Starting phenix.real_space_refine on Sun Aug 24 11:29:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eyy_28724/08_2025/8eyy_28724_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eyy_28724/08_2025/8eyy_28724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eyy_28724/08_2025/8eyy_28724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eyy_28724/08_2025/8eyy_28724.map" model { file = "/net/cci-nas-00/data/ceres_data/8eyy_28724/08_2025/8eyy_28724_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eyy_28724/08_2025/8eyy_28724_neut.cif" } resolution = 4.9 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= 0.003 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 6340 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 114 5.16 5 C 9083 2.51 5 N 2446 2.21 5 O 2658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14301 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 6284 Classifications: {'peptide': 775} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 732} Chain breaks: 6 Chain: "B" Number of atoms: 6540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 810, 6540 Classifications: {'peptide': 810} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 764} Chain breaks: 5 Chain: "C" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 370 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain breaks: 1 Chain: "D" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 361 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain breaks: 1 Chain: "E" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "F" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 370 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain breaks: 1 Time building chain proxies: 3.66, per 1000 atoms: 0.26 Number of scatterers: 14301 At special positions: 0 Unit cell: (141.48, 140.4, 178.2, 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 114 16.00 O 2658 8.00 N 2446 7.00 C 9083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 862 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 797 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 862 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 797 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 62 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 66 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 66 " distance=2.03 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 62 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 75 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 66 " distance=2.03 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS F 62 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 75 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 66 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 806.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3338 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 34 sheets defined 17.9% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.583A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 48 removed outlier: 4.120A pdb=" N ASP A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 132 through 137 removed outlier: 3.885A pdb=" N ILE A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.562A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N CYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.936A pdb=" N LEU A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 Processing helix chain 'A' and resid 435 through 446 removed outlier: 3.573A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 691 through 716 removed outlier: 3.746A pdb=" N TYR A 710 " --> pdb=" O THR A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'B' and resid 18 through 24 removed outlier: 3.592A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 48 removed outlier: 3.687A pdb=" N PHE B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 removed outlier: 3.713A pdb=" N ILE B 136 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.853A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.579A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.918A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 640 through 645 removed outlier: 4.037A pdb=" N PHE B 644 " --> pdb=" O ASP B 640 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 645 " --> pdb=" O SER B 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 640 through 645' Processing helix chain 'B' and resid 706 through 716 Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.805A pdb=" N ASP B 814 " --> pdb=" O ALA B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.769A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 71 through 75 Processing helix chain 'D' and resid 7 through 19 Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 67 through 72 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'E' and resid 7 through 19 Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 67 through 73 removed outlier: 3.573A pdb=" N LEU E 71 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 19 Processing helix chain 'F' and resid 71 through 75 