Starting phenix.real_space_refine on Thu Nov 20 02:53:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ack_9594/11_2025/6ack_9594.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ack_9594/11_2025/6ack_9594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ack_9594/11_2025/6ack_9594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ack_9594/11_2025/6ack_9594.map" model { file = "/net/cci-nas-00/data/ceres_data/6ack_9594/11_2025/6ack_9594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ack_9594/11_2025/6ack_9594.cif" } resolution = 4.5 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= -0.001 sd= 0.908 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 164 5.16 5 C 18987 2.51 5 N 4918 2.21 5 O 5646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29715 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8302 Classifications: {'peptide': 1065} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1013} Chain breaks: 3 Chain: "B" Number of atoms: 8302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8302 Classifications: {'peptide': 1065} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1013} Chain breaks: 3 Chain: "C" Number of atoms: 8241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8241 Classifications: {'peptide': 1057} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1006} Chain breaks: 5 Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Time building chain proxies: 6.72, per 1000 atoms: 0.23 Number of scatterers: 29715 At special positions: 0 Unit cell: (145.2, 205.92, 196.68, 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 164 16.00 O 5646 8.00 N 4918 7.00 C 18987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.02 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.02 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.02 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.04 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.02 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.01 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.02 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.02 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.02 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.01 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.02 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.01 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.02 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.01 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.04 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.02 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.02 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.04 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.04 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.01 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7102 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 45 sheets defined 28.0% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 371 through 377 removed outlier: 4.319A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A 376 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 377 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 604 through 612 removed outlier: 3.539A pdb=" N THR A 608 " --> pdb=" O THR A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 737 removed outlier: 4.370A pdb=" N ASN A 733 " --> pdb=" O THR A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 765 Processing helix chain 'A' and resid 798 through 808 Processing helix chain 'A' and resid 848 through 865 Processing helix chain 'A' and resid 880 through 890 Processing helix chain 'A' and resid 895 through 900 Processing helix chain 'A' and resid 901 through 922 removed outlier: 4.156A pdb=" N ALA A 912 " --> pdb=" O GLN A 908 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 950 removed outlier: 3.691A pdb=" N GLN A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 966 removed outlier: 3.813A pdb=" N ARG A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1017 removed outlier: 4.211A pdb=" N VAL A1015 " --> pdb=" O MET A1011 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY A1017 " --> pdb=" O GLU A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 373 through 377 removed outlier: 3.693A pdb=" N ASP B 376 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU B 377 " --> pdb=" O LEU B 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 373 through 377' Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 488 through 492 removed outlier: 3.623A pdb=" N GLN B 492 " --> pdb=" O ILE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 612 removed outlier: 3.761A pdb=" N THR B 608 " --> pdb=" O THR B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 737 Processing helix chain 'B' and resid 740 through 765 Processing helix chain 'B' and resid 798 through 807 Processing helix chain 'B' and resid 848 through 865 Processing helix chain 'B' and resid 880 through 890 removed outlier: 3.694A pdb=" N PHE B 888 " --> pdb=" O MET B 884 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 889 " --> pdb=" O ALA B 885 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 890 " --> pdb=" O TYR B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 900 removed outlier: 3.579A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU B 900 " --> pdb=" O ASN B 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 895 through 900' Processing helix chain 'B' and resid 901 through 922 removed outlier: 3.633A pdb=" N ALA B 912 " --> pdb=" O GLN B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 950 removed outlier: 4.213A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 965 removed outlier: 4.105A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG B 965 " --> pdb=" O ASP B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 1014 Processing helix chain 'C' and resid 281 through 288 Processing helix chain 'C' and resid 392 through 397 removed outlier: 4.391A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 604 through 612 removed outlier: 3.903A pdb=" N THR C 608 " --> pdb=" O THR C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 737 Processing helix chain 'C' and resid 740 through 764 Processing helix chain 'C' and resid 798 through 808 Processing helix chain 'C' and resid 848 through 865 Processing helix chain 'C' and resid 880 through 888 removed outlier: 3.637A pdb=" N MET C 884 " --> pdb=" O PHE C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 901 removed outlier: 3.766A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C 900 " --> pdb=" O ASN C 896 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 901 " --> pdb=" O VAL C 897 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 895 through 901' Processing helix chain 'C' and resid 901 through 922 removed outlier: 3.781A pdb=" N THR C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 950 removed outlier: 4.262A pdb=" N GLN C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 965 Processing helix chain 'C' and resid 968 through 1017 removed outlier: 3.561A pdb=" N GLU C 972 " --> pdb=" O LYS C 968 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL C1015 " --> pdb=" O MET C1011 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.661A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN D 53 " --> pdb=" O ASN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 4.153A pdb=" N ASN D 63 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.695A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER D 128 " --> pdb=" O SER D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 4.076A pdb=" N ALA D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.632A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 4.241A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 208 removed outlier: 3.638A pdb=" N ASP D 206 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR D 207 " --> pdb=" O TRP D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 252 removed outlier: 4.418A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 removed outlier: 4.003A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 400 through 412 removed outlier: 4.065A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 4.217A pdb=" N GLY D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 466 removed outlier: 4.088A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU D 450 " --> pdb=" O ILE D 446 " (cutoff:3.500A) Proline residue: D 451 - end of helix Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 503 through 508 removed outlier: 3.765A pdb=" N SER D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN D 508 " --> pdb=" O PHE D 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 503 through 508' Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.057A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.665A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 