 0.9380 (mmtt) cc_final: 0.8678 (mmtp) REVERT: C 188 MET cc_start: 0.9528 (ttp) cc_final: 0.9112 (mmm) REVERT: C 252 MET cc_start: 0.9319 (ttp) cc_final: 0.8961 (mmp) REVERT: C 427 MET cc_start: 0.8732 (mtp) cc_final: 0.8506 (ptp) REVERT: C 437 MET cc_start: 0.9521 (ttt) cc_final: 0.9221 (tpp) REVERT: C 440 GLU cc_start: 0.9344 (mm-30) cc_final: 0.8636 (tp30) REVERT: C 464 MET cc_start: 0.9406 (ppp) cc_final: 0.9038 (ppp) REVERT: C 545 LEU cc_start: 0.9706 (tp) cc_final: 0.9467 (tp) REVERT: C 564 ASP cc_start: 0.8984 (m-30) cc_final: 0.8240 (t70) REVERT: C 568 PHE cc_start: 0.9144 (m-80) cc_final: 0.8580 (m-80) REVERT: C 569 MET cc_start: 0.9181 (ttm) cc_final: 0.8600 (mtp) REVERT: C 574 MET cc_start: 0.9607 (ttt) cc_final: 0.9299 (tmm) REVERT: C 580 MET cc_start: 0.9568 (tmm) cc_final: 0.9321 (tmm) REVERT: C 628 HIS cc_start: 0.7240 (m170) cc_final: 0.6762 (m90) REVERT: C 650 LEU cc_start: 0.9512 (mm) cc_final: 0.9170 (pp) REVERT: C 654 LEU cc_start: 0.9756 (mp) cc_final: 0.9519 (mp) REVERT: C 657 MET cc_start: 0.9114 (mmm) cc_final: 0.8757 (tmm) REVERT: C 668 ASP cc_start: 0.8560 (m-30) cc_final: 0.8061 (m-30) REVERT: C 672 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8964 (mm-30) REVERT: C 779 GLN cc_start: 0.9535 (tm-30) cc_final: 0.9317 (tm-30) REVERT: D 158 CYS cc_start: 0.8635 (m) cc_final: 0.8294 (m) REVERT: D 160 LYS cc_start: 0.9358 (mmtt) cc_final: 0.8700 (mmtp) REVERT: D 188 MET cc_start: 0.9535 (ttp) cc_final: 0.9113 (mmm) REVERT: D 252 MET cc_start: 0.9323 (ttp) cc_final: 0.8964 (mmp) REVERT: D 427 MET cc_start: 0.8731 (mtp) cc_final: 0.8508 (ptp) REVERT: D 437 MET cc_start: 0.9521 (ttt) cc_final: 0.9219 (tpp) REVERT: D 440 GLU cc_start: 0.9340 (mm-30) cc_final: 0.8633 (tp30) REVERT: D 464 MET cc_start: 0.9400 (ppp) cc_final: 0.9033 (ppp) REVERT: D 545 LEU cc_start: 0.9700 (tp) cc_final: 0.9460 (tp) REVERT: D 564 ASP cc_start: 0.8892 (m-30) cc_final: 0.8242 (t70) REVERT: D 568 PHE cc_start: 0.9014 (m-80) cc_final: 0.8602 (m-10) REVERT: D 569 MET cc_start: 0.9222 (ttm) cc_final: 0.8649 (mtp) REVERT: D 574 MET cc_start: 0.9605 (ttt) cc_final: 0.9299 (tmm) REVERT: D 580 MET cc_start: 0.9575 (tmm) cc_final: 0.9325 (tmm) REVERT: D 628 HIS cc_start: 0.7242 (m170) cc_final: 0.6766 (m90) REVERT: D 650 LEU cc_start: 0.9524 (mm) cc_final: 0.9156 (pp) REVERT: D 657 MET cc_start: 0.9104 (mmm) cc_final: 0.8765 (tmm) REVERT: D 668 ASP cc_start: 0.8466 (m-30) cc_final: 0.7943 (m-30) REVERT: D 672 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8928 (mm-30) REVERT: D 779 GLN cc_start: 0.9536 (tm-30) cc_final: 0.9318 (tm-30) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.1348 time to fit residues: 76.3166 Evaluate side-chains 281 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 3 optimal weight: 7.9990 chunk 42 optimal weight: 0.1980 chunk 64 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 243 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 170 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.051181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.041186 restraints weight = 124225.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.042472 restraints weight = 73236.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.043406 restraints weight = 50616.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.044080 restraints weight = 38542.