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 14 removed outlier: 5.652A pdb=" N HIS A 32 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET A 11 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 82 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 14 removed outlier: 5.652A pdb=" N HIS A 32 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET A 11 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 64 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N MET A 98 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ARG A 65 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N SER A 116 " --> pdb=" O TYR A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 295 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 312 removed outlier: 3.554A pdb=" N ILE A 364 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 318 through 321 removed outlier: 6.507A pdb=" N LEU A 340 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ARG A 371 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ILE A 342 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS A 425 " --> pdb=" O TYR A 398 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 471 through 472 removed outlier: 6.194A pdb=" N GLU A 471 " --> pdb=" O LYS A 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 475 through 479 Processing sheet with id=AB2, first strand: chain 'A' and resid 500 through 509 removed outlier: 5.793A pdb=" N LEU A 571 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE A 503 " --> pdb=" O LYS A 569 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LYS A 569 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU A 505 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE A 567 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TYR A 507 " --> pdb=" O ALA A 565 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA A 565 " --> pdb=" O TYR A 507 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N GLU A 509 " --> pdb=" O GLN A 563 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLN A 563 " --> pdb=" O GLU A 509 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 601 through 607 removed outlier: 6.566A pdb=" N LYS A 616 " --> pdb=" O PRO A 603 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER A 605 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 614 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 761 through 764 removed outlier: 6.598A pdb=" N ARG A 796 " --> pdb=" O ASN A 789 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 761 through 764 removed outlier: 3.568A pdb=" N ALA A 805 " --> pdb=" O TYR A 781 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 817 through 824 removed outlier: 4.637A pdb=" N GLN A 835 " --> pdb=" O PRO A 819 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 859 through 864 removed outlier: 5.456A pdb=" N VAL A 888 " --> pdb=" O TRP A 899 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TRP A 899 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ALA A 890 " --> pdb=" O GLY A 897 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 859 through 864 Processing sheet with id=AB9, first strand: chain 'B' and resid 12 through 14 removed outlier: 5.918A pdb=" N ILE B 13 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N MET B 38 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU B 33 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N PHE B 64 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE B 35 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL B 66 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU B 37 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N MET B 98 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ARG B 65 " --> pdb=" O MET B 98 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU B 97 " --> pdb=" O ASN B 122 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 121 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN B 148 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AC2, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AC3, first strand: chain 'B' and resid 182 through 184 removed outlier: 6.491A pdb=" N HIS B 187 " --> pdb=" O TRP B 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 231 through 233 Processing sheet with id=AC5, first strand: chain 'B' and resid 245 through 248 Processing sheet with id=AC6, first strand: chain 'B' and resid 278 through 280 Processing sheet with id=AC7, first strand: chain 'B' and resid 292 through 294 Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 312 removed outlier: 3.793A pdb=" N ILE B 364 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 318 through 321 removed outlier: 7.517A pdb=" N PHE B 427 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYR B 401 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N HIS B 429 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU B 403 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AD2, first strand: chain 'B' and resid 475 through 480 removed outlier: 6.343A pdb=" N ARG B 488 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE B 478 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU B 486 " --> pdb=" O ILE B 478 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 530 through 534 Processing sheet with id=AD4, first strand: chain 'B' and resid 601 through 607 removed outlier: 5.414A pdb=" N ASP B 602 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS B 618 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 761 through 764 removed outlier: 3.938A pdb=" N GLY B 780 " --> pdb=" O GLN B 637 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 817 through 824 removed outlier: 4.416A pdb=" N GLN B 835 " --> pdb=" O PRO B 819 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 859 through 864 394 hydrogen bonds defined for protein. 