4.074A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 removed outlier: 4.034A pdb=" N SER D 563 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU D 564 " --> pdb=" O GLY D 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 560 through 564' Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.867A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 599 Proline residue: D 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35 removed outlier: 3.962A pdb=" N SER A 64 " --> pdb=" O SER A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.988A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 82 removed outlier: 4.137A pdb=" N SER A 111 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 130 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL A 123 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASN A 129 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N CYS A 159 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 222 removed outlier: 7.034A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A 186 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA A 90 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 138 through 140 Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 301 Processing sheet with id=AA7, first strand: chain 'A' and resid 305 through 306 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 312 removed outlier: 7.007A pdb=" N GLY A 311 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ASN A 528 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY A 534 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.612A pdb=" N CYS A 419 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AB2, first strand: chain 'A' and resid 628 through 629 removed outlier: 3.772A pdb=" N VAL A 628 " --> pdb=" O LEU A 636 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 640 through 641 removed outlier: 5.705A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A 659 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE A 650 " --> pdb=" O ALA A 658 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 700 through 701 Processing sheet with id=AB5, first strand: chain 'A' and resid 704 through 710 Processing sheet with id=AB6, first strand: chain 'A' and resid 704 through 710 removed outlier: 3.534A pdb=" N GLY A1041 " --> pdb=" O ALA A1038 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB8, first strand: chain 'A' and resid 1063 through 1064 Processing sheet with id=AB9, first strand: chain 'A' and resid 1078 through 1079 Processing sheet with id=AC1, first strand: chain 'B' and resid 32 through 34 removed outlier: 8.039A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU B 184 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY B 199 " --> pdb=" O GLU B 184 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE B 219 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 53 through 59 removed outlier: 4.192A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.861A pdb=" N ILE B 81 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 139 through 141 removed outlier: 6.594A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 298 through 304 removed outlier: 3.738A pdb=" N THR B 585 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 637 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 312 removed outlier: 6.516A pdb=" N GLY B 311 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ASN B 528 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY B 534 " --> pdb=" O PHE B 527 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.914A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 439 through 440 Processing sheet with id=AC9, first strand: chain 'B' and resid 650 through 652 removed outlier: 3.996A pdb=" N ILE B 650 " --> pdb=" O ALA B 658 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 700 through 701 removed outlier: 3.505A pdb=" N VAL B1050 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 705 through 709 Processing sheet with id=AD3, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AD4, first strand: chain 'C' and resid 31 through 34 removed outlier: 7.916A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 90 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 31 through 34 removed outlier: 7.916A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 90 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 51 through 56 removed outlier: 4.118A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 81 through 82 removed outlier: 5.544A pdb=" N VAL C 123 " --> pdb=" O SER C 165 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 298 through 306 removed outlier: 5.600A pdb=" N ILE C 299 " --> pdb=" O THR C 585 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N THR C 585 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLN C 301 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL C 583 " --> pdb=" O GLN C 301 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER C 303 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER C 582 " --> pdb=" O LEU C 597 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 313 Processing sheet with id=AE1, first strand: chain 'C' and resid 341 through 345 removed outlier: 6.424A pdb=" N ASN C 424 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N PHE C 361 " --> pdb=" O ASN C 424 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE3, first strand: chain 'C' and resid 538 through 540 Processing sheet with id=AE4, first strand: chain 'C' and resid 704 through 710 removed outlier: 3.691A pdb=" N ALA C1038 " --> pdb=" O GLY C1041 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 716 through 717 Processing sheet with id=AE6, first strand: chain 'C' and resid 1078 through 1079 Processing sheet with id=AE7, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AE8, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.976A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 347 through 350 1088 hydrogen bonds defined for protein. 3027 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: 6.90 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.26: 4899 1.26 - 1.40: 7920 1.40 - 1.55: 17381 1.55 - 1.70: 9 1.70 - 1.85: 231 Bond restraints: 30440 Sorted by residual: bond pdb=" C ALA C 676 " pdb=" O ALA C 676 " ideal model delta sigma weight residual 1.235 1.108 0.127 1.26e-02 6.30e+03 1.02e+02 bond pdb=" CA TYR C 677 " pdb=" C TYR C 677 " ideal model delta sigma weight residual 1.523 1.398 0.126 1.34e-02 5.57e+03 8.78e+01 bond pdb=" CA SER C 645 " pdb=" C SER C 645 " ideal model delta sigma weight residual 1.523 1.413 0.110 1.34e-02 5.57e+03 6.74e+01 bond pdb=" CA TYR C 677 " pdb=" CB TYR C 677 " ideal model delta sigma weight residual 1.530 1.419 0.111 1.69e-02 3.50e+03 4.34e+01 bond pdb=" N SER C 645 " pdb=" CA SER C 645 " ideal model delta sigma weight residual 1.457 1.374 0.083 1.29e-02 6.01e+03 4.18e+01 ... (remaining 30435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 39338 2.75 - 5.49: 1769 5.49 - 8.24: 235 8.24 - 10.99: 63 10.99 - 13.73: 11 Bond angle restraints: 41416 Sorted by residual: angle pdb=" N ILE A1112 " pdb=" CA ILE A1112 " pdb=" C ILE A1112 " ideal model delta sigma weight residual 113.20 102.43 10.77 9.60e-01 1.09e+00 1.26e+02 angle pdb=" C TYR C 646 " pdb=" N GLU C 647 " pdb=" CA GLU C 647 " ideal model delta sigma weight residual 122.79 109.06 13.73 1.63e+00 3.76e-01 7.10e+01 angle pdb=" O THR C 644 " pdb=" C THR C 644 " pdb=" N SER C 645 " ideal model delta sigma weight residual 122.91 132.25 -9.34 1.19e+00 7.06e-01 6.16e+01 angle pdb=" CA THR C 644 " pdb=" C THR C 644 " pdb=" N SER C 645 " ideal model delta sigma weight residual 114.98 104.49 10.49 1.34e+00 5.57e-01 6.13e+01 angle pdb=" N ILE A 891 " pdb=" CA ILE A 891 " pdb=" C ILE A 891 " ideal model delta sigma weight residual 112.90 106.04 6.86 9.60e-01 1.09e+00 5.11e+01 ... (remaining 41411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 16900 17.50 - 34.99: 987 34.99 - 52.49: 151 52.49 - 69.99: 28 69.99 - 87.48: 12 Dihedral angle restraints: 18078 sinusoidal: 7038 harmonic: 11040 Sorted by residual: dihedral pdb=" CA GLU B1074 " pdb=" C GLU B1074 " pdb=" N GLY B1075 " pdb=" CA GLY B1075 " ideal model delta harmonic sigma weight residual 180.00 -117.27 -62.73 0 5.00e+00 4.00e-02 1.57e+02 dihedral pdb=" CA GLU C1074 " pdb=" C GLU C1074 " pdb=" N GLY C1075 " pdb=" CA GLY C1075 " ideal model delta harmonic sigma weight residual -180.00 -117.49 -62.51 0 5.00e+00 4.00e-02 1.56e+02 dihedral pdb=" CA GLY B 726 " pdb=" C GLY B 726 " pdb=" N ASP B 727 " pdb=" CA ASP B 727 " ideal model delta harmonic sigma weight residual 180.00 125.46 54.54 0 5.00e+00 4.00e-02 1.19e+02 ... (remaining 18075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 