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.044584 restraints weight = 31356.724| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21696 Z= 0.163 Angle : 0.617 7.519 29340 Z= 0.323 Chirality : 0.038 0.173 3340 Planarity : 0.004 0.048 3668 Dihedral : 4.281 21.020 2872 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.55 (0.17), residues: 2632 helix: 2.21 (0.12), residues: 1992 sheet: None (None), residues: 0 loop : -3.07 (0.20), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 773 TYR 0.018 0.002 TYR B 662 PHE 0.007 0.001 PHE D 381 TRP 0.028 0.002 TRP D 681 HIS 0.006 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00341 (21696) covalent geometry : angle 0.61655 (29340) hydrogen bonds : bond 0.03853 ( 1428) hydrogen bonds : angle 3.88321 ( 4248) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8185 (pmm) cc_final: 0.7917 (pmm) REVERT: A 158 CYS cc_start: 0.8553 (m) cc_final: 0.8154 (m) REVERT: A 160 LYS cc_start: 0.9353 (mmtt) cc_final: 0.8645 (mmtp) REVERT: A 188 MET cc_start: 0.9520 (ttp) cc_final: 0.9138 (mmm) REVERT: A 309 VAL cc_start: 0.9854 (t) cc_final: 0.9561 (p) REVERT: A 314 CYS cc_start: 0.9366 (t) cc_final: 0.9059 (t) REVERT: A 427 MET cc_start: 0.8735 (mtp) cc_final: 0.8520 (ptp) REVERT: A 437 MET cc_start: 0.9538 (ttt) cc_final: 0.9241 (tpp) REVERT: A 440 GLU cc_start: 0.9350 (mm-30) cc_final: 0.8625 (tp30) REVERT: A 464 MET cc_start: 0.9423 (ppp) cc_final: 0.9066 (ppp) REVERT: A 545 LEU cc_start: 0.9716 (tp) cc_final: 0.9500 (tp) REVERT: A 564 ASP cc_start: 0.8899 (m-30) cc_final: 0.8428 (t70) REVERT: A 569 MET cc_start: 0.9138 (ttm) cc_final: 0.8593 (mtp) REVERT: A 574 MET cc_start: 0.9630 (ttt) cc_final: 0.9276 (tmm) REVERT: A 583 MET cc_start: 0.9495 (mmt) cc_final: 0.9033 (mmm) REVERT: A 643 ASN cc_start: 0.9540 (t0) cc_final: 0.9232 (t0) REVERT: A 650 LEU cc_start: 0.9443 (mm) cc_final: 0.9019 (pp) REVERT: A 668 ASP cc_start: 0.8451 (m-30) cc_final: 0.7884 (m-30) REVERT: A 672 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8968 (mm-30) REVERT: B 158 CYS cc_start: 0.8560 (m) cc_final: 0.8165 (m) REVERT: B 160 LYS cc_start: 0.9352 (mmtt) cc_final: 0.8647 (mmtp) REVERT: B 188 MET cc_start: 0.9523 (ttp) cc_final: 0.9139 (mmm) REVERT: B 309 VAL cc_start: 0.9854 (t) cc_final: 0.9562 (p) REVERT: B 314 CYS cc_start: 0.9372 (t) cc_final: 0.9064 (t) REVERT: B 427 MET cc_start: 0.8738 (mtp) cc_final: 0.8522 (ptp) REVERT: B 437 MET cc_start: 0.9541 (ttt) cc_final: 0.9247 (tpp) REVERT: B 440 GLU cc_start: 0.9349 (mm-30) cc_final: 0.8624 (tp30) REVERT: B 464 MET cc_start: 0.9427 (ppp) cc_final: 0.9069 (ppp) REVERT: B 545 LEU cc_start: 0.9710 (tp) cc_final: 0.9448 (tp) REVERT: B 564 ASP cc_start: 0.8969 (m-30) cc_final: 0.8294 (t70) REVERT: B 568 PHE cc_start: 0.9092 (m-80) cc_final: 0.8735 (m-10) REVERT: B 569 MET cc_start: 0.9185 (ttm) cc_final: 0.8605 (mtp) REVERT: B 574 MET cc_start: 0.9626 (ttt) cc_final: 0.9253 (tmm) REVERT: B 583 MET cc_start: 0.9492 (mmt) cc_final: 0.9031 (mmm) REVERT: B 643 ASN cc_start: 0.9547 (t0) cc_final: 0.9244 (t0) REVERT: B 650 LEU cc_start: 0.9449 (mm) cc_final: 0.8990 (tt) REVERT: B 654 LEU cc_start: 0.9768 (mp) cc_final: 0.9540 (mp) REVERT: B 657 MET cc_start: 0.9085 (mmm) cc_final: 0.8776 (tmm) REVERT: B 668 ASP cc_start: 0.8451 (m-30) cc_final: 0.7888 (m-30) REVERT: B 672 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8965 (mm-30) REVERT: C 158 CYS cc_start: 0.8553 (m) cc_final: 0.8154 (m) REVERT: C 160 LYS cc_start: 0.9350 (mmtt) cc_final: 0.8642 (mmtp) REVERT: C 188 MET cc_start: 0.9528 (ttp) cc_final: 0.9141 (mmm) REVERT: C 309 VAL cc_start: 0.9853 (t) cc_final: 0.9558 (p) REVERT: C 314 CYS cc_start: 0.9363 (t) cc_final: 0.9056 (t) REVERT: C 427 MET cc_start: 0.8735 (mtp) cc_final: 0.8520 (ptp) REVERT: C 437 MET cc_start: 0.9543 (ttt) cc_final: 0.9249 (tpp) REVERT: C 440 GLU cc_start: 0.9351 (mm-30) cc_final: 0.8626 (tp30) REVERT: C 464 MET cc_start: 0.9429 (ppp) cc_final: 0.9068 (ppp) REVERT: C 545 LEU cc_start: 0.9712 (tp) cc_final: 0.9497 (tp) REVERT: C 564 ASP cc_start: 0.8991 (m-30) cc_final: 0.8242 (t70) REVERT: C 568 PHE cc_start: 0.9167 (m-80) cc_final: 0.8678 (m-80) REVERT: C 569 MET cc_start: 0.9170 (ttm) cc_final: 0.8594 (mtp) REVERT: C 574 MET cc_start: 0.9629 (ttt) cc_final: 0.9252 (tmm) REVERT: C 583 MET cc_start: 0.9495 (mmt) cc_final: 0.9034 (mmm) REVERT: C 643 ASN cc_start: 0.9529 (t0) cc_final: 0.9228 (t0) REVERT: C 650 LEU cc_start: 0.9442 (mm) cc_final: 0.8890 (tt) REVERT: C 654 LEU cc_start: 