1011 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4673 1.34 - 1.46: 2939 1.46 - 1.58: 6894 1.58 - 1.70: 1 1.70 - 1.81: 138 Bond restraints: 14645 Sorted by residual: bond pdb=" CB PRO B 548 " pdb=" CG PRO B 548 " ideal model delta sigma weight residual 1.492 1.581 -0.089 5.00e-02 4.00e+02 3.15e+00 bond pdb=" CA TYR A 144 " pdb=" C TYR A 144 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.21e-02 6.83e+03 1.77e+00 bond pdb=" C TYR A 144 " pdb=" O TYR A 144 " ideal model delta sigma weight residual 1.234 1.221 0.013 1.14e-02 7.69e+03 1.22e+00 bond pdb=" CA ASN A 90 " pdb=" CB ASN A 90 " ideal model delta sigma weight residual 1.532 1.549 -0.017 1.56e-02 4.11e+03 1.18e+00 bond pdb=" C ASP A 602 " pdb=" O ASP A 602 " ideal model delta sigma weight residual 1.235 1.240 -0.005 4.70e-03 4.53e+04 1.15e+00 ... (remaining 14640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 19435 1.71 - 3.42: 352 3.42 - 5.14: 45 5.14 - 6.85: 6 6.85 - 8.56: 6 Bond angle restraints: 19844 Sorted by residual: angle pdb=" C THR B 580 " pdb=" N TYR B 581 " pdb=" CA TYR B 581 " ideal model delta sigma weight residual 121.54 129.60 -8.06 1.91e+00 2.74e-01 1.78e+01 angle pdb=" N PRO B 548 " pdb=" CA PRO B 548 " pdb=" C PRO B 548 " ideal model delta sigma weight residual 112.47 119.88 -7.41 2.06e+00 2.36e-01 1.29e+01 angle pdb=" CA PRO B 548 " pdb=" N PRO B 548 " pdb=" CD PRO B 548 " ideal model delta sigma weight residual 112.00 107.99 4.01 1.40e+00 5.10e-01 8.22e+00 angle pdb=" N GLU A 700 " pdb=" CA GLU A 700 " pdb=" CB GLU A 700 " ideal model delta sigma weight residual 110.28 114.72 -4.44 1.55e+00 4.16e-01 8.20e+00 angle pdb=" C LEU D 71 " pdb=" N GLU D 72 " pdb=" CA GLU D 72 " ideal model delta sigma weight residual 121.18 115.78 5.40 1.98e+00 2.55e-01 7.44e+00 ... (remaining 19839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 8057 17.49 - 34.99: 658 34.99 - 52.48: 106 52.48 - 69.98: 27 69.98 - 87.47: 17 Dihedral angle restraints: 8865 sinusoidal: 3692 harmonic: 5173 Sorted by residual: dihedral pdb=" CB CYS B 649 " pdb=" SG CYS B 649 " pdb=" SG CYS B 862 " pdb=" CB CYS B 862 " ideal model delta sinusoidal sigma weight residual -86.00 -173.47 87.47 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 274 " pdb=" CB CYS A 274 " ideal model delta sinusoidal sigma weight residual -86.00 -161.70 75.70 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CB CYS B 266 " pdb=" SG CYS B 266 " pdb=" SG CYS B 274 " pdb=" CB CYS B 274 " ideal model delta sinusoidal sigma weight residual 93.00 159.21 -66.21 1 1.00e+01 1.00e-02 5.73e+01 ... (remaining 8862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1704 0.049 - 0.099: 341 0.099 - 0.148: 102 0.148 - 0.198: 5 0.198 - 0.247: 1 Chirality restraints: 2153 Sorted by residual: chirality pdb=" CA PRO B 548 " pdb=" N PRO B 548 " pdb=" C PRO B 548 " pdb=" CB PRO B 548 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA ILE A 566 " pdb=" N ILE A 566 " pdb=" C ILE A 566 " pdb=" CB ILE A 566 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" CB ILE A 370 " pdb=" CA ILE A 370 " pdb=" CG1 ILE A 370 " pdb=" CG2 ILE A 370 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 2150 not shown) Planarity restraints: 2565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 547 " -0.085 5.00e-02 4.00e+02 1.28e-01 2.61e+01 pdb=" N PRO B 548 " 0.221 5.00e-02 4.00e+02 pdb=" CA PRO B 548 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO B 548 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 550 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO A 551 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 551 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 551 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 580 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C THR B 580 " -0.033 2.00e-02 2.50e+03 pdb=" O THR B 580 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR B 581 " 0.011 2.00e-02 2.50e+03 ... (remaining 2562 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 687 2.71 - 3.26: 15466 3.26 - 3.81: 25556 3.81 - 4.35: 32486 4.35 - 4.90: 50400 Nonbonded interactions: 124595 Sorted by model distance: nonbonded pdb=" OE1 GLU B 836 " pdb=" OH TYR B 847 " model vdw 2.165 3.040 nonbonded pdb=" NH1 ARG B 853 " pdb=" O PRO B 881 " model vdw 2.177 3.120 nonbonded pdb=" OG SER E 67 " pdb=" OE1 GLN E 70 " model vdw 