4383 0.135 - 0.269: 238 0.269 - 0.404: 5 0.404 - 0.538: 0 0.538 - 0.673: 2 Chirality restraints: 4628 Sorted by residual: chirality pdb=" CA TYR C 646 " pdb=" N TYR C 646 " pdb=" C TYR C 646 " pdb=" CB TYR C 646 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CA TYR C 677 " pdb=" N TYR C 677 " pdb=" C TYR C 677 " pdb=" CB TYR C 677 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.07e+00 chirality pdb=" CG LEU C 846 " pdb=" CB LEU C 846 " pdb=" CD1 LEU C 846 " pdb=" CD2 LEU C 846 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.65e+00 ... (remaining 4625 not shown) Planarity restraints: 5366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 677 " -0.018 2.00e-02 2.50e+03 3.06e-02 1.87e+01 pdb=" CG TYR C 677 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR C 677 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR C 677 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR C 677 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 677 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR C 677 " -0.028 2.00e-02 2.50e+03 pdb=" OH TYR C 677 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 644 " -0.018 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C THR C 644 " 0.070 2.00e-02 2.50e+03 pdb=" O THR C 644 " -0.029 2.00e-02 2.50e+03 pdb=" N SER C 645 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 585 " -0.058 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO B 586 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO B 586 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 586 " -0.047 5.00e-02 4.00e+02 ... (remaining 5363 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.21: 13 2.21 - 2.88: 11783 2.88 - 3.55: 43295 3.55 - 4.23: 74277 4.23 - 4.90: 119315 Nonbonded interactions: 248683 Sorted by model distance: nonbonded pdb=" O SER C 659 " pdb=" CG2 ILE C 674 " model vdw 1.533 3.460 nonbonded pdb=" O TYR C 646 " pdb=" OG SER C 680 " model vdw 1.617 3.040 nonbonded pdb=" CB TYR C 646 " pdb=" CE2 TYR C 677 " model vdw 2.022 3.740 nonbonded pdb=" O GLY C 655 " pdb=" O THR C 678 " model vdw 2.083 3.040 nonbonded pdb=" O THR C 644 " pdb=" O SER C 645 " model vdw 2.115 3.040 ... (remaining 248678 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 318 or resid 323 through 512 or resid 517 throu \ gh 1119)) selection = (chain 'B' and (resid 18 through 318 or resid 323 through 512 or resid 517 throu \ gh 1119)) selection = chain 'C' } 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 28.660 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 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 : 0.010 0.147 30482 Z= 0.513 Angle : 1.352 13.734 41500 Z= 0.765 Chirality : 0.068 0.673 4628 Planarity : 0.009 0.087 5366 Dihedral : 11.386 80.555 10850 Min Nonbonded Distance : 1.533 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.45 % Allowed : 16.09 % Favored : 83.46 % Rotamer: Outliers : 0.79 % Allowed : 3.07 % Favored : 96.13 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 2.23 % Twisted General : 1.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.81 (0.11), residues: 3754 helix: -2.49 (0.12), residues: 978 sheet: -2.40 (0.21), residues: 498 loop : -3.93 (0.10), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG C1089 TYR 0.063 0.005 TYR C 677 PHE 0.049 0.005 PHE A 909 TRP 0.034 0.004 TRP B 868 HIS 0.017 0.004 HIS C 641 Details of bonding type rmsd covalent geometry : bond 0.01033 (30440) covalent geometry : angle 1.34849 (41416) SS BOND : bond 0.00937 ( 42) SS BOND : angle 2.57710 ( 84) hydrogen bonds : bond 0.16443 ( 1062) hydrogen bonds : angle 8.98944 ( 3027) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 488 time to evaluate : 1.210 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.5080 (ttp) cc_final: 0.4865 (ppp) REVERT: A 361 PHE cc_start: 0.7233 (m-10) cc_final: 0.5981 (p90) REVERT: A 416 PHE cc_start: 0.8486 (m-10) cc_final: 0.8161 (m-10) REVERT: A 423 TRP cc_start: 0.5596 (p90) cc_final: 0.4979 (p90) REVERT: A 762 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7518 (mt-10) REVERT: A 766 GLN cc_start: 0.7676 (mt0) cc_final: 0.6972 (tm-30) REVERT: A 882 MET cc_start: 0.5574 (mmm) cc_final: 0.5017 (mtp) REVERT: A 899 TYR cc_start: 0.6946 (m-80) cc_final: 0.6036 (m-80) REVERT: A 1014 CYS cc_start: 0.6023 (m) cc_final: 0.4994 (m) REVERT: A 1092 PHE cc_start: 0.8093 (t80) cc_final: 0.7782 (t80) REVERT: B 85 ASP cc_start: 0.8928 (m-30) cc_final: 0.8665 (t0) REVERT: B 151 MET cc_start: 0.4012 (ptm) cc_final: 0.3762 (ptp) REVERT: B 161 PHE cc_start: 0.7928 (t80) cc_final: 0.7652 (t80) REVERT: B 220 PHE cc_start: 0.8603 (m-10) cc_final: 0.8312 (m-80) REVERT: B 296 ASP cc_start: 0.7811 (m-30) cc_final: 0.7220 (t70) REVERT: B 333 LYS cc_start: 0.8113 (tttt) cc_final: 0.7659 (tptt) REVERT: B 381 ASN cc_start: 0.8356 (m-40) cc_final: 0.7946 (t0) REVERT: B 415 ASP cc_start: 0.8019 (m-30) cc_final: 0.7628 (t0) REVERT: B 476 TRP cc_start: 0.8670 (m-90) cc_final: 0.8448 (m100) REVERT: B 747 ARG cc_start: 0.8641 (mtt180) cc_final: 0.7764 (mtp180) REVERT: B 1088 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8281 (pt0) REVERT: C 220 PHE cc_start: 0.8377 (m-10) cc_final: 0.8153 (m-10) REVERT: C 476 TRP cc_start: 0.7362 (m100) cc_final: 0.6857 (p90) REVERT: C 677 TYR cc_start: 0.3905 (OUTLIER) cc_final: 0.2766 (p90) REVERT: C 709 MET cc_start: 0.8331 (mmm) cc_final: 0.7859 (mmm) REVERT: C 752 ILE cc_start: 0.9384 (mt) cc_final: 0.8750 (mm) REVERT: C 761 ARG cc_start: 0.7895 (mmm160) cc_final: 0.7449 (tpt170) REVERT: C 763 VAL cc_start: 0.8512 (t) cc_final: 0.8250 (m) REVERT: C 770 MET cc_start: 0.7554 (mtp) cc_final: 0.7328 (mtp) REVERT: C 911 LYS cc_start: 0.9306 (mttt) cc_final: 0.8682 (mtmt) REVERT: C 1000 ILE cc_start: 0.9007 (tp) cc_final: 0.8784 (tt) REVERT: C 1085 PHE cc_start: 0.7401 (m-80) cc_final: 0.6867 (m-80) REVERT: D 82 MET cc_start: 0.4313 (ttt) cc_final: 0.3964 (mpp) REVERT: D 89 GLN cc_start: 0.6204 (tp-100) cc_final: 0.5510 (pt0) REVERT: D 121 ASN cc_start: 0.2882 (m-40) cc_final: 0.2585 (t0) REVERT: D 156 LEU cc_start: 0.7254 (mp) cc_final: 0.7047 (tp) REVERT: D 323 MET cc_start: 0.2920 (mmp) cc_final: -0.1391 (mtp) REVERT: D 570 LEU cc_start: -0.5285 (OUTLIER) cc_final: -0.5842 (tp) outliers start: 26 outliers final: 10 residues processed: 513 average time/residue: 0.2132 time to fit residues: 171.1976 Evaluate side-chains 293 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 281 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.0870 overall best weight: 1.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 155 ASN A 181 HIS A 505 ASN A 627 ASN A 632 GLN A 691 ASN A 756 GLN A 759 ASN A 769 GLN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 ASN A 939 GLN A 947 GLN A1040 HIS B 70 HIS B 147 GLN B 155 ASN B 214 ASN B 445 HIS B 627 ASN B 692 ASN B 733 ASN B 737 GLN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 GLN B 877 GLN ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1018 GLN ** B1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 HIS C 445 HIS C 473 ASN C 589 ASN ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 ASN C 699 ASN C 766 GLN ** C 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 838 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1018 GLN C1088 GLN C1101 ASN D 250 ASN D 380 GLN D 417 HIS D 522 GLN D 526 GLN D 572 ASN ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.094498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.070797 restraints weight = 178829.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.070433 restraints weight = 123562.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.070684 restraints weight = 102874.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.070971 restraints weight = 91536.