Starting phenix.real_space_refine on Sat Mar 7 06:17:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zlu_11274/03_2026/6zlu_11274.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zlu_11274/03_2026/6zlu_11274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zlu_11274/03_2026/6zlu_11274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zlu_11274/03_2026/6zlu_11274.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zlu_11274/03_2026/6zlu_11274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zlu_11274/03_2026/6zlu_11274.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 21700 atoms to isotropic. 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 80 5.16 5 C 13742 2.51 5 N 3652 2.21 5 O 4226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21700 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4457 Classifications: {'peptide': 555} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 535} Chain: "B" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6393 Classifications: {'peptide': 804} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 776} Restraints were copied for chains: C, D Time building chain proxies: 8.25, per 1000 atoms: 0.38 Number of scatterers: 21700 At special positions: 0 Unit cell: (157.29, 92.02, 136.96, 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 80 16.00 O 4226 8.00 N 3652 7.00 C 13742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 299 " distance=2.04 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 389 " distance=2.11 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 299 " distance=2.04 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 389 " distance=2.11 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 795.7 milliseconds 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4956 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 26 sheets defined 28.8% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 17 through 23 removed outlier: 3.994A pdb=" N ALA A 20 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 24 through 39 removed outlier: 4.558A pdb=" N TRP A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 37 " --> pdb=" O TYR A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.573A pdb=" N VAL A 53 " --> pdb=" O TRP A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 77 Processing helix chain 'A' and resid 84 through 110 removed outlier: 3.939A pdb=" N GLN A 110 " --> pdb=" O GLN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 118 through 142 Processing helix chain 'A' and resid 154 through 160 Processing helix chain 'A' and resid 166 through 185 removed outlier: 3.651A pdb=" N ASP A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 213 removed outlier: 4.046A pdb=" N TYR A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 236 removed outlier: 3.656A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.549A pdb=" N LEU A 258 " --> pdb=" O MET A 255 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.598A pdb=" N GLU A 262 " --> pdb=" O PRO A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 305 through 312 removed outlier: 3.735A pdb=" N PHE A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 344 Processing helix chain 'A' and resid 407 through 421 Processing helix chain 'A' and resid 425 through 442 Processing helix chain 'A' and resid 469 through 485 Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 500 through 514 removed outlier: 4.516A pdb=" N SER A 514 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 522 removed outlier: 3.888A pdb=" N ASN A 521 " --> pdb=" O ILE A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 543 removed outlier: 3.785A pdb=" N ASN A 543 " --> pdb=" O ILE A 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.523A pdb=" N ASN B 255 " --> pdb=" O PRO B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 300 Processing helix chain 'B' and resid 376 through 384 Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 535 through 539 Processing helix chain 'B' and resid 584 through 587 Processing helix chain 'B' and resid 602 through 608 removed outlier: 5.110A pdb=" N ASN B 605 " --> pdb=" O THR B 602 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N PHE B 606 " --> pdb=" O GLN B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 729 Processing helix chain 'B' and resid 779 through 786 removed outlier: 3.522A pdb=" N GLY B 786 " --> pdb=" O VAL B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 821 removed outlier: 3.714A pdb=" N VAL B 819 " --> pdb=" O SER B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 895 removed outlier: 3.863A pdb=" N LYS B 893 " --> pdb=" O ASP B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 914 removed outlier: 3.869A pdb=" N LEU B 911 " --> pdb=" O GLY B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 941 No H-bonds generated for 'chain 'B' and resid 939 through 941' Processing helix chain 'B' and resid 961 through 966 Processing helix chain 'B' and resid 967 through 969 No H-bonds generated for 'chain 'B' and resid 967 through 969' Processing helix chain 'C' and resid 17 through 23 removed outlier: 3.994A pdb=" N ALA C 20 " --> pdb=" O ASP C 17 " (cutoff:3.500A) Proline residue: C 22 - end of helix Processing helix chain 'C' and resid 24 through 39 removed outlier: 4.558A pdb=" N TRP C 36 " --> pdb=" O ALA C 32 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA C 37 " --> pdb=" O TYR C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 53 removed outlier: 3.573A pdb=" N VAL C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 77 Processing helix chain 'C' and resid 84 through 110 removed outlier: 3.939A pdb=" N GLN C 110 " --> pdb=" O GLN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 118 through 142 Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 166 through 185 removed outlier: 3.651A pdb=" N ASP C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 213 removed outlier: 4.046A pdb=" N TYR C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 236 removed outlier: 3.656A pdb=" N LEU C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 244 Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.549A pdb=" N LEU C 258 " --> pdb=" O MET C 255 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.598A pdb=" N GLU C 262 " --> pdb=" O PRO C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 289 Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 305 through 312 removed outlier: 3.735A pdb=" N PHE C 312 " --> pdb=" O LEU C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 344 Processing helix chain 'C' and resid 407 