2.184 3.040 nonbonded pdb=" O THR B 547 " pdb=" N SER B 549 " model vdw 2.193 3.120 nonbonded pdb=" O LEU B 87 " pdb=" OG1 THR B 325 " model vdw 2.194 3.040 ... (remaining 124590 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 518 or resid 527 through 542 or resid 547 throug \ h 658 or resid 705 through 908)) selection = (chain 'B' and (resid 5 through 151 or resid 198 through 201 or resid 208 throug \ h 518 or resid 527 through 908)) } ncs_group { reference = (chain 'C' and (resid 4 through 28 or resid 56 through 76)) selection = chain 'D' selection = (chain 'E' and resid 4 through 76) selection = (chain 'F' and (resid 4 through 28 or resid 56 through 76)) } 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=0.00 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: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.400 Find NCS groups from input model: 0.250 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: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 : 0.003 0.089 14684 Z= 0.119 Angle : 0.583 8.559 19922 Z= 0.310 Chirality : 0.044 0.247 2153 Planarity : 0.004 0.128 2565 Dihedral : 12.979 82.750 5410 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.16 % Favored : 92.61 % Rotamer: Outliers : 0.06 % Allowed : 0.37 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.21), residues: 1731 helix: -0.31 (0.34), residues: 239 sheet: -0.85 (0.27), residues: 362 loop : -0.82 (0.20), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 479 TYR 0.012 0.001 TYR E 16 PHE 0.015 0.001 PHE A 703 TRP 0.016 0.001 TRP A 414 HIS 0.005 0.001 HIS B 386 Details of bonding type rmsd covalent geometry : bond 0.00257 (14645) covalent geometry : angle 0.58152 (19844) SS BOND : bond 0.00193 ( 39) SS BOND : angle 0.82063 ( 78) hydrogen bonds : bond 0.17873 ( 365) hydrogen bonds : angle 8.44046 ( 1011) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 LEU cc_start: 0.8598 (mt) cc_final: 0.8392 (mt) REVERT: A 504 MET cc_start: 0.7752 (tpt) cc_final: 0.7438 (tpt) REVERT: A 555 MET cc_start: 0.9449 (mmp) cc_final: 0.9105 (mmp) REVERT: B 11 MET cc_start: 0.8731 (ppp) cc_final: 0.8237 (ppp) REVERT: B 38 MET cc_start: 0.9406 (mmp) cc_final: 0.9198 (mmm) REVERT: B 62 LEU cc_start: 0.9678 (tp) cc_final: 0.9442 (tp) REVERT: B 98 MET cc_start: 0.8915 (mmp) cc_final: 0.8497 (mmm) REVERT: B 110 MET cc_start: 0.9241 (mmp) cc_final: 0.8880 (mmm) REVERT: F 6 LEU cc_start: 0.9412 (mm) cc_final: 0.9156 (pt) outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.0788 time to fit residues: 9.0704 Evaluate side-chains 49 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 GLN A 860 HIS C 60 GLN F 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.029315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.019028 restraints weight = 224658.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.019833 restraints weight = 135693.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.020382 restraints weight = 95863.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.020756 restraints weight = 74782.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.021012 restraints weight = 62603.346| |-----------------------------------------------------------------------------| r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 14684 Z= 0.121 Angle : 0.566 9.885 19922 Z= 0.296 Chirality : 0.044 0.284 2153 Planarity : 0.005 0.133 2565 Dihedral : 4.948 28.486 1933 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.16 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.21), residues: 1731 helix: -0.14 (0.34), residues: 237 sheet: -0.72 (0.26), residues: 374 loop : -0.77 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 479 TYR 0.018 0.001 TYR B 144 PHE 0.013 0.001 PHE A 703 TRP 0.012 0.001 TRP A 899 HIS 0.007 0.001 HIS A 386 Details of bonding type rmsd covalent geometry : bond 0.00270 (14645) covalent geometry : angle 0.56535 (19844) SS BOND : bond 0.00214 ( 39) SS BOND : angle 0.65481 ( 78) hydrogen bonds : bond 0.03918 ( 365) hydrogen bonds : angle 7.10708 ( 1011) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9273 (mmp) cc_final: 0.8955 (mmm) REVERT: A 504 MET cc_start: 0.7571 (tpt) cc_final: 0.7237 (tpt) REVERT: A 555 MET cc_start: 0.9443 (mmp) cc_final: 0.9131 (mmp) REVERT: B 98 MET cc_start: 0.9064 (mmp) cc_final: 0.8751 (mmm) REVERT: B 110 MET cc_start: 0.9029 (mmp) cc_final: 0.8643 (mmm) REVERT: B 300 MET cc_start: 0.9127 (mmp) cc_final: 0.8918 (mmm) REVERT: E 15 LEU cc_start: 0.9676 (tp) cc_final: 0.9386 (tp) REVERT: F 6 LEU cc_start: 0.9550 (mm) cc_final: 0.9212 (pt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0974 time to fit residues: 10.3305 Evaluate side-chains 47 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 64 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 75 optimal weight: 20.0000 chunk 137 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 GLN C 60 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.028484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.018632 restraints weight = 239209.