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.071241 restraints weight = 79066.638| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 30482 Z= 0.163 Angle : 0.762 10.429 41500 Z= 0.405 Chirality : 0.048 0.332 4628 Planarity : 0.006 0.058 5366 Dihedral : 7.820 61.257 4064 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.51 % Favored : 88.20 % Rotamer: Outliers : 0.12 % Allowed : 3.14 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.95 (0.12), residues: 3754 helix: -1.33 (0.14), residues: 994 sheet: -2.12 (0.22), residues: 481 loop : -3.55 (0.11), residues: 2279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 563 TYR 0.030 0.002 TYR C 855 PHE 0.025 0.002 PHE C1077 TRP 0.021 0.002 TRP A 868 HIS 0.007 0.001 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00339 (30440) covalent geometry : angle 0.75773 (41416) SS BOND : bond 0.00498 ( 42) SS BOND : angle 1.86866 ( 84) hydrogen bonds : bond 0.05363 ( 1062) hydrogen bonds : angle 7.09861 ( 3027) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 439 time to evaluate : 1.134 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: symmetry clash REVERT: A 361 PHE cc_start: 0.7128 (m-10) cc_final: 0.5909 (p90) REVERT: A 451 PHE cc_start: 0.8165 (m-10) cc_final: 0.7965 (m-10) REVERT: A 723 TYR cc_start: 0.6667 (t80) cc_final: 0.6378 (t80) REVERT: A 736 LEU cc_start: 0.8962 (mt) cc_final: 0.8412 (pp) REVERT: A 746 ASN cc_start: 0.8783 (m-40) cc_final: 0.8308 (m-40) REVERT: A 762 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8344 (mt-10) REVERT: A 763 VAL cc_start: 0.9286 (t) cc_final: 0.9018 (t) REVERT: A 766 GLN cc_start: 0.7568 (mt0) cc_final: 0.6899 (tm-30) REVERT: A 932 ASP cc_start: 0.8216 (m-30) cc_final: 0.7912 (m-30) REVERT: A 947 GLN cc_start: 0.9268 (mm110) cc_final: 0.8948 (mm-40) REVERT: A 969 VAL cc_start: 0.8486 (m) cc_final: 0.8269 (p) REVERT: A 1013 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6650 (mm-30) REVERT: A 1032 MET cc_start: 0.8666 (tpp) cc_final: 0.7547 (tpt) REVERT: A 1092 PHE cc_start: 0.8064 (t80) cc_final: 0.7647 (t80) REVERT: B 51 THR cc_start: 0.6763 (t) cc_final: 0.6091 (p) REVERT: B 151 MET cc_start: 0.4209 (ptm) cc_final: 0.3298 (ptp) REVERT: B 161 PHE cc_start: 0.7856 (t80) cc_final: 0.7533 (t80) REVERT: B 166 ASP cc_start: 0.8774 (m-30) cc_final: 0.8564 (p0) REVERT: B 220 PHE cc_start: 0.8663 (m-10) cc_final: 0.7884 (m-10) REVERT: B 261 THR cc_start: 0.9404 (m) cc_final: 0.9174 (p) REVERT: B 296 ASP cc_start: 0.7208 (m-30) cc_final: 0.6966 (t70) REVERT: B 301 GLN cc_start: 0.8426 (tp40) cc_final: 0.7792 (tp40) REVERT: B 333 LYS cc_start: 0.7978 (tttt) cc_final: 0.7474 (tptt) REVERT: B 395 ARG cc_start: 0.8407 (mtm-85) cc_final: 0.8047 (ptp90) REVERT: B 415 ASP cc_start: 0.8105 (m-30) cc_final: 0.7599 (t0) REVERT: B 558 PHE cc_start: 0.7110 (m-10) cc_final: 0.6601 (m-10) REVERT: B 679 MET cc_start: 0.8026 (ttt) cc_final: 0.7717 (tmm) REVERT: B 752 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.8882 (mp) REVERT: B 768 LYS cc_start: 0.7833 (mmpt) cc_final: 0.7220 (mmmt) REVERT: B 932 ASP cc_start: 0.8076 (t0) cc_final: 0.6717 (t0) REVERT: B 936 GLN cc_start: 0.8519 (mt0) cc_final: 0.8194 (mt0) REVERT: B 1091 PHE cc_start: 0.7252 (t80) cc_final: 0.6933 (t80) REVERT: C 103 PHE cc_start: 0.7714 (m-10) cc_final: 0.7414 (m-80) REVERT: C 220 PHE cc_start: 0.8507 (m-10) cc_final: 0.8083 (m-10) REVERT: C 476 TRP cc_start: 0.7602 (m100) cc_final: 0.7170 (p90) REVERT: C 559 THR cc_start: 0.7491 (m) cc_final: 0.7093 (p) REVERT: C 709 MET cc_start: 0.8772 (mmm) cc_final: 0.7738 (mpp) REVERT: C 711 VAL cc_start: 0.7842 (m) cc_final: 0.7440 (p) REVERT: C 745 LEU cc_start: 0.8784 (mt) cc_final: 0.8097 (mt) REVERT: C 760 THR cc_start: 0.9363 (m) cc_final: 0.8850 (p) REVERT: C 763 VAL cc_start: 0.8243 (t) cc_final: 0.7875 (t) REVERT: C 770 MET cc_start: 0.7192 (mtp) cc_final: 0.6821 (mtp) REVERT: C 884 MET cc_start: 0.7894 (mmp) cc_final: 0.7482 (mmp) REVERT: C 946 LYS cc_start: 0.9356 (mtmm) cc_final: 0.8966 (mtmm) REVERT: C 1000 ILE cc_start: 0.8908 (tp) cc_final: 0.8634 (tt) REVERT: C 1059 THR cc_start: 0.5725 (t) cc_final: 0.5516 (t) REVERT: C 1085 PHE cc_start: 0.7302 (m-80) cc_final: 0.7032 (m-80) REVERT: C 1092 PHE cc_start: 0.8391 (t80) cc_final: 0.8181 (t80) REVERT: D 82 MET cc_start: 0.4078 (ttt) cc_final: 0.3623 (mpp) REVERT: D 89 GLN cc_start: 0.6507 (tp-100) cc_final: 0.5854 (pt0) REVERT: D 121 ASN cc_start: 0.2870 (m-40) cc_final: 0.2667 (t0) REVERT: D 156 LEU cc_start: 0.7244 (mp) cc_final: 0.7043 (tp) REVERT: D 323 MET cc_start: 0.2534 (mmp) cc_final: -0.1334 (ttm) REVERT: D 474 MET cc_start: 0.0932 (mmp) cc_final: 0.0586 (mmp) REVERT: D 480 MET cc_start: 0.2032 (ttt) cc_final: 0.1750 (ttp) outliers start: 4 outliers final: 0 residues processed: 441 average time/residue: 0.1966 time to fit residues: 140.1242 Evaluate side-chains 299 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 155 optimal weight: 9.9990 chunk 335 optimal weight: 50.0000 chunk 157 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 chunk 272 optimal weight: 0.0050 chunk 118 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 65 optimal weight: 8.9990 chunk 303 optimal weight: 0.7980 overall best weight: 1.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 HIS A 627 ASN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 GLN A 992 GLN B 70 HIS B 214 ASN ** B 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 GLN ** B 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 GLN B1101 ASN C 589 ASN ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 838 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 117 ASN D 330 ASN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.093936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.069684 restraints weight = 180298.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.069642 restraints weight = 139103.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.069737 restraints weight = 102489.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.070082 restraints weight = 89925.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.070380 restraints weight = 82997.524| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 30482 Z= 0.164 Angle : 0.713 11.585 41500 Z= 0.379 Chirality : 0.047 0.223 4628 Planarity : 0.005 0.062 5366 Dihedral : 7.148 58.112 4064 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.36 % Favored : 87.40 % Rotamer: Outliers : 0.09 % Allowed : 3.01 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.12), residues: 3754 helix: -0.80 (0.15), residues: 992 sheet: -2.03 (0.21), residues: 563 loop : -3.38 (0.11), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 747 TYR 0.029 0.002 TYR C 484 PHE 0.022 0.002 PHE A 888 TRP 0.013 0.001 TRP A 868 HIS 0.008 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00336 (30440) covalent geometry : angle 0.70882 (41416) SS BOND : bond 0.00509 ( 42) SS BOND : angle 1.92936 ( 84) hydrogen bonds : bond 0.04994 ( 1062) hydrogen bonds : angle 6.66232 ( 3027) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 387 time to evaluate : 1.457 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: A 51 THR cc_start: 0.8601 (t) cc_final: 0.8308 (m) REVERT: A 361 PHE cc_start: 0.7212 (m-10) cc_final: 0.5895 (p90) REVERT: A 416 PHE cc_start: 0.7867 (m-80) cc_final: 0.7604 (m-80) REVERT: A 704 ILE cc_start: 0.8292 (mt) cc_final: 0.7982 (mt) REVERT: A 746 ASN cc_start: 0.8601 (m-40) cc_final: 0.7974 (m-40) REVERT: A 939 GLN cc_start: 0.8447 (tp40) cc_final: 0.8102 (tp-100) REVERT: A 962 ILE cc_start: 0.9124 (pt) cc_final: 0.8833 (tp) REVERT: A 1013 GLU cc_start: 0.7313 (mm-30) cc_final: 0.5960 (tp30) REVERT: A 1032 MET cc_start: 0.8547 (tpp) cc_final: 0.7969 (tpp) REVERT: A 1092 PHE cc_start: 0.8071 (t80) cc_final: 0.7627 (t80) REVERT: B 51 THR cc_start: 0.6697 (t) cc_final: 0.6378 (p) REVERT: B 151 MET cc_start: 0.3604 (ptm) cc_final: 0.3242 (ptp) REVERT: B 161 PHE cc_start: 0.7869 (t80) cc_final: 0.7668 (t80) REVERT: B 220 PHE cc_start: 0.8471 (m-10) cc_final: 0.8022 (m-10) REVERT: B 261 THR cc_start: 0.9381 (m) cc_final: 0.9087 (p) REVERT: B 296 ASP cc_start: 0.7578 (m-30) cc_final: 0.7205 (t70) REVERT: B 301 GLN cc_start: 0.8310 (tp40) cc_final: 0.7743 (tp40) REVERT: B 415 ASP cc_start: 0.8167 (m-30) cc_final: 0.7570 (t0) REVERT: B 558 PHE cc_start: 0.6998 (m-10) cc_final: 0.6794 (m-80) REVERT: B 768 LYS cc_start: 0.7422 (mmpt) cc_final: 0.7152 (mmmt) REVERT: B 851 MET cc_start: 0.8659 (ptp) cc_final: 0.8022 (ptp) REVERT: B 932 ASP cc_start: 0.8190 (t0) cc_final: 0.6983 (t0) REVERT: B 936 GLN cc_start: 0.8420 (mt0) cc_final: 0.8177 (mt0) REVERT: B 1024 PHE cc_start: 0.5719 (t80) cc_final: 0.5336 (t80) REVERT: B 1101 ASN cc_start: 0.7241 (OUTLIER) cc_final: 0.6891 (m110) REVERT: C 37 MET cc_start: 0.7393 (mpp) cc_final: 0.7126 (mmt) REVERT: C 103 PHE cc_start: 0.7539 (m-10) cc_final: 0.7325 (m-80) REVERT: C 191 ASP cc_start: 0.6880 (m-30) cc_final: 0.6460 (p0) REVERT: C 476 TRP cc_start: 0.7584 (m100) cc_final: 0.7172 (p90) REVERT: C 549 GLN cc_start: 0.7997 (mt0) cc_final: 0.7549 (mt0) REVERT: C 558 PHE cc_start: 0.8694 (m-80) cc_final: 0.8387 (m-80) REVERT: C 559 THR cc_start: 0.7668 (m) cc_final: 0.7434 (p) REVERT: C 711 VAL cc_start: 0.8248 (m) cc_final: 0.7827 (p) REVERT: C 745 LEU cc_start: 0.8723 (mt) cc_final: 0.8137 (mt) REVERT: C 747 ARG cc_start: 0.8319 (ttp-110) cc_final: 0.8081 (ttp-110) REVERT: C 755 GLU cc_start: 0.9297 (pt0) cc_final: 0.9009 (pt0) REVERT: C 770 MET cc_start: 0.7115 (mtp) cc_final: 0.6716 (mtp) REVERT: C 946 LYS cc_start: 0.9333 (mtmm) cc_final: 0.8977 (mtmm) REVERT: C 1000 ILE cc_start: 0.8923 (tp) cc_final: 0.8619 (tt) REVERT: C 1023 ASP cc_start: 0.7041 (t70) cc_final: 0.6492 (t70) REVERT: C 1033 SER cc_start: 0.6840 (t) cc_final: 0.6145 (t) REVERT: C 1085 PHE cc_start: 0.7215 (m-80) cc_final: 0.6861 (m-80) REVERT: C 1092 PHE cc_start: 0.8333 (t80) cc_final: 0.8123 (t80) REVERT: D 82 MET cc_start: 0.4145 (ttt) cc_final: 0.3639 (mpp) REVERT: D 89 GLN cc_start: 0.6118 (tp-100) cc_final: 0.5430 (pt0) REVERT: D 323 MET cc_start: 0.2239 (mmp) cc_final: -0.1803 (ttm) REVERT: D 383 MET cc_start: 0.2476 (ptp) cc_final: 0.0412 (tmm) REVERT: D 474 MET cc_start: 0.0585 (mmp) cc_final: 0.0152 (mmp) REVERT: D 480 MET cc_start: 0.1994 (ttt) cc_final: 0.1675 (ttp) outliers start: 3 outliers final: 0 residues processed: 388 average time/residue: 0.1895 time to fit residues: 120.6297 Evaluate side-chains 283 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 114 optimal weight: 1.9990 chunk 304 optimal weight: 0.7980 chunk 263 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 chunk 244 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 214 optimal weight: 6.9990 chunk 365 optimal weight: 50.0000 chunk 113 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 ASN A1101 ASN B 70 HIS B 147 GLN B 214 ASN B 304 ASN ** B 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 GLN B1018 GLN B1040 HIS C 589 ASN ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.092857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.069652 restraints weight = 180343.