through 421 Processing helix chain 'C' and resid 425 through 442 Processing helix chain 'C' and resid 469 through 485 Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'C' and resid 500 through 514 removed outlier: 4.516A pdb=" N SER C 514 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 522 removed outlier: 3.888A pdb=" N ASN C 521 " --> pdb=" O ILE C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 543 removed outlier: 3.785A pdb=" N ASN C 543 " --> pdb=" O ILE C 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 251 through 255 removed outlier: 3.523A pdb=" N ASN D 255 " --> pdb=" O PRO D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 300 Processing helix chain 'D' and resid 376 through 384 Processing helix chain 'D' and resid 409 through 417 Processing helix chain 'D' and resid 535 through 539 Processing helix chain 'D' and resid 584 through 587 Processing helix chain 'D' and resid 602 through 608 removed outlier: 5.110A pdb=" N ASN D 605 " --> pdb=" O THR D 602 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N PHE D 606 " --> pdb=" O GLN D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 729 Processing helix chain 'D' and resid 779 through 786 removed outlier: 3.522A pdb=" N GLY D 786 " --> pdb=" O VAL D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 815 through 821 removed outlier: 3.714A pdb=" N VAL D 819 " --> pdb=" O SER D 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 889 through 895 removed outlier: 3.863A pdb=" N LYS D 893 " --> pdb=" O ASP D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 908 through 914 removed outlier: 3.869A pdb=" N LEU D 911 " --> pdb=" O GLY D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 941 No H-bonds generated for 'chain 'D' and resid 939 through 941' Processing helix chain 'D' and resid 961 through 966 Processing helix chain 'D' and resid 967 through 969 No H-bonds generated for 'chain 'D' and resid 967 through 969' Processing sheet with id=1, first strand: chain 'A' and resid 58 through 61 removed outlier: 6.024A pdb=" N GLY A 61 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE A 301 " --> pdb=" O GLY A 61 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.924A pdb=" N SER A 267 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ARG A 406 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP A 269 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 313 through 314 removed outlier: 4.053A pdb=" N ASN A 336 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 345 through 346 Processing sheet with id=5, first strand: chain 'A' and resid 390 through 392 Processing sheet with id=6, first strand: chain 'B' and resid 214 through 224 removed outlier: 4.368A pdb=" N ARG B 421 " --> pdb=" O ARG B 457 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG B 457 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N THR B 591 " --> pdb=" O GLY B 626 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLY B 626 " --> pdb=" O THR B 591 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA B 740 " --> pdb=" O LEU B 776 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP B 873 " --> pdb=" O LEU B 956 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU B 956 " --> pdb=" O ASP B 873 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR B 875 " --> pdb=" O ILE B 954 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE B 954 " --> pdb=" O THR B 875 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE B 877 " --> pdb=" O ARG B 952 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU B 983 " --> pdb=" O LEU B 951 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASN B 953 " --> pdb=" O ASN B 981 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN B 981 " --> pdb=" O ASN B 953 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLN B 955 " --> pdb=" O ALA B 979 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA B 979 " --> pdb=" O GLN B 955 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLY B 957 " --> pdb=" O CYS B 977 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N CYS B 977 " --> pdb=" O GLY B 957 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N THR B 959 " --> pdb=" O PHE B 975 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N PHE B 975 " --> pdb=" O THR B 959 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 972 " --> pdb=" O GLY B1015 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'B' and resid 259 through 265 removed outlier: 6.772A pdb=" N ALA B 260 " --> pdb=" O MET B 276 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N MET B 276 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN B 262 " --> pdb=" O TYR B 274 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 464 through 465 Processing sheet with id=9, first strand: chain 'B' and resid 638 through 640 removed outlier: 6.377A pdb=" N ILE B 638 " --> pdb=" O ASN B 676 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'B' and resid 719 through 722 Processing sheet with id=11, first strand: chain 'B' and resid 804 through 807 removed outlier: 6.580A pdb=" N GLN B 804 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.870A pdb=" N ARG B 834 " --> pdb=" O ASP B 810 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'B' and resid 885 through 887 Processing sheet with id=14, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.024A pdb=" N GLY C 61 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE C 301 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 267 through 271 removed outlier: 6.924A pdb=" N SER C 267 " --> pdb=" O ARG C 406 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ARG C 406 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP C 269 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 313 through 314 removed outlier: 4.053A pdb=" N ASN C 336 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'C' and resid 345 through 346 Processing sheet with id=18, first strand: chain 'C' and resid 390 through 392 Processing sheet with id=19, first strand: chain 'D' and resid 214 through 224 removed outlier: 4.368A pdb=" N ARG D 421 " --> pdb=" O ARG D 457 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG D 457 " --> pdb=" O ARG D 421 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE D 441 " --> pdb=" O PRO D 437 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N THR D 591 " --> pdb=" O GLY D 626 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLY D 626 " --> pdb=" O THR D 591 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA D 740 " --> pdb=" O LEU D 776 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP D 873 " --> pdb=" O LEU D 956 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU D 956 " --> pdb=" O ASP D 873 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR D 875 " --> pdb=" O ILE D 954 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE D 954 " --> pdb=" O THR D 875 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE D 877 " --> pdb=" O ARG D 952 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU D 983 " --> pdb=" O LEU D 951 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASN D 953 " --> pdb=" O ASN D 981 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN D 981 " --> pdb=" O ASN D 953 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLN D 955 " --> pdb=" O ALA D 979 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA D 979 " --> pdb=" O GLN D 955 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLY D 957 " --> pdb=" O CYS D 977 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N CYS D 977 " --> pdb=" O GLY D 957 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N THR D 959 " --> pdb=" O PHE D 975 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N PHE D 975 " --> pdb=" O THR D 959 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG D 972 " --> pdb=" O GLY D1015 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'D' and resid 259 through 265 removed outlier: 6.772A pdb=" N ALA D 260 " --> pdb=" O MET D 276 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N MET D 276 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN D 262 " --> pdb=" O TYR D 274 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'D' and resid 464 through 465 Processing sheet with id=22, first strand: chain 'D' and resid 638 through 640 removed outlier: 6.377A pdb=" N ILE D 638 " --> pdb=" O ASN D 676 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'D' and resid 719 through 722 Processing sheet with id=24, first strand: chain 'D' and resid 804 through 807 removed outlier: 6.580A pdb=" N GLN D 804 " --> pdb=" O ILE D 852 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'D' and resid 809 through 812 removed outlier: 4.870A pdb=" N ARG D 834 " --> pdb=" O ASP D 810 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'D' and resid 885 through 887 1060 hydrogen bonds defined for protein. 2904 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7044 1.34 - 1.47: 6006 1.47 - 1.60: 9050 1.60 - 1.73: 0 1.73 - 1.86: 142 Bond restraints: 22242 Sorted by residual: bond pdb=" CB ASN D 470 " pdb=" CG ASN D 470 " ideal model delta sigma weight residual 1.516 1.449 0.067 2.50e-02 1.60e+03 7.26e+00 bond pdb=" CB ASN B 470 " pdb=" CG ASN B 470 " ideal model delta sigma weight residual 1.516 1.449 0.067 2.50e-02 1.60e+03 7.26e+00 bond pdb=" CB ASN B 785 " pdb=" CG ASN B 785 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.27e+00 bond pdb=" CB ASN D 785 " pdb=" CG ASN D 785 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.27e+00 bond pdb=" C THR B 469 " pdb=" N ASN B 470 " ideal model delta sigma weight residual 1.336 1.306 0.030 1.55e-02 4.16e+03 3.85e+00 ... (remaining 22237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 27976 1.80 - 3.59: 1950 3.59 - 5.39: 186 5.39 - 7.18: 36 7.18 - 8.98: 22 Bond angle restraints: 30170 Sorted by residual: angle pdb=" CA TRP D 599 " pdb=" CB TRP D 599 " pdb=" CG TRP D 599 " ideal model delta sigma weight residual 113.60 122.41 -8.81 1.90e+00 2.77e-01 2.15e+01 angle pdb=" CA TRP B 599 " pdb=" CB TRP B 599 " pdb=" CG TRP B 599 " ideal model delta sigma weight residual 113.60 122.41 -8.81 1.90e+00 2.77e-01 2.15e+01 angle pdb=" CG ARG B 588 " pdb=" CD ARG B 588 " pdb=" NE ARG B 588 " ideal model delta sigma weight residual 112.00 103.31 8.69 2.20e+00 2.07e-01 1.56e+01 angle pdb=" CG ARG D 588 " pdb=" CD ARG D 588 " pdb=" NE ARG D 588 " ideal model delta sigma weight residual 112.00 103.31 8.69 2.20e+00 2.07e-01 1.56e+01 angle pdb=" C PRO B 405 " pdb=" N ASP B 406 " pdb=" CA ASP B 406 " ideal model delta sigma weight residual 121.54 129.00 -7.46 1.91e+00 2.74e-01 1.52e+01 ... (remaining 30165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 11306 17.80 - 35.60: 1268 35.60 - 53.39: 292 53.39 - 71.19: 76 71.19 - 88.99: 42 Dihedral angle restraints: 12984 sinusoidal: 5132 harmonic: 7852 Sorted by residual: dihedral pdb=" CA ASN B 470 " pdb=" C ASN B 470 " pdb=" N ASN B 471 " pdb=" CA ASN B 471 " ideal model delta harmonic sigma weight residual -180.00 -150.55 -29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ASN D 470 " pdb=" C ASN D 470 " pdb=" N ASN D 471 " pdb=" CA ASN D 471 " ideal model delta harmonic sigma weight residual -180.00 -150.55 -29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA THR D 645 " pdb=" C THR D 645 " pdb=" N THR D 646 " pdb=" CA THR D 646 " ideal model delta harmonic sigma weight residual -180.00 -152.70 -27.30 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 12981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2662 0.078 - 0.157: 434 0.157 - 0.235: 10 0.235 - 0.314: 4 0.314 - 0.392: 2 Chirality restraints: 3112 Sorted by residual: chirality pdb=" CB ILE B 377 " pdb=" CA ILE B 377 " pdb=" CG1 ILE B 377 " pdb=" CG2 ILE B 377 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CB ILE D 377 " pdb=" CA ILE D 377 " pdb=" CG1 ILE D 377 " pdb=" CG2 ILE D 377 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CB ILE C 275 " pdb=" CA ILE C 275 " pdb=" CG1 ILE C 275 " pdb=" CG2 ILE C 275 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 3109 not shown) Planarity restraints: 3968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 384 " 0.049 5.00e-02 4.00e+02 7.40e-02 8.76e+00 pdb=" N PRO B 385 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 385 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 385 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 384 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.76e+00 pdb=" N PRO D 385 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 385 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 385 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 303 " -0.048 5.00e-02 4.00e+02 7.35e-02 8.65e+00 pdb=" N PRO C 304 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 304 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 304 " -0.040 5.00e-02 4.00e+02 ... (remaining 3965 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.11: 26 2.11 - 2.81: 6400 2.81 - 3.51: 29591 3.51 - 4.20: 56690 4.20 - 4.90: 95950 Nonbonded interactions: 188657 Sorted by model distance: nonbonded pdb=" O CYS A 1 " pdb=" OH TYR B 589 " model vdw 1.417 3.040 nonbonded pdb=" O CYS C 1 " pdb=" OH TYR D 589 " model vdw 1.417 3.040 nonbonded pdb=" OG1 THR C 82 " pdb=" OE2 GLU D 846 " model vdw 1.616 3.040 nonbonded pdb=" OG1 THR A 82 " pdb=" OE2 GLU B 846 " model vdw 1.616 3.040 nonbonded pdb=" O GLY B 547 " pdb=" OD2 ASP D 537 " model vdw 1.667 3.040 ... (remaining 188652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.700 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4770 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 : 0.008 0.077 22246 Z= 0.372 Angle : 0.994 8.978 30178 Z= 0.559 Chirality : 0.055 0.392 3112 Planarity : 0.006 0.074 3968 Dihedral : 16.839 88.989 8016 Min Nonbonded Distance : 1.417 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.65 % Favored : 94.91 % Rotamer: Outliers : 0.09 % Allowed : 19.70 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.14), residues: 2710 helix: -2.71 (0.15), residues: 612 sheet: -0.23 (0.18), residues: 722 loop : -1.27 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 367 TYR 0.021 0.004 TYR D 712 PHE 0.026 0.004 PHE D 942 TRP 0.029 0.005 TRP D 425 HIS 0.009 0.002 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00800 (22242) covalent geometry : angle 0.99263 (30170) SS BOND : bond 0.05495 ( 4) SS BOND : angle 2.79299 ( 8) hydrogen bonds : bond 0.20675 ( 1060) hydrogen bonds : angle 8.62976 ( 2904) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 582 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 TRP cc_start: 0.4518 (m-10) cc_final: 0.3827 (m100) REVERT: B 273 LEU cc_start: 0.5763 (tp) cc_final: 0.5486 (pt) REVERT: B 422 TYR cc_start: 0.6631 (p90) cc_final: 0.6219 (p90) REVERT: B 511 LEU cc_start: 0.7838 (mt) cc_final: 0.7605 (mt) REVERT: B 841 ASN cc_start: 0.6442 (p0) cc_final: 0.6134 (m-40) REVERT: C 290 LEU cc_start: 0.5441 (mt) cc_final: 0.4958 (mt) REVERT: C 295 ILE cc_start: 0.2150 (tp) cc_final: 0.1866 (tp) REVERT: C 385 PRO cc_start: 0.5074 (Cg_exo) cc_final: 0.4788 (Cg_endo) REVERT: D 273 LEU cc_start: 0.6499 (tp) cc_final: 0.6044 (pt) REVERT: D 309 ASN cc_start: 0.8356 (t0) cc_final: 0.8147 (t0) REVERT: D 450 ASP cc_start: 0.6597 (t0) cc_final: 0.5784 (m-30) REVERT: D 770 THR cc_start: 0.2426 (t) cc_final: 0.1825 (m) REVERT: D 841 ASN cc_start: 0.6971 (p0) cc_final: 0.6499 (m-40) outliers start: 2 outliers final: 0 residues processed: 584 average time/residue: 0.1719 time to fit residues: 153.1828 Evaluate side-chains 340 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 43 ASN ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN A 263 ASN A 272 GLN A 302 HIS A 401 ASN ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN B 417 ASN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS B 512 ASN B 586 ASN B 680 ASN B 816 GLN C 43 ASN ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 470 ASN ** D 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 HIS D 512 ASN D 586 ASN D 676 ASN D 680 ASN ** D 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 ASN D 754 ASN D 816 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.182332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.157653 restraints weight = 55081.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.159994 restraints weight = 40770.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.160854 restraints weight = 31297.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.160822 restraints weight = 27262.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.160978 restraints weight = 28526.040| |-----------------------------------------------------------------------------| r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5745 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22246 Z= 0.161 Angle : 0.682 10.312 30178 Z= 0.371 Chirality : 0.047 0.257 3112 Planarity : 0.005 0.050 3968 Dihedral : 5.658 24.328 3014 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.21 % Favored : 97.68 % Rotamer: Outliers : 0.22 % Allowed : 2.31 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.15), residues: 2710 helix: -0.77 (0.18), residues: 644 sheet: 0.19 (0.17), residues: 750 loop : -0.52 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 600 TYR 0.033 0.002 TYR C 203 PHE 0.058 0.002 PHE A 178 TRP 0.023 0.002 TRP B 599 HIS 0.006 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00352 (22242) covalent geometry : angle 0.67689 (30170) SS BOND : bond 0.00413 ( 4) SS BOND : angle 4.93354 ( 8) hydrogen bonds : bond 0.04958 ( 1060) hydrogen bonds : angle 5.70745 ( 2904) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 457 time to evaluate : 0.855 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: A 38 THR cc_start: 0.8640 (p) cc_final: 0.8429 (p) REVERT: A 71 PHE cc_start: 0.7896 (m-80) cc_final: 0.7505 (m-80) REVERT: A 132 HIS cc_start: 0.6457 (t70) cc_final: 0.6212 (t70) REVERT: A 291 THR cc_start: 0.7872 (p) cc_final: 0.7668 (p) REVERT: A 412 LEU cc_start: 0.6146 (mt) cc_final: 0.5715 (mt) REVERT: B 273 LEU cc_start: 0.7543 (tp) cc_final: 0.6944 (pt) REVERT: B 276 MET cc_start: 0.5005 (mtp) cc_final: 0.4611 (mtm) REVERT: B 463 TYR cc_start: 0.5285 (p90) cc_final: 0.4864 (p90) REVERT: B 542 THR cc_start: 0.8407 (m) cc_final: 0.8152 (p) REVERT: B 643 TYR cc_start: 0.7962 (t80) cc_final: 0.7541 (t80) REVERT: B 645 THR cc_start: 0.7914 (p) cc_final: 0.7698 (p) REVERT: B 950 LYS cc_start: 0.8302 (mttp) cc_final: 0.7980 (tppt) REVERT: B 951 LEU cc_start: 0.8293 (tp) cc_final: 0.8035 (tp) REVERT: B 970 MET cc_start: 0.4221 (mtp) cc_final: 0.3824 (mtm) REVERT: C 28 LEU cc_start: 0.8298 (mt) cc_final: 0.8050 (mt) REVERT: C 168 ASP cc_start: 0.7527 (p0) cc_final: 0.7154 (p0) REVERT: C 290 LEU cc_start: 0.5943 (mt) cc_final: 0.5620 (mt) REVERT: C 471 ASP cc_start: 0.7931 (p0) cc_final: 0.7557 (p0) REVERT: D 273 LEU cc_start: 0.7840 (tp) cc_final: 0.7520 (pt) REVERT: D 643 TYR cc_start: 0.7209 (t80) cc_final: 0.6481 (t80) REVERT: D 713 LYS cc_start: 0.6784 (ttpt) cc_final: 0.6395 (tmtt) outliers start: 5 outliers final: 1 residues processed: 461 average time/residue: 0.1760 time to fit residues: 122.6230 Evaluate side-chains 304 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 3 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 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 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN A 121 GLN A 139 GLN A 263 ASN A 548 GLN B 230 ASN ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 GLN ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 936 GLN B 999 ASN C 121 GLN C 189 GLN ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS C 307 ASN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 ASN D 999 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.158965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.133059 restraints weight = 55717.