0.9721 (mp) cc_final: 0.9413 (mp) REVERT: C 657 MET cc_start: 0.9121 (mmm) cc_final: 0.8799 (tmm) REVERT: C 668 ASP cc_start: 0.8453 (m-30) cc_final: 0.7892 (m-30) REVERT: C 672 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8966 (mm-30) REVERT: D 158 CYS cc_start: 0.8579 (m) cc_final: 0.8204 (m) REVERT: D 160 LYS cc_start: 0.9346 (mmtt) cc_final: 0.8672 (mmtp) REVERT: D 168 LEU cc_start: 0.9743 (tp) cc_final: 0.9492 (tt) REVERT: D 169 MET cc_start: 0.8389 (mmp) cc_final: 0.8170 (mmm) REVERT: D 188 MET cc_start: 0.9526 (ttp) cc_final: 0.9140 (mmm) REVERT: D 309 VAL cc_start: 0.9853 (t) cc_final: 0.9577 (p) REVERT: D 427 MET cc_start: 0.8733 (mtp) cc_final: 0.8521 (ptp) REVERT: D 437 MET cc_start: 0.9541 (ttt) cc_final: 0.9245 (tpp) REVERT: D 440 GLU cc_start: 0.9351 (mm-30) cc_final: 0.8625 (tp30) REVERT: D 464 MET cc_start: 0.9423 (ppp) cc_final: 0.9065 (ppp) REVERT: D 545 LEU cc_start: 0.9706 (tp) cc_final: 0.9446 (tp) REVERT: D 564 ASP cc_start: 0.8886 (m-30) cc_final: 0.8203 (t70) REVERT: D 568 PHE cc_start: 0.9093 (m-80) cc_final: 0.8821 (m-10) REVERT: D 569 MET cc_start: 0.9186 (ttm) cc_final: 0.8602 (mtp) REVERT: D 574 MET cc_start: 0.9631 (ttt) cc_final: 0.9274 (tmm) REVERT: D 583 MET cc_start: 0.9490 (mmt) cc_final: 0.9030 (mmm) REVERT: D 643 ASN cc_start: 0.9547 (t0) cc_final: 0.9235 (t0) REVERT: D 650 LEU cc_start: 0.9461 (mm) cc_final: 0.9042 (pp) REVERT: D 657 MET cc_start: 0.9111 (mmm) cc_final: 0.8768 (tmm) REVERT: D 668 ASP cc_start: 0.8447 (m-30) cc_final: 0.7893 (m-30) REVERT: D 672 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8918 (mm-30) outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 0.1313 time to fit residues: 71.9378 Evaluate side-chains 276 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 0.0470 chunk 160 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN A 628 HIS B 159 GLN B 628 HIS C 159 GLN C 628 HIS D 159 GLN D 628 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.052451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.042090 restraints weight = 123927.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.043425 restraints weight = 73814.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.044388 restraints weight = 51302.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.045098 restraints weight = 38971.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.045606 restraints weight = 31830.491| |-----------------------------------------------------------------------------| r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21696 Z= 0.127 Angle : 0.608 10.560 29340 Z= 0.317 Chirality : 0.039 0.168 3340 Planarity : 0.004 0.048 3668 Dihedral : 4.119 20.198 2872 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.63 (0.17), residues: 2632 helix: 2.26 (0.12), residues: 1992 sheet: None (None), residues: 0 loop : -2.99 (0.20), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 769 TYR 0.018 0.002 TYR B 662 PHE 0.013 0.001 PHE D 31 TRP 0.022 0.001 TRP D 681 HIS 0.005 0.001 HIS D 311 Details of bonding type rmsd covalent geometry : bond 0.00273 (21696) covalent geometry : angle 0.60831 (29340) hydrogen bonds : bond 0.03883 ( 1428) hydrogen bonds : angle 3.76975 ( 4248) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 CYS cc_start: 0.8481 (m) cc_final: 0.8278 (m) REVERT: A 160 LYS cc_start: 0.9309 (mmtt) cc_final: 0.8836 (mmtp) REVERT: A 188 MET cc_start: 0.9512 (ttp) cc_final: 0.9121 (mmm) REVERT: A 252 MET cc_start: 0.9397 (ttm) cc_final: 0.9086 (mmp) REVERT: A 309 VAL cc_start: 0.9847 (t) cc_final: 0.9544 (p) REVERT: A 314 CYS cc_start: 0.9357 (t) cc_final: 0.9055 (t) REVERT: A 427 MET cc_start: 0.8720 (mtp) cc_final: 0.8498 (ptp) REVERT: A 437 MET cc_start: 0.9506 (ttt) cc_final: 0.9204 (tpp) REVERT: A 440 GLU cc_start: 0.9351 (mm-30) cc_final: 0.8671 (tp30) REVERT: A 464 MET cc_start: 0.9414 (ppp) cc_final: 0.9056 (ppp) REVERT: A 564 ASP cc_start: 0.8885 (m-30) cc_final: 0.8372 (t70) REVERT: A 568 PHE cc_start: 0.9055 (m-10) cc_final: 0.8249 (m-10) REVERT: A 574 MET cc_start: 0.9622 (ttt) cc_final: 0.9280 (tmm) REVERT: A 580 MET cc_start: 0.9564 (tmm) cc_final: 0.9327 (tmm) REVERT: A 583 MET cc_start: 0.9427 (mmt) cc_final: 0.8933 (mmm) REVERT: A 628 HIS cc_start: 0.7311 (m170) cc_final: 0.6949 (m90) REVERT: A 643 ASN cc_start: 0.9494 (t0) cc_final: 0.9176 (t0) REVERT: A 657 MET cc_start: 0.9149 (mmp) cc_final: 0.8850 (ppp) REVERT: A 668 ASP cc_start: 0.8367 (m-30) cc_final: 0.7796 (m-30) REVERT: A 672 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8916 (mm-30) REVERT: A 781 ASP cc_start: 0.9648 (t70) cc_final: 0.9374 (t0) REVERT: B 160 LYS cc_start: 0.9311 (mmtt) cc_final: 0.8839 (mmtp) REVERT: B 188 MET cc_start: 0.9512 (ttp) cc_final: 0.9120 (mmm) REVERT: B 252 MET cc_start: 0.9397 (ttm) cc_final: 0.9083 (mmp) REVERT: B 309 VAL cc_start: 0.9846 (t) cc_final: 0.9544 (p) REVERT: B 314 CYS cc_start: 0.9365 (t) cc_final: 0.9064 (t) REVERT: B 427 MET cc_start: 0.8723 (mtp) cc_final: 0.8500 (ptp) REVERT: B 437 MET cc_start: 0.9507 (ttt) cc_final: 0.9208 (tpp) REVERT: B 440 GLU cc_start: 0.9350 (mm-30) cc_final: 0.8668 (tp30) REVERT: B 464 MET cc_start: 0.9416 (ppp) cc_final: 0.9058 (ppp) REVERT: B 564 ASP cc_start: 0.8936 (m-30) cc_final: 0.8235 (t70) REVERT: B 568 PHE cc_start: 0.9146 (m-80) cc_final: 0.8632 (m-10) REVERT: B 574 MET cc_start: 0.9620 (ttt) cc_final: 0.9273 (tmm) REVERT: B 580 MET cc_start: 0.9566 (tmm) cc_final: 0.9327 (tmm) REVERT: B 583 MET cc_start: 0.9425 (mmt) cc_final: 0.8932 (mmm) REVERT: B 628 HIS cc_start: 0.7316 (m170) cc_final: 0.6954 (m90) REVERT: B 643 ASN cc_start: 0.9509 (t0) cc_final: 0.9190 (t0) REVERT: B 650 LEU cc_start: 0.9408 (mm) cc_final: 0.8994 (tt) REVERT: B 657 MET cc_start: 0.9185 (mmm) cc_final: 0.8761 (tmm) REVERT: B 668 ASP cc_start: 0.8366 (m-30) cc_final: 0.7804 (m-30) REVERT: B 672 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8921 (mm-30) REVERT: B 781 ASP cc_start: 0.9649 (t70) cc_final: 0.9374 (t0) REVERT: C 158 CYS cc_start: 0.8487 (m) cc_final: 0.8282 (m) REVERT: C 160 LYS cc_start: 0.9308 (mmtt) cc_final: 0.8835 (mmtp) REVERT: C 188 MET cc_start: 0.9521 (ttp) cc_final: 0.9124 (mmm) REVERT: C 252 MET cc_start: 0.9398 (ttm) cc_final: 0.9086 (mmp) REVERT: C 309 VAL cc_start: 0.9848 (t) cc_final: 0.9546 (p) REVERT: C 314 CYS cc_start: 0.9358 (t) cc_final: 0.9055 (t) REVERT: C 427 MET cc_start: 0.8722 (mtp) cc_final: 0.8498 (ptp) REVERT: C 437 MET cc_start: 0.9510 (ttt) cc_final: 0.9211 (tpp) REVERT: C 440 GLU cc_start: 0.9354 (mm-30) cc_final: 0.8678 (tp30) REVERT: C 464 MET cc_start: 0.9419 (ppp) cc_final: 0.9060 (ppp) REVERT: C 564 ASP cc_start: 0.8965 (m-30) cc_final: 0.8172 (t70) REVERT: C 568 PHE cc_start: 0.9195 (m-80) cc_final: 0.8809 (m-80) REVERT: C 569 MET cc_start: 0.9162 (ttm) cc_final: 0.8585 (mtp) REVERT: C 574 MET cc_start: 0.9623 (ttt) cc_final: 0.9275 (tmm) REVERT: C 580 MET cc_start: 0.9558 (tmm) cc_final: 0.9317 (tmm) REVERT: C 583 MET cc_start: 0.9445 (mmt) cc_final: 0.8980 (mmm) REVERT: C 628 HIS cc_start: 0.7325 (m170) cc_final: 0.6962 (m90) REVERT: C 643 ASN cc_start: 0.9507 (t0) cc_final: 0.9187 (t0) REVERT: C 650 LEU cc_start: 0.9403 (mm) cc_final: 0.8968 (tt) REVERT: C 657 MET cc_start: 0.9253 (mmm) cc_final: 0.8649 (tmm) REVERT: C 668 ASP cc_start: 0.8375 (m-30) cc_final: 0.7809 (m-30) REVERT: C 672 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8922 (mm-30) REVERT: C 781 ASP cc_start: 0.9649 (t70) cc_final: 0.9372 (t0) REVERT: D 158 CYS cc_start: 0.8533 (m) cc_final: 0.8330 (m) REVERT: D 160 LYS cc_start: 0.9361 (mmtt) cc_final: 0.8919 (mmtp) REVERT: D 188 MET cc_start: 0.9515 (ttp) cc_final: 0.9122 (mmm) REVERT: D 252 MET cc_start: 0.9398 (ttm) cc_final: 0.9086 (mmp) REVERT: D 309 VAL cc_start: 0.9847 (t) cc_final: 0.9542 (p) REVERT: D 314 CYS cc_start: 0.9357 (t) cc_final: 0.9044 (t) REVERT: D 427 