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.069578 restraints weight = 145147.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.069675 restraints weight = 106736.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.070031 restraints weight = 96416.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.070231 restraints weight = 85784.511| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 30482 Z= 0.188 Angle : 0.713 10.166 41500 Z= 0.378 Chirality : 0.047 0.211 4628 Planarity : 0.005 0.062 5366 Dihedral : 6.921 56.740 4064 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.20 % Favored : 87.53 % Rotamer: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.12), residues: 3754 helix: -0.59 (0.15), residues: 999 sheet: -1.95 (0.22), residues: 516 loop : -3.28 (0.11), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 563 TYR 0.021 0.002 TYR C 484 PHE 0.019 0.002 PHE A 558 TRP 0.024 0.001 TRP A 868 HIS 0.008 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00389 (30440) covalent geometry : angle 0.71019 (41416) SS BOND : bond 0.00529 ( 42) SS BOND : angle 1.66126 ( 84) hydrogen bonds : bond 0.04900 ( 1062) hydrogen bonds : angle 6.53077 ( 3027) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 1.180 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: A 51 THR cc_start: 0.8748 (t) cc_final: 0.8475 (m) REVERT: A 361 PHE cc_start: 0.7358 (m-10) cc_final: 0.6823 (m-10) REVERT: A 746 ASN cc_start: 0.8666 (m-40) cc_final: 0.8211 (m-40) REVERT: A 962 ILE cc_start: 0.9143 (pt) cc_final: 0.8786 (tp) REVERT: A 996 ARG cc_start: 0.9292 (mmt90) cc_final: 0.9069 (mmm-85) REVERT: A 1013 GLU cc_start: 0.7354 (mm-30) cc_final: 0.5707 (tp30) REVERT: A 1032 MET cc_start: 0.8423 (tpp) cc_final: 0.7975 (tpp) REVERT: A 1092 PHE cc_start: 0.8124 (t80) cc_final: 0.7753 (t80) REVERT: B 151 MET cc_start: 0.3518 (ptm) cc_final: 0.3029 (ptp) REVERT: B 296 ASP cc_start: 0.7612 (m-30) cc_final: 0.7229 (t70) REVERT: B 301 GLN cc_start: 0.8354 (tp40) cc_final: 0.7831 (tp40) REVERT: B 333 LYS cc_start: 0.7570 (tttt) cc_final: 0.7139 (tptt) REVERT: B 558 PHE cc_start: 0.7192 (m-10) cc_final: 0.6954 (m-80) REVERT: B 581 VAL cc_start: 0.9376 (m) cc_final: 0.9080 (p) REVERT: B 713 MET cc_start: 0.8525 (ppp) cc_final: 0.8010 (ppp) REVERT: B 719 ASP cc_start: 0.7649 (t70) cc_final: 0.7447 (t0) REVERT: B 721 ASN cc_start: 0.7412 (t0) cc_final: 0.7128 (p0) REVERT: B 768 LYS cc_start: 0.7442 (mmpt) cc_final: 0.7065 (mmmt) REVERT: B 927 LEU cc_start: 0.8101 (mt) cc_final: 0.7829 (mt) REVERT: B 983 LEU cc_start: 0.9146 (pp) cc_final: 0.8538 (tp) REVERT: C 191 ASP cc_start: 0.7075 (m-30) cc_final: 0.6704 (p0) REVERT: C 220 PHE cc_start: 0.8417 (m-10) cc_final: 0.8061 (m-10) REVERT: C 476 TRP cc_start: 0.7448 (m100) cc_final: 0.7022 (p90) REVERT: C 559 THR cc_start: 0.7737 (m) cc_final: 0.7520 (p) REVERT: C 679 MET cc_start: 0.7886 (tmm) cc_final: 0.7429 (tmm) REVERT: C 711 VAL cc_start: 0.8025 (m) cc_final: 0.7718 (p) REVERT: C 745 LEU cc_start: 0.8619 (mt) cc_final: 0.8154 (mt) REVERT: C 755 GLU cc_start: 0.9112 (pt0) cc_final: 0.8762 (pt0) REVERT: C 770 MET cc_start: 0.7722 (mtp) cc_final: 0.7445 (mtp) REVERT: C 855 TYR cc_start: 0.7709 (m-80) cc_final: 0.7499 (m-80) REVERT: C 946 LYS cc_start: 0.9336 (mtmm) cc_final: 0.8994 (mtmm) REVERT: C 1085 PHE cc_start: 0.6992 (m-80) cc_final: 0.6597 (m-80) REVERT: D 82 MET cc_start: 0.4840 (ttt) cc_final: 0.4197 (mpp) REVERT: D 89 GLN cc_start: 0.6145 (tp-100) cc_final: 0.5394 (pt0) REVERT: D 323 MET cc_start: 0.2570 (mmp) cc_final: -0.0632 (mtp) REVERT: D 383 MET cc_start: 0.2569 (ptp) cc_final: 0.1988 (ptp) REVERT: D 480 MET cc_start: 0.1732 (ttt) cc_final: 0.1504 (ttp) outliers start: 1 outliers final: 0 residues processed: 361 average time/residue: 0.1850 time to fit residues: 110.5527 Evaluate side-chains 256 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 315 optimal weight: 9.9990 chunk 268 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 244 optimal weight: 0.0980 chunk 257 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 273 optimal weight: 8.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN B 304 ASN ** B 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 GLN ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 GLN B1090 ASN C 589 ASN ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 838 ASN C 877 GLN ** C 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 993 GLN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.090980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.067487 restraints weight = 182907.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.066152 restraints weight = 135943.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.066856 restraints weight = 120467.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.066992 restraints weight = 100560.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.067227 restraints weight = 91993.110| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 30482 Z= 0.237 Angle : 0.767 13.955 41500 Z= 0.406 Chirality : 0.048 0.268 4628 Planarity : 0.005 0.061 5366 Dihedral : 7.021 56.215 4064 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.93 % Favored : 85.80 % Rotamer: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.12), residues: 3754 helix: -0.65 (0.15), residues: 1000 sheet: -1.86 (0.22), residues: 500 loop : -3.28 (0.12), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 183 TYR 0.028 0.002 TYR B 855 PHE 0.019 0.002 PHE C 741 TRP 0.021 0.002 TRP A 868 HIS 0.010 0.002 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00487 (30440) covalent geometry : angle 0.76348 (41416) SS BOND : bond 0.00499 ( 42) SS BOND : angle 1.84054 ( 84) hydrogen bonds : bond 0.05170 ( 1062) hydrogen bonds : angle 6.62841 ( 3027) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 328 time to evaluate : 1.207 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: A 51 THR cc_start: 0.8805 (t) cc_final: 0.8521 (m) REVERT: A 361 PHE cc_start: 0.7442 (m-10) cc_final: 0.6815 (m-10) REVERT: A 367 TYR cc_start: 0.8153 (m-80) cc_final: 0.7908 (m-80) REVERT: A 417 MET cc_start: 0.5357 (mmp) cc_final: 0.4975 (mmp) REVERT: A 451 PHE cc_start: 0.8316 (m-10) cc_final: 0.7997 (m-10) REVERT: A 939 GLN cc_start: 0.8727 (tp-100) cc_final: 0.8500 (tp40) REVERT: A 1032 MET cc_start: 0.8172 (tpp) cc_final: 0.7868 (tpp) REVERT: A 1092 PHE cc_start: 0.8249 (t80) cc_final: 0.7867 (t80) REVERT: B 151 MET cc_start: 0.4109 (ptm) cc_final: 0.3800 (ptp) REVERT: B 296 ASP cc_start: 0.7575 (m-30) cc_final: 0.7194 (t70) REVERT: B 301 GLN cc_start: 0.8264 (tp40) cc_final: 0.7706 (tp40) REVERT: B 333 LYS cc_start: 0.7520 (tttt) cc_final: 0.7068 (tptt) REVERT: B 558 PHE cc_start: 0.7098 (m-10) cc_final: 0.6773 (m-10) REVERT: B 581 VAL cc_start: 0.9348 (m) cc_final: 0.9074 (p) REVERT: B 713 MET cc_start: 0.8306 (ppp) cc_final: 0.7824 (ppp) REVERT: B 755 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8482 (mt-10) REVERT: B 768 LYS cc_start: 0.7432 (mmpt) cc_final: 0.7136 (mmmt) REVERT: B 851 MET cc_start: 0.8970 (ptp) cc_final: 0.8225 (ptm) REVERT: B 884 MET cc_start: 0.5411 (mmp) cc_final: 0.4953 (mmp) REVERT: B 927 LEU cc_start: 0.8233 (mt) cc_final: 0.7990 (mt) REVERT: B 983 LEU cc_start: 0.9159 (pp) cc_final: 0.8771 (pp) REVERT: C 191 ASP cc_start: 0.7049 (m-30) cc_final: 0.6561 (p0) REVERT: C 220 PHE cc_start: 0.8648 (m-10) cc_final: 0.8255 (m-10) REVERT: C 476 TRP cc_start: 0.7514 (m100) cc_final: 0.7009 (p90) REVERT: C 679 MET cc_start: 0.8098 (tmm) cc_final: 0.7705 (tmm) REVERT: C 745 LEU cc_start: 0.8737 (mt) cc_final: 0.8164 (mt) REVERT: C 747 ARG cc_start: 0.8298 (ttp-110) cc_final: 0.7904 (ttp-110) REVERT: C 755 GLU cc_start: 0.9154 (pt0) cc_final: 0.8885 (pt0) REVERT: C 770 MET cc_start: 0.7873 (mtp) cc_final: 0.7587 (mtp) REVERT: C 933 VAL cc_start: 0.8847 (p) cc_final: 0.8634 (m) REVERT: C 946 LYS cc_start: 0.9448 (mtmm) cc_final: 0.9076 (mttp) REVERT: C 1085 PHE cc_start: 0.7335 (m-80) cc_final: 0.6910 (m-80) REVERT: D 82 MET cc_start: 0.4690 (ttt) cc_final: 0.4118 (mpp) REVERT: D 89 GLN cc_start: 0.6293 (tp-100) cc_final: 0.5519 (pt0) REVERT: D 297 MET cc_start: -0.2066 (tmm) cc_final: -0.2539 (tmm) outliers start: 1 outliers final: 0 residues processed: 329 average time/residue: 0.1795 time to fit residues: 98.2439 Evaluate side-chains 242 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 237 optimal weight: 9.9990 chunk 335 optimal weight: 40.0000 chunk 85 optimal weight: 4.9990 chunk 230 optimal weight: 10.0000 chunk 296 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 354 optimal weight: 30.0000 chunk 6 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN B 766 GLN ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1090 ASN C 589 ASN ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 ASN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.090606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.067549 restraints weight = 182549.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.066436 restraints weight = 125881.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.066812 restraints weight = 112360.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.066949 restraints weight = 100566.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.067206 restraints weight = 89335.586| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 30482 Z= 0.242 Angle : 0.776 12.392 41500 Z= 0.410 Chirality : 0.048 0.242 4628 Planarity : 0.005 0.062 5366 Dihedral : 7.046 57.882 4064 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.21 % Allowed : 14.28 % Favored : 85.51 % Rotamer: Outliers : 0.03 % Allowed : 1.92 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.40 (0.12), residues: 3754 helix: -0.69 (0.15), residues: 1006 sheet: -2.01 (0.22), residues: 496 loop : -3.25 (0.12), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 887 TYR 0.027 0.002 TYR C 484 PHE 0.028 0.002 PHE B 741 TRP 0.024 0.001 TRP C 868 HIS 0.015 0.002 HIS B1040 Details of bonding type rmsd covalent geometry : bond 0.00500 (30440) covalent geometry : angle 0.77142 (41416) SS BOND : bond 0.00536 ( 42) SS BOND : angle 2.05317 ( 84) hydrogen bonds : bond 0.05177 ( 1062) hydrogen bonds : angle 6.61567 ( 3027) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 330 time to evaluate : 1.140 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: A 51 THR cc_start: 0.8771 (t) cc_final: 0.8511 (m) REVERT: A 361 PHE cc_start: 0.7558 (m-10) cc_final: 0.6879 (m-10) REVERT: A 367 TYR cc_start: 0.8251 (m-80) cc_final: 0.7962 (m-80) REVERT: A 932 ASP cc_start: 0.7948 (m-30) cc_final: 0.7743 (m-30) REVERT: A 947 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8784 (mm-40) REVERT: A 1013 GLU cc_start: 0.7558 (mm-30) cc_final: 0.5774 (tp30) REVERT: A 1032 MET cc_start: 0.8196 (tpp) cc_final: 0.7978 (tpp) REVERT: A 1092 PHE cc_start: 0.8368 (t80) cc_final: 0.7884 (t80) REVERT: B 151 MET cc_start: 0.4131 (ptm) cc_final: 0.3741 (ptp) REVERT: B 161 PHE cc_start: 0.8016 (t80) cc_final: 0.7793 (t80) REVERT: B 196 VAL cc_start: 0.8804 (t) cc_final: 0.8598 (t) REVERT: B 220 PHE cc_start: 0.8439 (m-10) cc_final: 0.8091 (m-10) REVERT: B 263 MET cc_start: 0.6616 (tmm) cc_final: 0.6341 (tmm) REVERT: B 296 ASP cc_start: 0.7512 (m-30) cc_final: 0.7204 (t70) REVERT: B 301 GLN cc_start: 0.8266 (tp40) cc_final: 0.7613 (tp40) REVERT: B 333 LYS cc_start: 0.7532 (tttt) cc_final: 0.7134 (tptt) REVERT: B 558 PHE cc_start: 0.6983 (m-10) cc_final: 0.6744 (m-10) REVERT: B 719 ASP cc_start: 0.8020 (t0) cc_final: 0.7522 (t0) REVERT: B 721 ASN cc_start: 0.7374 (t0) cc_final: 0.7117 (p0) REVERT: B 752 ILE cc_start: 0.9493 (mt) cc_final: 0.9245 (mt) REVERT: B 758 ARG cc_start: 0.8634 (mmp-170) cc_final: 0.8400 (mmm160) REVERT: B 768 LYS cc_start: 0.7279 (mmpt) cc_final: 0.7039 (mmmt) REVERT: B 851 MET cc_start: 0.8703 (ptp) cc_final: 0.7680 (ptm) REVERT: B 983 LEU cc_start: 0.9271 (pp) cc_final: 0.8886 (pp) REVERT: B 1070 TYR cc_start: 0.8438 (m-80) cc_final: 0.8200 (m-80) REVERT: C 37 MET cc_start: 0.7983 (ptm) cc_final: 0.7702 (mmt) REVERT: C 191 ASP cc_start: 0.6924 (m-30) cc_final: 0.6600 (p0) REVERT: C 476 TRP cc_start: 0.7515 (m100) cc_final: 0.6906 (p90) REVERT: C 679 MET cc_start: 0.8237 (tmm) cc_final: 0.7780 (tmm) REVERT: C 745 LEU cc_start: 0.8810 (mt) cc_final: 0.8280 (mt) REVERT: C 747 ARG cc_start: 0.8483 (ttp-110) cc_final: 0.8247 (ttp-110) REVERT: C 755 GLU cc_start: 0.9030 (pt0) cc_final: 0.8824 (pt0) REVERT: C 770 MET cc_start: 0.8141 (mtp) cc_final: 0.7858 (mtm) REVERT: C 855 TYR cc_start: 0.7509 (m-80) cc_final: 0.7271 (m-80) REVERT: C 932 ASP cc_start: 0.8718 (m-30) cc_final: 0.8508 (m-30) REVERT: C 946 LYS cc_start: 0.9458 (mtmm) cc_final: 0.9078 (mttp) REVERT: C 1085 PHE cc_start: 0.7335 (m-80) cc_final: 0.6949 (m-80) REVERT: D 82 MET cc_start: 0.4805 (ttt) cc_final: 0.4206 (mpp) REVERT: D 89 GLN cc_start: 0.6326 (tp-100) cc_final: 0.5547 (pt0) REVERT: D 323 MET cc_start: 0.2593 (mmp) cc_final: -0.0350 (ttm) REVERT: D 366 MET cc_start: 0.0534 (mmt) cc_final: -0.0058 (mmt) REVERT: D 383 MET cc_start: 0.3117 (ptp) cc_final: 0.2668 (ptp) outliers start: 1 outliers final: 0 residues processed: 331 average time/residue: 0.1850 time to fit residues: 101.7169 Evaluate side-chains 239 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 354 optimal weight: 7.9990 chunk 375 optimal weight: 50.0000 chunk 245 optimal weight: 0.9980 chunk 163 optimal weight: 9.9990 chunk 271 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 305 optimal weight: 0.6980 chunk 113 optimal weight: 20.0000 chunk 333 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN B 766 GLN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1090 ASN C 589 ASN ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 769 GLN ** C 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.090833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.067576 restraints weight = 181726.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.067515 restraints weight = 145434.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.067235 restraints weight = 121430.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.067513 restraints weight = 115438.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.067656 restraints weight = 107353.693| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 30482 Z= 0.224 Angle : 0.762 11.566 41500 Z= 0.403 Chirality : 0.048 0.227 4628 Planarity : 0.005 0.063 5366 Dihedral : 6.976 57.992 4064 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.38 % Favored : 85.38 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.28 (0.13), residues: 3754 helix: -0.54 (0.16), residues: 989 sheet: -1.94 (0.22), residues: 507 loop : -3.18 (0.12), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 887 TYR 0.025 0.002 TYR B 855 PHE 0.022 0.002 PHE C 741 TRP 0.026 0.001 TRP C 868 HIS 0.011 0.002 HIS B1040 Details of bonding type rmsd covalent geometry : bond 0.00464 (30440) covalent geometry : angle 0.75700 (41416) SS BOND : bond 0.00509 ( 42) SS BOND : angle 2.01816 ( 84) hydrogen bonds : bond 0.05087 ( 1062) hydrogen bonds : angle 6.52229 ( 3027) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.289 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 51 THR cc_start: 0.8861 (t) cc_final: 0.8652 (m) REVERT: A 263 MET cc_start: 0.4590 (ppp) cc_final: 0.3461 (ppp) REVERT: A 361 PHE cc_start: 0.7627 (m-10) cc_final: 0.7175 (m-80) REVERT: A 367 TYR cc_start: 0.8242 (m-80) cc_final: 0.8029 (m-80) REVERT: A 503 LEU cc_start: 0.9107 (tp) cc_final: 0.8846 (mm) REVERT: A 723 TYR cc_start: 0.6705 (t80) cc_final: 0.6465 (t80) REVERT: A 932 ASP cc_start: 0.7922 (m-30) cc_final: 0.7591 (m-30) REVERT: A 939 GLN cc_start: 0.8800 (tp40) cc_final: 0.8521 (tp40) REVERT: A 947 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8760 (mm-40) REVERT: A 962 ILE cc_start: 0.9312 (pt) cc_final: 0.9079 (tp) REVERT: A 1032 MET cc_start: 0.8241 (tpp) cc_final: 0.8016 (tpp) REVERT: A 1092 PHE cc_start: 0.8389 (t80) cc_final: 0.7830 (t80) REVERT: B 161 PHE cc_start: 0.7929 (t80) cc_final: 0.7670 (t80) REVERT: B 196 VAL cc_start: 0.8902 (t) cc_final: 0.8655 (t) REVERT: B 220 PHE cc_start: 0.8455 (m-10) cc_final: 0.8103 (m-10) REVERT: B 296 ASP cc_start: 0.7477 (m-30) cc_final: 0.7120 (t70) REVERT: B 301 GLN cc_start: 0.8242 (tp40) cc_final: 0.7587 (tp40) REVERT: B 558 PHE cc_start: 0.7101 (m-10) cc_final: 0.6688 (m-80) REVERT: B 752 ILE