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.019353 restraints weight = 148519.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.019853 restraints weight = 106869.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.020201 restraints weight = 84360.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.020389 restraints weight = 71040.802| |-----------------------------------------------------------------------------| r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 14684 Z= 0.206 Angle : 0.623 10.164 19922 Z= 0.323 Chirality : 0.043 0.286 2153 Planarity : 0.005 0.135 2565 Dihedral : 5.128 27.686 1933 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 21.90 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.86 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.21), residues: 1731 helix: -0.25 (0.33), residues: 236 sheet: -0.94 (0.26), residues: 353 loop : -0.81 (0.20), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 479 TYR 0.026 0.002 TYR B 847 PHE 0.017 0.002 PHE A 400 TRP 0.019 0.002 TRP A 414 HIS 0.006 0.001 HIS A 386 Details of bonding type rmsd covalent geometry : bond 0.00432 (14645) covalent geometry : angle 0.62204 (19844) SS BOND : bond 0.00290 ( 39) SS BOND : angle 0.76647 ( 78) hydrogen bonds : bond 0.04111 ( 365) hydrogen bonds : angle 7.14697 ( 1011) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9287 (mmp) cc_final: 0.8995 (mmm) REVERT: A 504 MET cc_start: 0.7457 (tpt) cc_final: 0.7195 (tpt) REVERT: A 555 MET cc_start: 0.9498 (mmp) cc_final: 0.9107 (mmm) REVERT: B 11 MET cc_start: 0.8763 (ppp) cc_final: 0.8525 (ppp) REVERT: B 62 LEU cc_start: 0.9629 (tp) cc_final: 0.9406 (tp) REVERT: B 94 VAL cc_start: 0.9419 (p) cc_final: 0.9175 (p) REVERT: B 98 MET cc_start: 0.9188 (mmp) cc_final: 0.8813 (mmm) REVERT: E 15 LEU cc_start: 0.9679 (tp) cc_final: 0.9390 (tp) REVERT: F 6 LEU cc_start: 0.9568 (mm) cc_final: 0.9224 (pt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1098 time to fit residues: 9.4927 Evaluate side-chains 42 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 14 optimal weight: 0.0670 chunk 12 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 117 optimal weight: 0.4980 chunk 61 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 overall best weight: 2.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN D 60 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.028889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.018818 restraints weight = 233197.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.019593 restraints weight = 142531.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.020103 restraints weight = 101486.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.020445 restraints weight = 79819.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.020692 restraints weight = 67538.684| |-----------------------------------------------------------------------------| r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 14684 Z= 0.152 Angle : 0.577 10.612 19922 Z= 0.301 Chirality : 0.043 0.282 2153 Planarity : 0.005 0.137 2565 Dihedral : 5.061 28.094 1933 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.51 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.21), residues: 1731 helix: -0.21 (0.34), residues: 236 sheet: -0.89 (0.27), residues: 346 loop : -0.85 (0.20), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 479 TYR 0.018 0.001 TYR B 847 PHE 0.014 0.001 PHE A 703 TRP 0.015 0.001 TRP A 414 HIS 0.008 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00329 (14645) covalent geometry : angle 0.57504 (19844) SS BOND : bond 0.00309 ( 39) SS BOND : angle 0.89845 ( 78) hydrogen bonds : bond 0.03671 ( 365) hydrogen bonds : angle 6.90724 ( 1011) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9361 (mmp) cc_final: 0.9046 (mmm) REVERT: A 504 MET cc_start: 0.7469 (tpt) cc_final: 0.7190 (tpt) REVERT: A 555 MET cc_start: 0.9437 (mmp) cc_final: 0.9175 (mmp) REVERT: B 98 MET cc_start: 0.9176 (mmp) cc_final: 0.8714 (mmm) REVERT: B 300 MET cc_start: 0.9220 (mmp) cc_final: 0.8982 (mmm) REVERT: E 15 LEU cc_start: 0.9675 (tp) cc_final: 0.9370 (tp) REVERT: F 6 LEU cc_start: 0.9600 (mm) cc_final: 0.9243 (pt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1208 time to fit residues: 10.7439 Evaluate side-chains 43 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 101 optimal weight: 0.0970 chunk 59 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 629 HIS A 831 HIS A 860 HIS ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN B 470 ASN ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN C 73 ASN D 60 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.029423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.019029 restraints weight = 217728.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.019859 restraints weight = 132274.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.020405 restraints weight = 93200.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.020791 restraints weight = 73008.