MET cc_start: 0.8719 (mtp) cc_final: 0.8500 (ptp) REVERT: D 437 MET cc_start: 0.9509 (ttt) cc_final: 0.9207 (tpp) REVERT: D 440 GLU cc_start: 0.9354 (mm-30) cc_final: 0.8675 (tp30) REVERT: D 464 MET cc_start: 0.9413 (ppp) cc_final: 0.9056 (ppp) REVERT: D 545 LEU cc_start: 0.9724 (tp) cc_final: 0.9467 (tp) REVERT: D 564 ASP cc_start: 0.8864 (m-30) cc_final: 0.8190 (t70) REVERT: D 568 PHE cc_start: 0.9196 (m-80) cc_final: 0.8774 (m-10) REVERT: D 569 MET cc_start: 0.9138 (ttm) cc_final: 0.8530 (mtp) REVERT: D 574 MET cc_start: 0.9624 (ttt) cc_final: 0.9282 (tmm) REVERT: D 580 MET cc_start: 0.9568 (tmm) cc_final: 0.9327 (tmm) REVERT: D 583 MET cc_start: 0.9421 (mmt) cc_final: 0.8932 (mmm) REVERT: D 628 HIS cc_start: 0.7311 (m170) cc_final: 0.6950 (m90) REVERT: D 643 ASN cc_start: 0.9502 (t0) cc_final: 0.9177 (t0) REVERT: D 650 LEU cc_start: 0.9413 (mm) cc_final: 0.8932 (pp) REVERT: D 657 MET cc_start: 0.9227 (mmm) cc_final: 0.8738 (tmm) REVERT: D 781 ASP cc_start: 0.9650 (t70) cc_final: 0.9379 (t0) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.1306 time to fit residues: 73.2960 Evaluate side-chains 280 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 225 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 233 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 chunk 251 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 chunk 256 optimal weight: 0.9990 chunk 134 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.051040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.040836 restraints weight = 127820.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.042123 restraints weight = 76208.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.043041 restraints weight = 53166.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.043704 restraints weight = 40767.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.044204 restraints weight = 33557.635| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21696 Z= 0.195 Angle : 0.670 10.336 29340 Z= 0.351 Chirality : 0.040 0.176 3340 Planarity : 0.004 0.047 3668 Dihedral : 4.387 21.372 2872 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.45 (0.17), residues: 2632 helix: 2.11 (0.12), residues: 1992 sheet: None (None), residues: 0 loop : -2.99 (0.20), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 266 TYR 0.018 0.002 TYR C 662 PHE 0.011 0.001 PHE A 576 TRP 0.032 0.002 TRP D 681 HIS 0.010 0.002 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00405 (21696) covalent geometry : angle 0.66976 (29340) hydrogen bonds : bond 0.04116 ( 1428) hydrogen bonds : angle 4.10588 ( 4248) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 CYS cc_start: 0.8608 (m) cc_final: 0.8160 (m) REVERT: A 160 LYS cc_start: 0.9373 (mmtt) cc_final: 0.8692 (mmtp) REVERT: A 188 MET cc_start: 0.9497 (ttp) cc_final: 0.9145 (mmm) REVERT: A 252 MET cc_start: 0.9391 (ttm) cc_final: 0.9126 (mmp) REVERT: A 309 VAL cc_start: 0.9831 (t) cc_final: 0.9567 (p) REVERT: A 437 MET cc_start: 0.9559 (ttt) cc_final: 0.9233 (tpp) REVERT: A 440 GLU cc_start: 0.9365 (mm-30) cc_final: 0.8609 (tp30) REVERT: A 464 MET cc_start: 0.9439 (ppp) cc_final: 0.9120 (ppp) REVERT: A 564 ASP cc_start: 0.8895 (m-30) cc_final: 0.8214 (t70) REVERT: A 569 MET cc_start: 0.9188 (ttm) cc_final: 0.8638 (mtp) REVERT: A 574 MET cc_start: 0.9665 (ttt) cc_final: 0.9267 (tmm) REVERT: A 583 MET cc_start: 0.9524 (mmt) cc_final: 0.9053 (mmm) REVERT: A 628 HIS cc_start: 0.7472 (m170) cc_final: 0.7081 (m90) REVERT: A 643 ASN cc_start: 0.9525 (t0) cc_final: 0.9260 (t0) REVERT: A 650 LEU cc_start: 0.9389 (mm) cc_final: 0.8895 (pp) REVERT: A 657 MET cc_start: 0.9190 (mmp) cc_final: 0.8591 (tmm) REVERT: A 668 ASP cc_start: 0.8446 (m-30) cc_final: 0.7838 (m-30) REVERT: A 672 GLU cc_start: 0.9259 (mm-30) cc_final: 0.8995 (mm-30) REVERT: A 781 ASP cc_start: 0.9681 (t70) cc_final: 0.9438 (t0) REVERT: B 158 CYS cc_start: 0.8618 (m) cc_final: 0.8182 (m) REVERT: B 160 LYS cc_start: 0.9370 (mmtt) cc_final: 0.8693 (mmtp) REVERT: B 188 MET cc_start: 0.9495 (ttp) cc_final: 0.9144 (mmm) REVERT: B 252 MET cc_start: 0.9394 (ttm) cc_final: 0.9126 (mmp) REVERT: B 309 VAL cc_start: 0.9832 (t) cc_final: 0.9566 (p) REVERT: B 437 MET cc_start: 0.9560 (ttt) cc_final: 0.9237 (tpp) REVERT: B 440 GLU cc_start: 0.9361 (mm-30) cc_final: 0.8606 (tp30) REVERT: B 464 MET cc_start: 0.9443 (ppp) cc_final: 0.9123 (ppp) REVERT: B 564 ASP cc_start: 0.8950 (m-30) cc_final: 0.8261 (t70) REVERT: B 568 PHE cc_start: 0.9191 (m-80) cc_final: 0.8702 (m-10) REVERT: B 569 MET cc_start: 0.9214 (ttm) cc_final: 0.8658 (mtp) REVERT: B 574 MET cc_start: 0.9622 (ttt) cc_final: 0.9257 (tmm) REVERT: B 583 MET cc_start: 0.9509 (mmt) cc_final: 0.9036 (mmm) REVERT: B 628 HIS cc_start: 0.7470 (m170) cc_final: 0.7077 (m90) REVERT: B 643 ASN cc_start: 0.9532 (t0) cc_final: 0.9276 (t0) REVERT: B 650 LEU cc_start: 0.9404 (mm) cc_final: 0.8928 (tt) REVERT: B 657 MET cc_start: 0.9213 (mmm) cc_final: 0.8769 (tmm) REVERT: B 668 ASP cc_start: 0.8447 (m-30) cc_final: 0.7836 (m-30) REVERT: B 672 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8963 (mm-30) REVERT: B 781 ASP cc_start: 0.9678 (t70) cc_final: 0.9438 (t0) REVERT: C 158 CYS cc_start: 0.8610 (m) cc_final: 0.8164 (m) REVERT: C 160 LYS cc_start: 0.9371 (mmtt) cc_final: 0.8690 (mmtp) REVERT: C 188 MET cc_start: 0.9498 (ttp) cc_final: 0.9144 (mmm) REVERT: C 252 MET cc_start: 0.9394 (ttm) cc_final: 0.9128 (mmp) REVERT: C 309 VAL cc_start: 0.9833 (t) cc_final: 0.9566 (p) REVERT: C 437 MET cc_start: 0.9562 (ttt) cc_final: 0.9240 (tpp) REVERT: C 440 GLU cc_start: 0.9363 (mm-30) cc_final: 0.8608 (tp30) REVERT: C 464 MET cc_start: 0.9446 (ppp) cc_final: 0.9123 (ppp) REVERT: C 564 ASP cc_start: 0.8998 (m-30) cc_final: 0.8221 (t70) REVERT: C 568 PHE cc_start: 0.9212 (m-80) cc_final: 0.8744 (m-80) REVERT: C 569 MET cc_start: 0.9188 (ttm) cc_final: 0.8648 (mtp) REVERT: C 574 MET cc_start: 0.9627 (ttt) cc_final: 0.9258 (tmm) REVERT: C 583 MET cc_start: 0.9512 (mmt) cc_final: 0.9043 (mmm) REVERT: C 628 HIS cc_start: 0.7482 (m170) cc_final: 0.7086 (m90) REVERT: C 643 ASN cc_start: 0.9535 (t0) cc_final: 0.9256 (t0) REVERT: C 650 LEU cc_start: 0.9394 (mm) cc_final: 0.8871 (pp) REVERT: C 657 MET cc_start: 0.9268 (mmm) cc_final: 0.8801 (tmm) REVERT: C 668 ASP cc_start: 0.8445 (m-30) cc_final: 0.7844 (m-30) REVERT: C 672 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8962 (mm-30) REVERT: C 781 ASP cc_start: 0.9681 (t70) cc_final: 0.9439 (t0) REVERT: D 158 CYS cc_start: 0.8655 (m) cc_final: 0.8251 (m) REVERT: D 160 LYS cc_start: 0.9239 (mmtt) cc_final: 0.8591 (mmtp) REVERT: D 188 MET cc_start: 0.9499 (ttp) cc_final: 0.9143 (mmm) REVERT: D 252 MET cc_start: 0.9392 (ttm) cc_final: 0.9127 (mmp) REVERT: D 309 VAL cc_start: 0.9833 (t) cc_final: 0.9566 (p) REVERT: D 437 MET cc_start: 0.9561 (ttt) cc_final: 0.9237 (tpp) REVERT: D 440 GLU cc_start: 0.9363 (mm-30) cc_final: 0.8609 (tp30) REVERT: D 464 MET cc_start: 0.9441 (ppp) cc_final: 0.9119 (ppp) REVERT: D 545 LEU cc_start: 0.9720 (tp) cc_final: 0.9497 (tp) REVERT: D 564 ASP cc_start: 0.8902 (m-30) cc_final: 0.8238 (t70) REVERT: D 568 PHE cc_start: 0.9244 (m-80) cc_final: 0.8860 (m-10) REVERT: D 569 MET cc_start: 0.9195 (ttm) cc_final: 0.8645 (mtp) REVERT: D 574 MET cc_start: 0.9626 (ttt) cc_final: 0.9261 (tmm) REVERT: D 583 MET cc_start: 0.9507 (mmt) cc_final: 0.9035 (mmm) REVERT: D 628 HIS cc_start: 0.7478 (m170) cc_final: 0.7083 (m90) REVERT: D 643 ASN cc_start: 0.9531 (t0) cc_final: 0.9269 (t0) REVERT: D 650 LEU cc_start: 0.9398 (mm) cc_final: 0.8956 (tt) REVERT: D 657 MET cc_start: 0.9253 (mmm) cc_final: 0.8772 (tmm) REVERT: D 781 ASP cc_start: 0.9680 (t70) cc_final: 0.9439 (t0) outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.1235 time to fit residues: 69.3156 Evaluate side-chains 283 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 195 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 231 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 143 optimal weight: 8.9990 chunk 180 optimal weight: 0.9980 chunk 213 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.052889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.042448 restraints weight = 124243.