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.132403 restraints weight = 57483.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.133751 restraints weight = 44520.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.134090 restraints weight = 35528.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.134169 restraints weight = 33091.219| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.6797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 22246 Z= 0.294 Angle : 0.830 13.731 30178 Z= 0.450 Chirality : 0.051 0.278 3112 Planarity : 0.006 0.078 3968 Dihedral : 5.891 24.240 3014 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.99 % Favored : 96.90 % Rotamer: Outliers : 0.22 % Allowed : 3.88 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.15), residues: 2710 helix: -0.70 (0.18), residues: 650 sheet: 0.49 (0.18), residues: 732 loop : -0.53 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 515 TYR 0.041 0.002 TYR D 458 PHE 0.050 0.003 PHE C 178 TRP 0.020 0.002 TRP B 599 HIS 0.008 0.003 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00592 (22242) covalent geometry : angle 0.82589 (30170) SS BOND : bond 0.01258 ( 4) SS BOND : angle 5.39134 ( 8) hydrogen bonds : bond 0.05638 ( 1060) hydrogen bonds : angle 5.75216 ( 2904) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 387 time to evaluate : 0.752 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: A 111 MET cc_start: 0.4029 (ttm) cc_final: 0.2918 (mmp) REVERT: A 168 ASP cc_start: 0.7729 (p0) cc_final: 0.7244 (p0) REVERT: A 325 TYR cc_start: 0.7362 (p90) cc_final: 0.6942 (p90) REVERT: B 243 GLN cc_start: 0.8594 (tp40) cc_final: 0.8105 (tm-30) REVERT: B 643 TYR cc_start: 0.8073 (t80) cc_final: 0.7591 (t80) REVERT: B 970 MET cc_start: 0.4766 (mtp) cc_final: 0.4463 (mtm) REVERT: C 168 ASP cc_start: 0.7639 (p0) cc_final: 0.7387 (p0) REVERT: C 242 MET cc_start: 0.6290 (mmt) cc_final: 0.5661 (mmt) REVERT: D 229 MET cc_start: 0.8655 (tpp) cc_final: 0.8108 (tpp) REVERT: D 273 LEU cc_start: 0.7990 (tp) cc_final: 0.7325 (pt) REVERT: D 388 ILE cc_start: 0.8595 (mm) cc_final: 0.8324 (mm) REVERT: D 427 MET cc_start: 0.6903 (mpp) cc_final: 0.6577 (mtm) REVERT: D 481 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7292 (tt0) REVERT: D 617 LYS cc_start: 0.7907 (mmmt) cc_final: 0.7660 (mmpt) REVERT: D 681 ASP cc_start: 0.7823 (p0) cc_final: 0.7580 (p0) REVERT: D 897 TRP cc_start: 0.7397 (t-100) cc_final: 0.6572 (t60) outliers start: 5 outliers final: 4 residues processed: 392 average time/residue: 0.1581 time to fit residues: 94.8364 Evaluate side-chains 261 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 257 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 56 optimal weight: 0.0020 chunk 20 optimal weight: 4.9990 chunk 214 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 151 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN A 263 ASN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN B 247 ASN B 270 ASN B 361 GLN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN B 501 HIS B 642 ASN C 11 GLN ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN C 327 ASN C 401 ASN D 247 ASN ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 825 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.157328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.133743 restraints weight = 55184.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.132430 restraints weight = 66484.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.133717 restraints weight = 57464.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.134023 restraints weight = 42274.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.134210 restraints weight = 40621.954| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.7612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 22246 Z= 0.157 Angle : 0.643 11.483 30178 Z= 0.345 Chirality : 0.046 0.241 3112 Planarity : 0.004 0.072 3968 Dihedral : 5.288 26.490 3014 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.69 % Favored : 97.23 % Rotamer: Outliers : 0.13 % Allowed : 2.27 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.15), residues: 2710 helix: -0.16 (0.19), residues: 654 sheet: 0.51 (0.18), residues: 750 loop : -0.43 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 340 TYR 0.036 0.002 TYR A 203 PHE 0.024 0.002 PHE A 178 TRP 0.027 0.002 TRP B 599 HIS 0.006 0.001 HIS B 799 Details of bonding type rmsd covalent geometry : bond 0.00359 (22242) covalent geometry : angle 0.63364 (30170) SS BOND : bond 0.01547 ( 4) SS BOND : angle 6.89182 ( 8) hydrogen bonds : bond 0.04397 ( 1060) hydrogen bonds : angle 5.23732 ( 2904) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 357 time to evaluate : 0.790 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: A 111 MET cc_start: 0.3263 (ttm) cc_final: 0.2425 (mmp) REVERT: A 152 MET cc_start: 0.7645 (ptm) cc_final: 0.6615 (ptt) REVERT: A 325 TYR cc_start: 0.7380 (p90) cc_final: 0.6919 (p90) REVERT: B 237 TYR cc_start: 0.6951 (t80) cc_final: 0.6738 (t80) REVERT: B 250 GLU cc_start: 0.6925 (tp30) cc_final: 0.6405 (mp0) REVERT: B 273 LEU cc_start: 0.7666 (tp) cc_final: 0.6704 (pt) REVERT: B 413 VAL cc_start: 0.8052 (t) cc_final: 0.7463 (m) REVERT: B 529 LEU cc_start: 0.7701 (mp) cc_final: 0.7256 (pt) REVERT: B 542 THR cc_start: 0.8991 (m) cc_final: 0.8676 (p) REVERT: B 736 ILE cc_start: 0.7302 (mm) cc_final: 0.7055 (mm) REVERT: C 35 ILE cc_start: 0.8214 (tp) cc_final: 0.7924 (tp) REVERT: D 229 MET cc_start: 0.8551 (tpp) cc_final: 0.8299 (tpp) REVERT: D 273 LEU cc_start: 0.7980 (tp) cc_final: 0.7283 (pt) REVERT: D 388 ILE cc_start: 0.8587 (mm) cc_final: 0.8303 (mm) REVERT: D 427 MET cc_start: 0.7375 (mpp) cc_final: 0.6964 (mtm) REVERT: D 481 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6998 (tt0) REVERT: D 534 MET cc_start: 0.8091 (mmm) cc_final: 0.7709 (mmm) REVERT: D 572 SER cc_start: 0.6326 (t) cc_final: 0.5582 (t) REVERT: D 897 TRP cc_start: 0.7248 (t-100) cc_final: 0.6584 (t60) outliers start: 3 outliers final: 1 residues processed: 360 average time/residue: 0.1500 time to fit residues: 84.2482 Evaluate side-chains 259 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 258 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 10 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 157 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 GLN A 120 ASN A 167 ASN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 ASN ** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 GLN B 501 HIS ** B 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 864 ASN C 121 GLN ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 ASN D 642 ASN D 676 ASN ** D 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 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 = 0.4108 r_free = 0.4108 target = 0.142234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.116360 restraints weight = 55854.