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.021064 restraints weight = 60962.882| |-----------------------------------------------------------------------------| r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.098 14684 Z= 0.104 Angle : 0.540 10.825 19922 Z= 0.282 Chirality : 0.044 0.282 2153 Planarity : 0.004 0.138 2565 Dihedral : 4.826 26.119 1933 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.16 % Favored : 92.61 % Rotamer: Outliers : 0.06 % Allowed : 2.23 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.21), residues: 1731 helix: -0.16 (0.34), residues: 238 sheet: -0.73 (0.27), residues: 350 loop : -0.85 (0.20), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 479 TYR 0.015 0.001 TYR B 847 PHE 0.015 0.001 PHE A 703 TRP 0.009 0.001 TRP A 834 HIS 0.020 0.001 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00240 (14645) covalent geometry : angle 0.53931 (19844) SS BOND : bond 0.00209 ( 39) SS BOND : angle 0.71216 ( 78) hydrogen bonds : bond 0.03273 ( 365) hydrogen bonds : angle 6.52774 ( 1011) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9361 (mmp) cc_final: 0.9000 (mmm) REVERT: A 500 LEU cc_start: 0.9595 (tt) cc_final: 0.9354 (mt) REVERT: A 504 MET cc_start: 0.7491 (tpt) cc_final: 0.7171 (tpt) REVERT: A 555 MET cc_start: 0.9343 (mmp) cc_final: 0.9128 (mmp) REVERT: B 11 MET cc_start: 0.8691 (ppp) cc_final: 0.8385 (ppp) REVERT: B 62 LEU cc_start: 0.9662 (tp) cc_final: 0.9451 (tp) REVERT: B 98 MET cc_start: 0.9152 (mmp) cc_final: 0.8737 (mmm) REVERT: B 300 MET cc_start: 0.9111 (mmp) cc_final: 0.8898 (mmm) REVERT: E 15 LEU cc_start: 0.9645 (tp) cc_final: 0.9320 (tp) REVERT: F 6 LEU cc_start: 0.9575 (mm) cc_final: 0.9231 (pt) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.1055 time to fit residues: 10.9153 Evaluate side-chains 47 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 131 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 141 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 chunk 18 optimal weight: 0.0040 chunk 148 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 overall best weight: 2.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 HIS ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN D 60 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.029149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.018936 restraints weight = 225881.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.019731 restraints weight = 136795.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.020267 restraints weight = 96763.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.020644 restraints weight = 75526.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.020894 restraints weight = 63147.586| |-----------------------------------------------------------------------------| r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 14684 Z= 0.124 Angle : 0.545 11.000 19922 Z= 0.283 Chirality : 0.043 0.283 2153 Planarity : 0.004 0.140 2565 Dihedral : 4.773 27.092 1933 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.68 % Favored : 92.20 % Rotamer: Outliers : 0.06 % Allowed : 2.36 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.21), residues: 1731 helix: -0.22 (0.34), residues: 240 sheet: -0.68 (0.26), residues: 362 loop : -0.82 (0.20), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 479 TYR 0.015 0.001 TYR B 581 PHE 0.013 0.001 PHE A 703 TRP 0.016 0.001 TRP A 414 HIS 0.004 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00279 (14645) covalent geometry : angle 0.54410 (19844) SS BOND : bond 0.00221 ( 39) SS BOND : angle 0.68169 ( 78) hydrogen bonds : bond 0.03289 ( 365) hydrogen bonds : angle 6.47035 ( 1011) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9379 (mmp) cc_final: 0.9025 (mmm) REVERT: A 504 MET cc_start: 0.7477 (tpt) cc_final: 0.7170 (tpt) REVERT: A 555 MET cc_start: 0.9424 (mmp) cc_final: 0.9126 (mmm) REVERT: B 11 MET cc_start: 0.8661 (ppp) cc_final: 0.8391 (ppp) REVERT: B 98 MET cc_start: 0.9196 (mmp) cc_final: 0.8748 (mmm) REVERT: E 15 LEU cc_start: 0.9658 (tp) cc_final: 0.9341 (tp) REVERT: F 6 LEU cc_start: 0.9596 (mm) cc_final: 0.9214 (pt) outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 0.1022 time to fit residues: 9.9013 Evaluate side-chains 45 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 148 optimal weight: 8.9990 chunk 92 optimal weight: 0.1980 chunk 133 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 GLN A 527 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.028601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.018607 restraints weight = 233122.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.019353 restraints weight = 143763.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.019854 restraints weight = 102773.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.020201 restraints weight = 80929.