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.043822 restraints weight = 73413.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.044767 restraints weight = 50815.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.045506 restraints weight = 38967.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.046038 restraints weight = 31711.802| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21696 Z= 0.121 Angle : 0.617 10.939 29340 Z= 0.316 Chirality : 0.038 0.164 3340 Planarity : 0.004 0.047 3668 Dihedral : 4.053 19.467 2872 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.17), residues: 2632 helix: 2.22 (0.12), residues: 1996 sheet: None (None), residues: 0 loop : -2.95 (0.20), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 773 TYR 0.017 0.002 TYR C 662 PHE 0.033 0.001 PHE B 538 TRP 0.021 0.002 TRP D 681 HIS 0.009 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00257 (21696) covalent geometry : angle 0.61651 (29340) hydrogen bonds : bond 0.03823 ( 1428) hydrogen bonds : angle 3.77543 ( 4248) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 CYS cc_start: 0.8449 (m) cc_final: 0.8006 (m) REVERT: A 160 LYS cc_start: 0.9300 (mmtt) cc_final: 0.8626 (mmtp) REVERT: A 188 MET cc_start: 0.9433 (ttp) cc_final: 0.9140 (mmm) REVERT: A 252 MET cc_start: 0.9334 (ttm) cc_final: 0.8870 (mmp) REVERT: A 314 CYS cc_start: 0.9224 (t) cc_final: 0.8860 (t) REVERT: A 437 MET cc_start: 0.9467 (ttt) cc_final: 0.9199 (tpp) REVERT: A 440 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8636 (tp30) REVERT: A 464 MET cc_start: 0.9492 (ppp) cc_final: 0.9043 (ppp) REVERT: A 564 ASP cc_start: 0.8785 (m-30) cc_final: 0.8252 (t70) REVERT: A 568 PHE cc_start: 0.8894 (m-10) cc_final: 0.8598 (m-10) REVERT: A 574 MET cc_start: 0.9629 (ttt) cc_final: 0.9307 (tmm) REVERT: A 583 MET cc_start: 0.9352 (mmt) cc_final: 0.8851 (mmm) REVERT: A 628 HIS cc_start: 0.7153 (m170) cc_final: 0.6762 (m90) REVERT: A 643 ASN cc_start: 0.9489 (t0) cc_final: 0.9186 (t0) REVERT: A 650 LEU cc_start: 0.9357 (mm) cc_final: 0.8827 (tt) REVERT: A 654 LEU cc_start: 0.9484 (mp) cc_final: 0.9267 (mm) REVERT: A 657 MET cc_start: 0.9210 (mmp) cc_final: 0.8804 (ppp) REVERT: A 781 ASP cc_start: 0.9693 (t70) cc_final: 0.9431 (t0) REVERT: B 158 CYS cc_start: 0.8456 (m) cc_final: 0.8003 (m) REVERT: B 160 LYS cc_start: 0.9299 (mmtt) cc_final: 0.8627 (mmtp) REVERT: B 188 MET cc_start: 0.9431 (ttp) cc_final: 0.9138 (mmm) REVERT: B 252 MET cc_start: 0.9335 (ttm) cc_final: 0.8868 (mmp) REVERT: B 314 CYS cc_start: 0.9230 (t) cc_final: 0.8866 (t) REVERT: B 437 MET cc_start: 0.9468 (ttt) cc_final: 0.9201 (tpp) REVERT: B 440 GLU cc_start: 0.9314 (mm-30) cc_final: 0.8633 (tp30) REVERT: B 464 MET cc_start: 0.9502 (ppp) cc_final: 0.9051 (ppp) REVERT: B 564 ASP cc_start: 0.8847 (m-30) cc_final: 0.8120 (t70) REVERT: B 568 PHE cc_start: 0.9217 (m-80) cc_final: 0.8721 (m-10) REVERT: B 569 MET cc_start: 0.9167 (ttm) cc_final: 0.8565 (mtp) REVERT: B 574 MET cc_start: 0.9625 (ttt) cc_final: 0.9301 (tmm) REVERT: B 583 MET cc_start: 0.9349 (mmt) cc_final: 0.8849 (mmm) REVERT: B 628 HIS cc_start: 0.7163 (m170) cc_final: 0.6767 (m90) REVERT: B 643 ASN cc_start: 0.9495 (t0) cc_final: 0.9196 (t0) REVERT: B 650 LEU cc_start: 0.9324 (mm) cc_final: 0.8789 (tt) REVERT: B 657 MET cc_start: 0.9284 (mmm) cc_final: 0.8801 (tmm) REVERT: B 781 ASP cc_start: 0.9689 (t70) cc_final: 0.9429 (t0) REVERT: C 158 CYS cc_start: 0.8451 (m) cc_final: 0.8005 (m) REVERT: C 160 LYS cc_start: 0.9299 (mmtt) cc_final: 0.8624 (mmtp) REVERT: C 188 MET cc_start: 0.9439 (ttp) cc_final: 0.9142 (mmm) REVERT: C 252 MET cc_start: 0.9334 (ttm) cc_final: 0.8870 (mmp) REVERT: C 314 CYS cc_start: 0.9229 (t) cc_final: 0.8865 (t) REVERT: C 437 MET cc_start: 0.9471 (ttt) cc_final: 0.9204 (tpp) REVERT: C 440 GLU cc_start: 0.9319 (mm-30) cc_final: 0.8642 (tp30) REVERT: C 464 MET cc_start: 0.9499 (ppp) cc_final: 0.9048 (ppp) REVERT: C 564 ASP cc_start: 0.8980 (m-30) cc_final: 0.8368 (t70) REVERT: C 569 MET cc_start: 0.9111 (ttm) cc_final: 0.8560 (mtp) REVERT: C 574 MET cc_start: 0.9635 (ttt) cc_final: 0.9302 (tmm) REVERT: C 583 MET cc_start: 0.9342 (mmt) cc_final: 0.8777 (mmm) REVERT: C 628 HIS cc_start: 0.7160 (m170) cc_final: 0.6767 (m90) REVERT: C 643 ASN cc_start: 0.9496 (t0) cc_final: 0.9198 (t0) REVERT: C 650 LEU cc_start: 0.9316 (mm) cc_final: 0.8683 (tt) REVERT: C 657 MET cc_start: 0.9231 (mmm) cc_final: 0.9018 (mmm) REVERT: C 781 ASP cc_start: 0.9688 (t70) cc_final: 0.9425 (t0) REVERT: D 158 CYS cc_start: 0.8540 (m) cc_final: 0.8333 (m) REVERT: D 160 LYS cc_start: 0.9336 (mmtt) cc_final: 0.8896 (mmtp) REVERT: D 188 MET cc_start: 0.9440 (ttp) cc_final: 0.9140 (mmm) REVERT: D 252 MET cc_start: 0.9333 (ttm) cc_final: 0.8869 (mmp) REVERT: D 314 CYS cc_start: 0.9222 (t) cc_final: 0.8856 (t) REVERT: D 437 MET cc_start: 0.9469 (ttt) cc_final: 0.9200 (tpp) REVERT: D 440 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8634 (tp30) REVERT: D 464 MET cc_start: 0.9495 (ppp) cc_final: 0.9047 (ppp) REVERT: D 564 ASP cc_start: 0.8874 (m-30) cc_final: 0.8121 (t70) REVERT: D 568 PHE cc_start: 0.9220 (m-80) cc_final: 0.8751 (m-10) REVERT: D 569 MET cc_start: 0.9094 (ttm) cc_final: 0.8475 (mtp) REVERT: D 574 MET cc_start: 0.9628 (ttt) cc_final: 0.9306 (tmm) REVERT: D 583 MET cc_start: 0.9350 (mmt) cc_final: 0.8850 (mmm) REVERT: D 628 HIS cc_start: 0.7154 (m170) cc_final: 0.6762 (m90) REVERT: D 643 ASN cc_start: 0.9497 (t0) cc_final: 0.9194 (t0) REVERT: D 650 LEU cc_start: 0.9317 (mm) cc_final: 0.8775 (tt) REVERT: D 657 MET cc_start: 0.9290 (mmm) cc_final: 0.8816 (tmm) REVERT: D 781 ASP cc_start: 0.9698 (t70) cc_final: 0.9432 (t0) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.1270 time to fit residues: 76.1436 Evaluate side-chains 297 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 70 optimal weight: 0.6980 chunk 196 optimal weight: 0.7980 chunk 22 optimal weight: 0.0010 chunk 18 optimal weight: 0.6980 chunk 71 optimal weight: 10.0000 chunk 85 optimal weight: 0.2980 chunk 20 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 175 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 797 GLN ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.053432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.043074 restraints weight = 119998.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.044454 restraints weight = 70615.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.045453 restraints weight = 48544.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.046196 restraints weight = 36697.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.046751 restraints weight = 29582.508| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.6105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21696 Z= 0.118 Angle : 0.615 7.723 29340 Z= 0.317 Chirality : 0.038 0.159 3340 Planarity : 0.004 0.049 3668 Dihedral : 3.887 18.085 2872 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.67 (0.17), residues: 2632 helix: 2.24 (0.12), residues: 1992 sheet: None (None), residues: 0 loop : -2.81 (0.20), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 104 TYR 0.018 0.001 TYR B 662 PHE 0.013 0.001 PHE C 579 TRP 0.018 0.001 TRP D 322 HIS 0.008 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00238 (21696) covalent geometry : angle 0.61504 (29340) hydrogen bonds : bond 0.03725 ( 1428) hydrogen bonds : angle 3.78619 ( 4248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2940.31 seconds wall clock time: 52 minutes 0.64 seconds (3120.64 seconds total)