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.115120 restraints weight = 59720.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.116005 restraints weight = 58624.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.116511 restraints weight = 41609.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.116692 restraints weight = 38698.441| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.9661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 22246 Z= 0.303 Angle : 0.869 17.470 30178 Z= 0.462 Chirality : 0.053 0.249 3112 Planarity : 0.006 0.066 3968 Dihedral : 6.220 30.728 3014 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.32 % Favored : 95.61 % Rotamer: Outliers : 0.09 % Allowed : 4.18 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.15), residues: 2710 helix: -0.79 (0.18), residues: 656 sheet: 0.38 (0.18), residues: 724 loop : -0.94 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 100 TYR 0.030 0.003 TYR B 658 PHE 0.039 0.003 PHE A 178 TRP 0.030 0.003 TRP B 599 HIS 0.016 0.003 HIS B 799 Details of bonding type rmsd covalent geometry : bond 0.00674 (22242) covalent geometry : angle 0.85856 (30170) SS BOND : bond 0.03964 ( 4) SS BOND : angle 8.20192 ( 8) hydrogen bonds : bond 0.06231 ( 1060) hydrogen bonds : angle 5.98771 ( 2904) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 349 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.3862 (ttm) cc_final: 0.3303 (mmp) REVERT: A 116 TYR cc_start: 0.6931 (t80) cc_final: 0.6468 (t80) REVERT: A 203 TYR cc_start: 0.7213 (t80) cc_final: 0.6823 (t80) REVERT: A 325 TYR cc_start: 0.7613 (p90) cc_final: 0.7131 (p90) REVERT: A 445 MET cc_start: 0.7182 (tmm) cc_final: 0.6964 (tmm) REVERT: B 250 GLU cc_start: 0.7288 (tp30) cc_final: 0.6712 (mp0) REVERT: B 516 ASP cc_start: 0.7969 (m-30) cc_final: 0.7751 (m-30) REVERT: B 741 MET cc_start: 0.4695 (tpt) cc_final: 0.4477 (tpt) REVERT: C 88 ASN cc_start: 0.7882 (t0) cc_final: 0.7630 (t0) REVERT: C 325 TYR cc_start: 0.7658 (p90) cc_final: 0.7253 (p90) REVERT: D 273 LEU cc_start: 0.8114 (tp) cc_final: 0.7477 (pt) REVERT: D 388 ILE cc_start: 0.8766 (mm) cc_final: 0.8426 (mm) REVERT: D 502 ARG cc_start: 0.6424 (tmm160) cc_final: 0.6014 (tmm160) REVERT: D 876 MET cc_start: 0.7671 (mpp) cc_final: 0.7435 (mpp) REVERT: D 929 ARG cc_start: 0.6901 (ttt180) cc_final: 0.4839 (tpm170) outliers start: 2 outliers final: 0 residues processed: 351 average time/residue: 0.1448 time to fit residues: 79.3416 Evaluate side-chains 250 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 84 optimal weight: 9.9990 chunk 228 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 191 optimal weight: 0.0000 chunk 181 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 244 optimal weight: 40.0000 overall best weight: 2.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS B 642 ASN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 ASN C 420 GLN ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 512 ASN ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.141282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.119373 restraints weight = 53883.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.117961 restraints weight = 82801.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.118783 restraints weight = 77469.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.119116 restraints weight = 52892.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.119428 restraints weight = 49384.069| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 1.0311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 22246 Z= 0.216 Angle : 0.729 14.457 30178 Z= 0.389 Chirality : 0.048 0.234 3112 Planarity : 0.005 0.049 3968 Dihedral : 5.755 31.981 3014 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.36 % Favored : 96.57 % Rotamer: Outliers : 0.04 % Allowed : 2.14 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.16), residues: 2710 helix: -0.34 (0.20), residues: 632 sheet: 0.37 (0.18), residues: 734 loop : -0.85 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 437 TYR 0.034 0.002 TYR A 203 PHE 0.022 0.002 PHE A 485 TRP 0.024 0.002 TRP D 599 HIS 0.010 0.002 HIS B 799 Details of bonding type rmsd covalent geometry : bond 0.00489 (22242) covalent geometry : angle 0.71935 (30170) SS BOND : bond 0.02162 ( 4) SS BOND : angle 7.42128 ( 8) hydrogen bonds : bond 0.05056 ( 1060) hydrogen bonds : angle 5.62962 ( 2904) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 0.839 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: A 116 TYR cc_start: 0.7142 (t80) cc_final: 0.6783 (t80) REVERT: A 325 TYR cc_start: 0.6896 (p90) cc_final: 0.6505 (p90) REVERT: A 445 MET cc_start: 0.7625 (tmm) cc_final: 0.7342 (tmm) REVERT: B 529 LEU cc_start: 0.8095 (mt) cc_final: 0.7499 (pt) REVERT: B 722 MET cc_start: 0.7974 (mtt) cc_final: 0.7746 (mtm) REVERT: B 897 TRP cc_start: 0.7382 (t-100) cc_final: 0.7090 (t60) REVERT: D 273 LEU cc_start: 0.7845 (tp) cc_final: 0.7268 (pt) REVERT: D 529 LEU cc_start: 0.8445 (mm) cc_final: 0.7642 (pt) REVERT: D 722 MET cc_start: 0.7585 (mtt) cc_final: 0.7235 (mtm) REVERT: D 741 MET cc_start: 0.5928 (tpt) cc_final: 0.5624 (tpt) REVERT: D 929 ARG cc_start: 0.6813 (ttt180) cc_final: 0.5516 (tpm170) outliers start: 1 outliers final: 1 residues processed: 311 average time/residue: 0.1544 time to fit residues: 75.2594 Evaluate side-chains 236 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 247 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 264 optimal weight: 20.0000 chunk 234 optimal weight: 0.0970 chunk 226 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN A 263 ASN A 401 ASN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 GLN ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 480 GLN ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 955 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.142469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.120229 restraints weight = 53901.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.118522 restraints weight = 78006.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.119663 restraints weight = 65407.