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.020448 restraints weight = 68102.806| |-----------------------------------------------------------------------------| r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 14684 Z= 0.197 Angle : 0.616 11.164 19922 Z= 0.317 Chirality : 0.043 0.282 2153 Planarity : 0.005 0.140 2565 Dihedral : 5.013 27.236 1933 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.32 % Favored : 91.51 % Rotamer: Outliers : 0.06 % Allowed : 1.67 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.21), residues: 1731 helix: -0.26 (0.33), residues: 244 sheet: -0.81 (0.26), residues: 356 loop : -0.89 (0.20), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 578 TYR 0.028 0.002 TYR B 884 PHE 0.016 0.002 PHE A 400 TRP 0.016 0.002 TRP A 414 HIS 0.005 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00418 (14645) covalent geometry : angle 0.61397 (19844) SS BOND : bond 0.00281 ( 39) SS BOND : angle 0.98357 ( 78) hydrogen bonds : bond 0.03649 ( 365) hydrogen bonds : angle 6.66171 ( 1011) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9417 (mmp) cc_final: 0.9079 (mmm) REVERT: A 504 MET cc_start: 0.7496 (tpt) cc_final: 0.7225 (tpt) REVERT: A 555 MET cc_start: 0.9443 (mmp) cc_final: 0.9141 (mmm) REVERT: B 11 MET cc_start: 0.8711 (ppp) cc_final: 0.8268 (ppp) REVERT: B 38 MET cc_start: 0.9332 (mmp) cc_final: 0.9110 (mmm) REVERT: B 98 MET cc_start: 0.9160 (mmp) cc_final: 0.8865 (mmm) REVERT: B 300 MET cc_start: 0.9176 (mmp) cc_final: 0.8942 (mmm) REVERT: B 884 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: E 15 LEU cc_start: 0.9691 (tp) cc_final: 0.9413 (tp) REVERT: F 6 LEU cc_start: 0.9588 (mm) cc_final: 0.9234 (pt) outliers start: 1 outliers final: 0 residues processed: 53 average time/residue: 0.1090 time to fit residues: 9.5298 Evaluate side-chains 41 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 40 optimal weight: 0.1980 chunk 114 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 112 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.028931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.018814 restraints weight = 227526.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.019585 restraints weight = 140585.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.020104 restraints weight = 100262.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.020460 restraints weight = 78861.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.020707 restraints weight = 66380.831| |-----------------------------------------------------------------------------| r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 14684 Z= 0.137 Angle : 0.562 11.204 19922 Z= 0.291 Chirality : 0.043 0.279 2153 Planarity : 0.004 0.141 2565 Dihedral : 4.929 27.313 1933 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.28 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.21), residues: 1731 helix: -0.20 (0.34), residues: 240 sheet: -0.71 (0.26), residues: 356 loop : -0.89 (0.20), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 579 TYR 0.024 0.001 TYR B 884 PHE 0.013 0.001 PHE A 703 TRP 0.010 0.001 TRP B 553 HIS 0.004 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00306 (14645) covalent geometry : angle 0.55997 (19844) SS BOND : bond 0.00215 ( 39) SS BOND : angle 0.96009 ( 78) hydrogen bonds : bond 0.03332 ( 365) hydrogen bonds : angle 6.50996 ( 1011) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9404 (mmp) cc_final: 0.9049 (mmm) REVERT: A 504 MET cc_start: 0.7510 (tpt) cc_final: 0.7222 (tpt) REVERT: A 555 MET cc_start: 0.9384 (mmp) cc_final: 0.9154 (mmm) REVERT: A 581 TYR cc_start: 0.9307 (m-10) cc_final: 0.9040 (m-80) REVERT: B 11 MET cc_start: 0.8730 (ppp) cc_final: 0.8249 (ppp) REVERT: B 38 MET cc_start: 0.9420 (mmp) cc_final: 0.9216 (mmm) REVERT: B 98 MET cc_start: 0.9017 (mmp) cc_final: 0.8710 (mmm) REVERT: B 300 MET cc_start: 0.9201 (mmp) cc_final: 0.8963 (mmm) REVERT: E 15 LEU cc_start: 0.9685 (tp) cc_final: 0.9390 (tp) REVERT: F 6 LEU cc_start: 0.9608 (mm) cc_final: 0.9252 (pt) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0956 time to fit residues: 9.4037 Evaluate side-chains 44 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 83 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 144 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.028787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.018681 restraints weight = 230875.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.019458 restraints weight = 142814.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.019974 restraints weight = 101595.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.020322 restraints weight = 79657.