cc_start: 0.9398 (mt) cc_final: 0.8978 (mt) REVERT: B 755 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8722 (mp0) REVERT: B 758 ARG cc_start: 0.8735 (mmp-170) cc_final: 0.8525 (mmm160) REVERT: B 768 LYS cc_start: 0.7475 (mmpt) cc_final: 0.7074 (mmmt) REVERT: B 851 MET cc_start: 0.8245 (ptp) cc_final: 0.7892 (ptp) REVERT: B 882 MET cc_start: 0.6670 (mmm) cc_final: 0.6457 (mmp) REVERT: B 983 LEU cc_start: 0.9403 (pp) cc_final: 0.9137 (pp) REVERT: C 191 ASP cc_start: 0.6896 (m-30) cc_final: 0.6580 (p0) REVERT: C 220 PHE cc_start: 0.8683 (m-10) cc_final: 0.8244 (m-10) REVERT: C 476 TRP cc_start: 0.7568 (m100) cc_final: 0.6946 (p90) REVERT: C 558 PHE cc_start: 0.9007 (m-80) cc_final: 0.8694 (m-80) REVERT: C 745 LEU cc_start: 0.8851 (mt) cc_final: 0.8326 (mt) REVERT: C 747 ARG cc_start: 0.8532 (ttp-110) cc_final: 0.8176 (ttp-110) REVERT: C 755 GLU cc_start: 0.9199 (pt0) cc_final: 0.8918 (pt0) REVERT: C 927 LEU cc_start: 0.9254 (tp) cc_final: 0.9036 (tp) REVERT: C 946 LYS cc_start: 0.9496 (mtmm) cc_final: 0.9137 (mttp) REVERT: C 1032 MET cc_start: 0.6407 (tpp) cc_final: 0.6091 (mmm) REVERT: C 1085 PHE cc_start: 0.7323 (m-80) cc_final: 0.6945 (m-80) REVERT: D 82 MET cc_start: 0.4544 (ttt) cc_final: 0.3993 (mpp) REVERT: D 89 GLN cc_start: 0.6295 (tp-100) cc_final: 0.5497 (pt0) REVERT: D 323 MET cc_start: 0.3039 (mmp) cc_final: 0.0151 (ttm) REVERT: D 366 MET cc_start: 0.1079 (mmt) cc_final: 0.0690 (mmt) REVERT: D 383 MET cc_start: 0.1860 (ptp) cc_final: 0.1539 (ptp) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.1838 time to fit residues: 97.9543 Evaluate side-chains 235 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 125 optimal weight: 4.9990 chunk 273 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 264 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 40 optimal weight: 0.0870 chunk 130 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 589 ASN ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 ASN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.093553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.069571 restraints weight = 179768.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.070260 restraints weight = 135252.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.069995 restraints weight = 102914.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.070349 restraints weight = 94857.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.070473 restraints weight = 88118.019| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 30482 Z= 0.146 Angle : 0.714 12.043 41500 Z= 0.373 Chirality : 0.047 0.217 4628 Planarity : 0.005 0.064 5366 Dihedral : 6.612 58.844 4064 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.28 % Favored : 87.48 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.13), residues: 3754 helix: -0.16 (0.16), residues: 975 sheet: -1.83 (0.23), residues: 509 loop : -3.04 (0.12), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 887 TYR 0.032 0.002 TYR C 484 PHE 0.027 0.002 PHE C1024 TRP 0.062 0.002 TRP A 868 HIS 0.010 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00312 (30440) covalent geometry : angle 0.71013 (41416) SS BOND : bond 0.00392 ( 42) SS BOND : angle 1.72915 ( 84) hydrogen bonds : bond 0.04507 ( 1062) hydrogen bonds : angle 6.21365 ( 3027) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 1.304 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 361 PHE cc_start: 0.7588 (m-10) cc_final: 0.6837 (m-10) REVERT: A 750 SER cc_start: 0.8680 (p) cc_final: 0.8420 (p) REVERT: A 939 GLN cc_start: 0.8722 (tp40) cc_final: 0.8491 (tp40) REVERT: A 1000 ILE cc_start: 0.9110 (mt) cc_final: 0.8307 (mt) REVERT: A 1013 GLU cc_start: 0.7654 (mm-30) cc_final: 0.6582 (tp30) REVERT: A 1032 MET cc_start: 0.8160 (tpp) cc_final: 0.7934 (tpp) REVERT: B 161 PHE cc_start: 0.7883 (t80) cc_final: 0.7546 (t80) REVERT: B 196 VAL cc_start: 0.8847 (t) cc_final: 0.8574 (t) REVERT: B 220 PHE cc_start: 0.8414 (m-10) cc_final: 0.8110 (m-10) REVERT: B 261 THR cc_start: 0.9294 (m) cc_final: 0.9011 (p) REVERT: B 263 MET cc_start: 0.6525 (tmm) cc_final: 0.6289 (tmm) REVERT: B 301 GLN cc_start: 0.8136 (tp40) cc_final: 0.7486 (tp40) REVERT: B 451 PHE cc_start: 0.7426 (m-80) cc_final: 0.7219 (m-10) REVERT: B 558 PHE cc_start: 0.7093 (m-10) cc_final: 0.6770 (m-80) REVERT: B 733 ASN cc_start: 0.9166 (m110) cc_final: 0.8857 (t0) REVERT: B 768 LYS cc_start: 0.7315 (mmpt) cc_final: 0.6967 (mmmt) REVERT: B 851 MET cc_start: 0.8563 (ptp) cc_final: 0.7438 (ptm) REVERT: B 868 TRP cc_start: 0.6425 (t-100) cc_final: 0.6102 (t-100) REVERT: B 932 ASP cc_start: 0.8506 (t70) cc_final: 0.7546 (t0) REVERT: B 933 VAL cc_start: 0.8952 (t) cc_final: 0.8627 (p) REVERT: B 936 GLN cc_start: 0.8775 (mt0) cc_final: 0.8242 (mt0) REVERT: B 983 LEU cc_start: 0.9423 (pp) cc_final: 0.9034 (pp) REVERT: C 103 PHE cc_start: 0.7553 (m-10) cc_final: 0.7283 (m-80) REVERT: C 191 ASP cc_start: 0.7016 (m-30) cc_final: 0.6771 (p0) REVERT: C 193 PHE cc_start: 0.4554 (m-10) cc_final: 0.4218 (m-10) REVERT: C 220 PHE cc_start: 0.8680 (m-10) cc_final: 0.8286 (m-10) REVERT: C 476 TRP cc_start: 0.7585 (m100) cc_final: 0.7055 (p90) REVERT: C 558 PHE cc_start: 0.9156 (m-80) cc_final: 0.8871 (m-80) REVERT: C 709 MET cc_start: 0.8060 (mtt) cc_final: 0.7594 (mpp) REVERT: C 745 LEU cc_start: 0.8940 (mt) cc_final: 0.8458 (mt) REVERT: C 747 ARG cc_start: 0.8694 (ttp-110) cc_final: 0.8440 (ttp-110) REVERT: C 752 ILE cc_start: 0.9435 (mt) cc_final: 0.8661 (mt) REVERT: C 755 GLU cc_start: 0.9073 (pt0) cc_final: 0.8640 (pp20) REVERT: C 927 LEU cc_start: 0.9258 (tp) cc_final: 0.9051 (mm) REVERT: C 932 ASP cc_start: 0.8872 (m-30) cc_final: 0.8656 (m-30) REVERT: C 946 LYS cc_start: 0.9384 (mtmm) cc_final: 0.9029 (mttp) REVERT: C 1027 LYS cc_start: 0.9238 (mttt) cc_final: 0.8467 (tptt) REVERT: C 1085 PHE cc_start: 0.7226 (m-80) cc_final: 0.6860 (m-80) REVERT: D 82 MET cc_start: 0.4796 (ttt) cc_final: 0.4248 (mpp) REVERT: D 89 GLN cc_start: 0.6327 (tp-100) cc_final: 0.5523 (pt0) REVERT: D 249 MET cc_start: -0.0158 (mtt) cc_final: -0.0403 (mmt) REVERT: D 332 MET cc_start: 0.0114 (ttp) cc_final: -0.0106 (ttp) REVERT: D 366 MET cc_start: 0.0422 (mmt) cc_final: 0.0019 (mmt) REVERT: D 376 MET cc_start: 0.3263 (pmm) cc_final: 0.2445 (pmm) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.1860 time to fit residues: 111.2433 Evaluate side-chains 259 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 142 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 230 optimal weight: 0.0970 chunk 82 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 302 optimal weight: 7.9990 chunk 303 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 GLN B 877 GLN ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 ASN ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 524 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.093195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.069940 restraints weight = 179872.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.069654 restraints weight = 131745.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.069645 restraints weight = 102113.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.069870 restraints weight = 102819.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.070140 restraints weight = 89944.601| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 30482 Z= 0.156 Angle : 0.714 11.268 41500 Z= 0.374 Chirality : 0.047 0.247 4628 Planarity : 0.005 0.065 5366 Dihedral : 6.457 56.459 4064 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.76 % Favored : 87.00 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.13), residues: 3754 helix: -0.07 (0.16), residues: 969 sheet: -1.90 (0.22), residues: 541 loop : -3.00 (0.12), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 758 TYR 0.029 0.002 TYR B 855 PHE 0.030 0.002 PHE A 805 TRP 0.051 0.002 TRP A 868 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00332 (30440) covalent geometry : angle 0.71079 (41416) SS BOND : bond 0.00387 ( 42) SS BOND : angle 1.71389 ( 84) hydrogen bonds : bond 0.04484 ( 1062) hydrogen bonds : angle 6.15443 ( 3027) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 1.179 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 263 MET cc_start: 0.4506 (ppp) cc_final: 0.3450 (ppp) REVERT: A 361 PHE cc_start: 0.7756 (m-10) cc_final: 0.7170 (m-80) REVERT: A 939 GLN cc_start: 0.8723 (tp40) cc_final: 0.8406 (tp40) REVERT: A 1013 GLU cc_start: 0.7592 (mm-30) cc_final: 0.5775 (tp30) REVERT: A 1032 MET cc_start: 0.8073 (tpp) cc_final: 0.7780 (ttp) REVERT: B 161 PHE cc_start: 0.7933 (t80) cc_final: 0.7544 (t80) REVERT: B 196 VAL cc_start: 0.8904 (t) cc_final: 0.8613 (t) REVERT: B 220 PHE cc_start: 0.8421 (m-10) cc_final: 0.8102 (m-10) REVERT: B 301 GLN cc_start: 0.8049 (tp40) cc_final: 0.7446 (tp40) REVERT: B 558 PHE cc_start: 