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.120051 restraints weight = 49042.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.120277 restraints weight = 45450.706| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 1.0626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 22246 Z= 0.163 Angle : 0.671 14.345 30178 Z= 0.355 Chirality : 0.046 0.230 3112 Planarity : 0.004 0.061 3968 Dihedral : 5.438 34.850 3014 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.43 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.16), residues: 2710 helix: -0.01 (0.20), residues: 636 sheet: 0.36 (0.18), residues: 728 loop : -0.77 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 772 TYR 0.033 0.002 TYR C 203 PHE 0.034 0.002 PHE C 178 TRP 0.023 0.002 TRP B 599 HIS 0.005 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00377 (22242) covalent geometry : angle 0.65791 (30170) SS BOND : bond 0.02102 ( 4) SS BOND : angle 8.19918 ( 8) hydrogen bonds : bond 0.04521 ( 1060) hydrogen bonds : angle 5.38384 ( 2904) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.806 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: A 325 TYR cc_start: 0.7086 (p90) cc_final: 0.6728 (p90) REVERT: A 445 MET cc_start: 0.7701 (tmm) cc_final: 0.7421 (tmm) REVERT: A 481 ARG cc_start: 0.7481 (tpt170) cc_final: 0.7217 (tpt170) REVERT: B 427 MET cc_start: 0.7900 (mtm) cc_final: 0.7318 (ttp) REVERT: B 529 LEU cc_start: 0.8029 (mt) cc_final: 0.7386 (pt) REVERT: B 599 TRP cc_start: 0.4020 (t-100) cc_final: 0.3641 (t-100) REVERT: B 897 TRP cc_start: 0.7357 (t-100) cc_final: 0.7139 (t60) REVERT: D 273 LEU cc_start: 0.7946 (tp) cc_final: 0.7285 (pt) REVERT: D 502 ARG cc_start: 0.6064 (tmm160) cc_final: 0.5022 (tmm160) REVERT: D 529 LEU cc_start: 0.8343 (mm) cc_final: 0.7535 (pt) REVERT: D 722 MET cc_start: 0.7619 (mtt) cc_final: 0.7295 (mtm) REVERT: D 905 LEU cc_start: 0.8268 (mp) cc_final: 0.8009 (mt) REVERT: D 929 ARG cc_start: 0.7271 (ttt180) cc_final: 0.6465 (ttt90) REVERT: D 976 TYR cc_start: 0.6638 (p90) cc_final: 0.6351 (p90) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.1419 time to fit residues: 69.7560 Evaluate side-chains 234 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 98 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 230 optimal weight: 6.9990 chunk 95 optimal weight: 30.0000 chunk 212 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 825 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.141628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.118526 restraints weight = 53662.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.116691 restraints weight = 72627.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.118100 restraints weight = 68601.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.118236 restraints weight = 47871.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.119212 restraints weight = 44326.406| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 1.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 22246 Z= 0.155 Angle : 0.655 15.177 30178 Z= 0.347 Chirality : 0.046 0.220 3112 Planarity : 0.004 0.091 3968 Dihedral : 5.263 37.732 3014 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.36 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.16), residues: 2710 helix: 0.19 (0.20), residues: 630 sheet: 0.27 (0.18), residues: 744 loop : -0.69 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 481 TYR 0.031 0.002 TYR C 203 PHE 0.020 0.002 PHE A 485 TRP 0.020 0.002 TRP B 599 HIS 0.005 0.001 HIS B 799 Details of bonding type rmsd covalent geometry : bond 0.00352 (22242) covalent geometry : angle 0.64370 (30170) SS BOND : bond 0.02501 ( 4) SS BOND : angle 7.60997 ( 8) hydrogen bonds : bond 0.04305 ( 1060) hydrogen bonds : angle 5.28144 ( 2904) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.748 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: A 325 TYR cc_start: 0.7251 (p90) cc_final: 0.6852 (p90) REVERT: A 445 MET cc_start: 0.7855 (tmm) cc_final: 0.7504 (tmm) REVERT: B 529 LEU cc_start: 0.8031 (mt) cc_final: 0.7379 (pt) REVERT: B 688 THR cc_start: 0.7868 (m) cc_final: 0.7229 (t) REVERT: B 722 MET cc_start: 0.7859 (mtm) cc_final: 0.7544 (mtm) REVERT: B 970 MET cc_start: 0.5909 (ppp) cc_final: 0.5571 (ppp) REVERT: D 273 LEU cc_start: 0.8005 (tp) cc_final: 0.7354 (pt) REVERT: D 388 ILE cc_start: 0.8617 (mm) cc_final: 0.8388 (mm) REVERT: D 502 ARG cc_start: 0.6251 (tmm160) cc_final: 0.5168 (tmm160) REVERT: D 722 MET cc_start: 0.7788 (mtt) cc_final: 0.7464 (mtm) REVERT: D 878 TRP cc_start: 0.7015 (m100) cc_final: 0.6581 (m100) REVERT: D 929 ARG cc_start: 0.7339 (ttt180) cc_final: 0.6811 (ttt90) REVERT: D 939 SER cc_start: 0.6552 (p) cc_final: 0.6165 (t) REVERT: D 976 TYR cc_start: 0.6970 (p90) cc_final: 0.6741 (p90) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.1363 time to fit residues: 66.1094 Evaluate side-chains 234 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 135 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 252 optimal weight: 6.9990 chunk 49 optimal weight: 0.0370 chunk 241 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 237 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 overall best weight: 2.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 382 ASN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 ASN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 GLN C 382 ASN ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 825 GLN D 955 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.137628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.114475 restraints weight = 55520.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.113752 restraints weight = 84454.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.114711 restraints weight = 76226.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.115491 restraints weight = 52290.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.115767 restraints weight = 48286.098| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 1.