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.020570 restraints weight = 67190.120| |-----------------------------------------------------------------------------| r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 14684 Z= 0.149 Angle : 0.574 11.248 19922 Z= 0.296 Chirality : 0.043 0.279 2153 Planarity : 0.004 0.141 2565 Dihedral : 4.947 28.072 1933 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.03 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.21), residues: 1731 helix: -0.24 (0.33), residues: 240 sheet: -0.73 (0.27), residues: 348 loop : -0.90 (0.20), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 579 TYR 0.014 0.001 TYR B 884 PHE 0.014 0.001 PHE A 703 TRP 0.012 0.001 TRP A 414 HIS 0.003 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00331 (14645) covalent geometry : angle 0.57202 (19844) SS BOND : bond 0.00215 ( 39) SS BOND : angle 0.87367 ( 78) hydrogen bonds : bond 0.03349 ( 365) hydrogen bonds : angle 6.52802 ( 1011) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9422 (mmp) cc_final: 0.9057 (mmm) REVERT: A 504 MET cc_start: 0.7429 (tpt) cc_final: 0.7154 (tpt) REVERT: A 581 TYR cc_start: 0.9311 (m-10) cc_final: 0.9050 (m-80) REVERT: B 11 MET cc_start: 0.8598 (ppp) cc_final: 0.8132 (ppp) REVERT: B 38 MET cc_start: 0.9373 (mmp) cc_final: 0.9157 (mmm) REVERT: B 62 LEU cc_start: 0.9647 (tp) cc_final: 0.9432 (tp) REVERT: B 98 MET cc_start: 0.8985 (mmp) cc_final: 0.8701 (mmm) REVERT: B 300 MET cc_start: 0.9159 (mmp) cc_final: 0.8899 (mmm) REVERT: E 15 LEU cc_start: 0.9662 (tp) cc_final: 0.9355 (tp) REVERT: F 6 LEU cc_start: 0.9576 (mm) cc_final: 0.9247 (pt) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0993 time to fit residues: 9.4669 Evaluate side-chains 44 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 55 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN D 10 HIS ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.029152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.018848 restraints weight = 218655.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.019651 restraints weight = 133958.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.020199 restraints weight = 95152.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.020592 restraints weight = 74201.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.020862 restraints weight = 61835.085| |-----------------------------------------------------------------------------| r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.101 14684 Z= 0.104 Angle : 0.551 11.275 19922 Z= 0.284 Chirality : 0.044 0.278 2153 Planarity : 0.004 0.141 2565 Dihedral : 4.759 27.149 1933 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.93 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.21), residues: 1731 helix: -0.10 (0.34), residues: 233 sheet: -0.59 (0.27), residues: 354 loop : -0.87 (0.20), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 479 TYR 0.014 0.001 TYR B 884 PHE 0.014 0.001 PHE A 703 TRP 0.011 0.001 TRP A 414 HIS 0.003 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00247 (14645) covalent geometry : angle 0.54972 (19844) SS BOND : bond 0.00177 ( 39) SS BOND : angle 0.76572 ( 78) hydrogen bonds : bond 0.03067 ( 365) hydrogen bonds : angle 6.24871 ( 1011) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9408 (mmp) cc_final: 0.9011 (mmm) REVERT: A 504 MET cc_start: 0.7534 (tpt) cc_final: 0.7223 (tpt) REVERT: A 581 TYR cc_start: 0.9334 (m-10) cc_final: 0.9109 (m-10) REVERT: B 11 MET cc_start: 0.8388 (ppp) cc_final: 0.8131 (ppp) REVERT: B 62 LEU cc_start: 0.9639 (tp) cc_final: 0.9430 (tp) REVERT: B 98 MET cc_start: 0.8871 (mmp) cc_final: 0.8655 (mmm) REVERT: B 300 MET cc_start: 0.9145 (mmp) cc_final: 0.8943 (mmm) REVERT: E 15 LEU cc_start: 0.9666 (tp) cc_final: 0.9355 (tp) REVERT: F 6 LEU cc_start: 0.9587 (mm) cc_final: 0.9236 (pt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0973 time to fit residues: 9.9138 Evaluate side-chains 49 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 161 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 10 optimal weight: 30.0000 chunk 56 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.027935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2416 r_free = 0.2416 target = 0.018261 restraints weight = 246160.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.018975 restraints weight = 152597.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.019444 restraints weight = 109071.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.019759 restraints weight = 86335.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.019975 restraints weight = 73263.614| |-----------------------------------------------------------------------------| r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 14684 Z= 0.291 Angle : 0.749 11.701 19922 Z= 0.381 Chirality : 0.045 0.278 2153 Planarity : 0.005 0.142 2565 Dihedral : 5.425 29.175 1933 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 28.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.13 % Favored : 90.76 % Rotamer: Outliers : 0.06 % Allowed : 0.43 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.21), residues: 1731 helix: -0.45 (0.32), residues: 243 sheet: -0.87 (0.26), residues: 362 loop : -1.05 (0.20), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 578 TYR 0.020 0.002 TYR B 245 PHE 0.019 0.002 PHE A 76 TRP 0.028 0.003 TRP A 529 HIS 0.007 0.001 HIS A 440 Details of bonding type rmsd covalent geometry : bond 0.00605 (14645) covalent geometry : angle 0.74692 (19844) SS BOND : bond 0.00349 ( 39) SS BOND : angle 1.14233 ( 78) hydrogen bonds : bond 0.04197 ( 365) hydrogen bonds : angle 7.00104 ( 1011) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2425.74 seconds wall clock time: 43 minutes 3.42 seconds (2583.42 seconds total)