0.7187 (m-10) cc_final: 0.6882 (m-80) REVERT: B 733 ASN cc_start: 0.9171 (m110) cc_final: 0.8860 (t0) REVERT: B 752 ILE cc_start: 0.9454 (mt) cc_final: 0.9188 (mt) REVERT: B 768 LYS cc_start: 0.7358 (mmpt) cc_final: 0.7080 (mmmt) REVERT: B 851 MET cc_start: 0.8721 (ptp) cc_final: 0.7808 (ptm) REVERT: B 868 TRP cc_start: 0.6264 (t-100) cc_final: 0.5731 (t-100) REVERT: B 932 ASP cc_start: 0.8204 (t70) cc_final: 0.7230 (t0) REVERT: B 933 VAL cc_start: 0.8925 (t) cc_final: 0.8598 (p) REVERT: B 936 GLN cc_start: 0.8605 (mt0) cc_final: 0.8101 (mt0) REVERT: B 983 LEU cc_start: 0.9388 (pp) cc_final: 0.9044 (pp) REVERT: B 1016 LEU cc_start: 0.8927 (mt) cc_final: 0.8605 (mt) REVERT: B 1091 PHE cc_start: 0.7386 (t80) cc_final: 0.7167 (t80) REVERT: C 103 PHE cc_start: 0.7516 (m-10) cc_final: 0.7248 (m-80) REVERT: C 191 ASP cc_start: 0.7126 (m-30) cc_final: 0.6897 (p0) REVERT: C 193 PHE cc_start: 0.4586 (m-10) cc_final: 0.4257 (m-10) REVERT: C 476 TRP cc_start: 0.7604 (m100) cc_final: 0.6991 (p90) REVERT: C 558 PHE cc_start: 0.9015 (m-80) cc_final: 0.8731 (m-80) REVERT: C 709 MET cc_start: 0.7954 (mtt) cc_final: 0.7396 (mpp) REVERT: C 745 LEU cc_start: 0.9113 (mt) cc_final: 0.8630 (mt) REVERT: C 747 ARG cc_start: 0.8814 (ttp-110) cc_final: 0.8568 (ttp-110) REVERT: C 752 ILE cc_start: 0.9388 (mt) cc_final: 0.8692 (mt) REVERT: C 755 GLU cc_start: 0.9107 (pt0) cc_final: 0.8577 (pp20) REVERT: C 770 MET cc_start: 0.7836 (mtm) cc_final: 0.6574 (mtp) REVERT: C 927 LEU cc_start: 0.9307 (tp) cc_final: 0.9063 (tp) REVERT: C 946 LYS cc_start: 0.9366 (mtmm) cc_final: 0.9039 (mttp) REVERT: C 1027 LYS cc_start: 0.9100 (mttt) cc_final: 0.8515 (tptt) REVERT: C 1033 SER cc_start: 0.7247 (t) cc_final: 0.5748 (t) REVERT: C 1085 PHE cc_start: 0.7127 (m-80) cc_final: 0.6809 (m-80) REVERT: D 82 MET cc_start: 0.4809 (ttt) cc_final: 0.4270 (mpp) REVERT: D 89 GLN cc_start: 0.6344 (tp-100) cc_final: 0.5538 (pt0) REVERT: D 249 MET cc_start: 0.0028 (mtt) cc_final: -0.0215 (mmt) REVERT: D 323 MET cc_start: 0.3242 (mmp) cc_final: 0.0508 (ttm) REVERT: D 366 MET cc_start: 0.0549 (mmt) cc_final: 0.0347 (mmt) REVERT: D 383 MET cc_start: 0.2091 (ptp) cc_final: 0.1801 (ptp) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.1853 time to fit residues: 105.9385 Evaluate side-chains 251 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 75 optimal weight: 0.0270 chunk 341 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 78 optimal weight: 0.4980 chunk 56 optimal weight: 0.1980 chunk 354 optimal weight: 10.0000 chunk 306 optimal weight: 1.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 ASN ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 ASN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.094649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.070410 restraints weight = 177736.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.070128 restraints weight = 127962.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.070478 restraints weight = 116373.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.070862 restraints weight = 88517.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.071046 restraints weight = 81055.855| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30482 Z= 0.132 Angle : 0.693 11.761 41500 Z= 0.363 Chirality : 0.047 0.340 4628 Planarity : 0.005 0.066 5366 Dihedral : 6.251 56.661 4064 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.75 % Favored : 88.07 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.13), residues: 3754 helix: 0.11 (0.16), residues: 972 sheet: -1.62 (0.23), residues: 514 loop : -2.92 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 887 TYR 0.028 0.001 TYR B 855 PHE 0.029 0.001 PHE A 805 TRP 0.019 0.001 TRP A 868 HIS 0.008 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00282 (30440) covalent geometry : angle 0.68968 (41416) SS BOND : bond 0.00350 ( 42) SS BOND : angle 1.71613 ( 84) hydrogen bonds : bond 0.04214 ( 1062) hydrogen bonds : angle 5.97382 ( 3027) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7508 Ramachandran restraints generated. 3754 Oldfield, 0 Emsley, 3754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 1.880 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 361 PHE cc_start: 0.7721 (m-10) cc_final: 0.6943 (m-10) REVERT: A 736 LEU cc_start: 0.9026 (mt) cc_final: 0.8767 (mt) REVERT: A 755 GLU cc_start: 0.8577 (pm20) cc_final: 0.8315 (pm20) REVERT: A 939 GLN cc_start: 0.8598 (tp40) cc_final: 0.8290 (tp40) REVERT: A 992 GLN cc_start: 0.9007 (mp10) cc_final: 0.8789 (mp10) REVERT: A 1013 GLU cc_start: 0.7178 (mm-30) cc_final: 0.5185 (tp30) REVERT: A 1032 MET cc_start: 0.8328 (tpp) cc_final: 0.7755 (ttp) REVERT: B 161 PHE cc_start: 0.8008 (t80) cc_final: 0.7586 (t80) REVERT: B 196 VAL cc_start: 0.8749 (t) cc_final: 0.8474 (t) REVERT: B 261 THR cc_start: 0.9300 (m) cc_final: 0.9033 (p) REVERT: B 263 MET cc_start: 0.6513 (tmm) cc_final: 0.6283 (tmm) REVERT: B 300 TYR cc_start: 0.7428 (m-80) cc_final: 0.7116 (m-80) REVERT: B 301 GLN cc_start: 0.7924 (tp40) cc_final: 0.7462 (tp40) REVERT: B 558 PHE cc_start: 0.7125 (m-10) cc_final: 0.6810 (m-80) REVERT: B 745 LEU cc_start: 0.8753 (mt) cc_final: 0.8321 (mt) REVERT: B 851 MET cc_start: 0.8545 (ptp) cc_final: 0.7314 (ptp) REVERT: B 868 TRP cc_start: 0.6271 (t-100) cc_final: 0.5784 (t-100) REVERT: B 932 ASP cc_start: 0.7968 (t70) cc_final: 0.7013 (t0) REVERT: B 933 VAL cc_start: 0.8723 (t) cc_final: 0.8404 (p) REVERT: B 936 GLN cc_start: 0.8231 (mt0) cc_final: 0.7955 (mt0) REVERT: B 983 LEU cc_start: 0.9123 (pp) cc_final: 0.8729 (pp) REVERT: B 1091 PHE cc_start: 0.7244 (t80) cc_final: 0.6900 (t80) REVERT: C 103 PHE cc_start: 0.7422 (m-80) cc_final: 0.7172 (m-80) REVERT: C 476 TRP cc_start: 0.7893 (m100) cc_final: 0.7181 (p90) REVERT: C 709 MET cc_start: 0.8038 (mtt) cc_final: 0.7501 (mpp) REVERT: C 745 LEU cc_start: 0.8644 (mt) cc_final: 0.8114 (mt) REVERT: C 747 ARG cc_start: 0.8371 (ttp-110) cc_final: 0.8068 (ttp-110) REVERT: C 752 ILE cc_start: 0.9299 (mt) cc_final: 0.8515 (mt) REVERT: C 755 GLU cc_start: 0.8814 (pt0) cc_final: 0.8440 (pp20) REVERT: C 882 MET cc_start: 0.5885 (mmm) cc_final: 0.5681 (mmm) REVERT: C 946 LYS cc_start: 0.9343 (mtmm) cc_final: 0.9005 (mttp) REVERT: C 1027 LYS cc_start: 0.9088 (mttt) cc_final: 0.8593 (tptt) REVERT: C 1085 PHE cc_start: 0.6891 (m-80) cc_final: 0.6512 (m-80) REVERT: D 82 MET cc_start: 0.4495 (ttt) cc_final: 0.3982 (mpp) REVERT: D 89 GLN cc_start: 0.6379 (tp-100) cc_final: 0.5567 (pt0) REVERT: D 323 MET cc_start: 0.3372 (mmp) cc_final: 0.0275 (ttm) REVERT: D 332 MET cc_start: 0.0098 (ttp) cc_final: -0.0109 (ttp) REVERT: D 383 MET cc_start: 0.2901 (ptp) cc_final: 0.2557 (ptp) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.1798 time to fit residues: 105.0756 Evaluate side-chains 254 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 323 optimal weight: 0.7980 chunk 334 optimal weight: 30.0000 chunk 179 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 300 optimal weight: 6.9990 chunk 185 optimal weight: 0.8980 chunk 209 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 264 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN B 611 HIS B 759 ASN ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 ASN ** C 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 ASN ** C 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 910 ASN ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.093735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.069595 restraints weight = 179803.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.070255 restraints weight = 126474.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.069924 restraints weight = 96461.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.070046 restraints weight = 93471.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.070306 restraints weight = 82379.977| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30482 Z= 0.154 Angle : 0.709 11.445 41500 Z= 0.370 Chirality : 0.047 0.458 4628 Planarity : 0.005 0.068 5366 Dihedral : 6.211 55.543 4064 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.76 % Favored : 87.05 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.13), residues: 3754 helix: 0.04 (0.16), residues: 981 sheet: -1.62 (0.23), residues: 529 loop : -2.89 (0.12), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 887 TYR 0.027 0.001 TYR B 855 PHE 0.026 0.002 PHE A 805 TRP 0.016 0.001 TRP C 868 HIS 0.008 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00329 (30440) covalent geometry : angle 0.70582 (41416) SS BOND : bond 0.00367 ( 42) SS BOND : angle 1.71759 ( 84) hydrogen bonds : bond 0.04314 ( 1062) hydrogen bonds : angle 6.01468 ( 3027) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5647.24 seconds wall clock time: 98 minutes 35.82 seconds (5915.82 seconds total)