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.170 22246 Z= 0.222 Angle : 0.757 19.987 30178 Z= 0.398 Chirality : 0.048 0.248 3112 Planarity : 0.005 0.066 3968 Dihedral : 5.633 37.700 3014 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.16), residues: 2710 helix: 0.09 (0.20), residues: 630 sheet: 0.24 (0.18), residues: 734 loop : -0.85 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 481 TYR 0.045 0.002 TYR B 712 PHE 0.027 0.002 PHE C 178 TRP 0.021 0.002 TRP B 599 HIS 0.009 0.002 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00509 (22242) covalent geometry : angle 0.73592 (30170) SS BOND : bond 0.03096 ( 4) SS BOND : angle 10.85499 ( 8) hydrogen bonds : bond 0.05045 ( 1060) hydrogen bonds : angle 5.49851 ( 2904) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.800 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: A 325 TYR cc_start: 0.7130 (p90) cc_final: 0.6722 (p90) REVERT: A 445 MET cc_start: 0.7799 (tmm) cc_final: 0.7477 (tmm) REVERT: A 454 TYR cc_start: 0.3498 (m-80) cc_final: 0.2585 (m-80) REVERT: B 529 LEU cc_start: 0.8162 (mt) cc_final: 0.7452 (pt) REVERT: B 970 MET cc_start: 0.6157 (ppp) cc_final: 0.5705 (ppp) REVERT: C 325 TYR cc_start: 0.7284 (p90) cc_final: 0.7015 (p90) REVERT: D 273 LEU cc_start: 0.8234 (tp) cc_final: 0.7596 (pt) REVERT: D 502 ARG cc_start: 0.6377 (tmm160) cc_final: 0.5304 (tmm160) REVERT: D 529 LEU cc_start: 0.8273 (mm) cc_final: 0.7449 (pp) REVERT: D 599 TRP cc_start: 0.3823 (t-100) cc_final: 0.2745 (t-100) REVERT: D 905 LEU cc_start: 0.8706 (mt) cc_final: 0.8496 (mt) REVERT: D 929 ARG cc_start: 0.7581 (ttt180) cc_final: 0.7035 (ptt90) REVERT: D 976 TYR cc_start: 0.7195 (p90) cc_final: 0.6696 (p90) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.1452 time to fit residues: 68.9446 Evaluate side-chains 226 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 99 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 249 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 256 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 268 optimal weight: 0.1980 chunk 247 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 ASN ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 ASN ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 744 GLN ** D 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 825 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.139834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.117663 restraints weight = 54245.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.117330 restraints weight = 81018.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.118140 restraints weight = 70266.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.118640 restraints weight = 48652.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.119082 restraints weight = 44063.701| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 1.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 22246 Z= 0.152 Angle : 0.683 16.099 30178 Z= 0.360 Chirality : 0.046 0.253 3112 Planarity : 0.004 0.073 3968 Dihedral : 5.337 37.959 3014 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.14 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.16), residues: 2710 helix: 0.24 (0.20), residues: 636 sheet: 0.13 (0.18), residues: 752 loop : -0.77 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 481 TYR 0.032 0.001 TYR B 712 PHE 0.030 0.002 PHE A 485 TRP 0.044 0.002 TRP A 366 HIS 0.004 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00343 (22242) covalent geometry : angle 0.66831 (30170) SS BOND : bond 0.03265 ( 4) SS BOND : angle 8.75374 ( 8) hydrogen bonds : bond 0.04260 ( 1060) hydrogen bonds : angle 5.27429 ( 2904) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5420 Ramachandran restraints generated. 2710 Oldfield, 0 Emsley, 2710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.821 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 325 TYR cc_start: 0.6773 (p90) cc_final: 0.6502 (p90) REVERT: A 454 TYR cc_start: 0.3181 (m-80) cc_final: 0.2380 (m-80) REVERT: B 229 MET cc_start: 0.8253 (tpp) cc_final: 0.8017 (tpp) REVERT: B 273 LEU cc_start: 0.7633 (tp) cc_final: 0.7002 (pt) REVERT: B 445 SER cc_start: 0.6423 (t) cc_final: 0.5229 (m) REVERT: B 529 LEU cc_start: 0.8043 (mt) cc_final: 0.7375 (pt) REVERT: B 629 GLU cc_start: 0.7630 (tt0) cc_final: 0.7353 (mt-10) REVERT: D 388 ILE cc_start: 0.8651 (mm) cc_final: 0.8407 (mm) REVERT: D 502 ARG cc_start: 0.6072 (tmm160) cc_final: 0.5143 (tmm160) REVERT: D 529 LEU cc_start: 0.8239 (mm) cc_final: 0.7511 (pp) REVERT: D 599 TRP cc_start: 0.3509 (t-100) cc_final: 0.2711 (t-100) REVERT: D 775 ILE cc_start: 0.5604 (mp) cc_final: 0.4780 (tt) REVERT: D 853 TYR cc_start: 0.5741 (t80) cc_final: 0.5334 (t80) REVERT: D 905 LEU cc_start: 0.8655 (mt) cc_final: 0.8451 (mt) REVERT: D 929 ARG cc_start: 0.7338 (ttt180) cc_final: 0.6425 (ttt90) REVERT: D 976 TYR cc_start: 0.7045 (p90) cc_final: 0.6585 (p90) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.1394 time to fit residues: 68.2929 Evaluate side-chains 235 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 194 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 241 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 239 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 252 optimal weight: 0.9990 chunk 59 optimal weight: 0.0050 chunk 262 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 189 GLN A 470 GLN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 ASN ** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 GLN B 901 ASN C 134 HIS ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 825 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.137343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.113239 restraints weight = 53880.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.112835 restraints weight = 84248.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.113734 restraints weight = 76759.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.114250 restraints weight = 52803.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.114788 restraints weight = 47589.644| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 1.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 22246 Z= 0.183 Angle : 0.708 14.314 30178 Z= 0.373 Chirality : 0.047 0.232 3112 Planarity : 0.005 0.066 3968 Dihedral : 5.400 37.364 3014 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.39 % Favored : 95.54 % Rotamer: Outliers : 0.13 % Allowed : 0.39 % Favored : 99.48 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.16), residues: 2710 helix: 0.26 (0.21), residues: 632 sheet: 0.26 (0.18), residues: 734 loop : -0.83 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 772 TYR 0.031 0.002 TYR B 712 PHE 0.026 0.002 PHE A 178 TRP 0.031 0.002 TRP A 366 HIS 0.007 0.002 HIS B 799 Details of bonding type rmsd covalent geometry : bond 0.00416 (22242) covalent geometry : angle 0.69637 (30170) SS BOND : bond 0.02841 ( 4) SS BOND : angle 8.03938 ( 8) hydrogen bonds : bond 0.04546 ( 1060) hydrogen bonds : angle 5.30533 ( 2904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3180.09 seconds wall clock time: 56 minutes 27.87 seconds (3387.87 seconds total)