Starting phenix.real_space_refine on Tue May 20 04:33:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eyy_28724/05_2025/8eyy_28724_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eyy_28724/05_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_28724/05_2025/8eyy_28724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eyy_28724/05_2025/8eyy_28724.map" model { file = "/net/cci-nas-00/data/ceres_data/8eyy_28724/05_2025/8eyy_28724_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eyy_28724/05_2025/8eyy_28724_neut.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.07, per 1000 atoms: 0.56 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: 3.43 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 2.03 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: 4.84 Time building geometry restraints manager: 4.00 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 32.480 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.750 ------------------------------------------------------------------------------- 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 : 21.05 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.001 TRP A 414 HIS 0.005 0.001 HIS B 386 PHE 0.015 0.001 PHE A 703 TYR 0.012 0.001 TYR E 16 ARG 0.013 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.17873 ( 365) hydrogen bonds : angle 8.44046 ( 1011) SS BOND : bond 0.00193 ( 39) SS BOND : angle 0.82063 ( 78) covalent geometry : bond 0.00257 (14645) covalent geometry : angle 0.58152 (19844) *********************** 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 : 1.782 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: 0.2160 time to fit residues: 25.0580 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 : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.0870 chunk 131 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- 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 ** 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 = 0.2961 r_free = 0.2961 target = 0.028917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.018854 restraints weight = 230661.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.019614 restraints weight = 141433.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.020122 restraints weight = 100844.133| |-----------------------------------------------------------------------------| r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 14684 Z= 0.157 Angle : 0.587 9.883 19922 Z= 0.307 Chirality : 0.043 0.286 2153 Planarity : 0.005 0.133 2565 Dihedral : 5.055 29.077 1933 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.28 % Favored : 92.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.21), residues: 1731 helix: -0.19 (0.34), residues: 237 sheet: -0.83 (0.26), residues: 364 loop : -0.80 (0.20), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 414 HIS 0.007 0.001 HIS A 386 PHE 0.012 0.001 PHE A 400 TYR 0.014 0.001 TYR B 144 ARG 0.009 0.001 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.04425 ( 365) hydrogen bonds : angle 7.33577 ( 1011) SS BOND : bond 0.00241 ( 39) SS BOND : angle 0.69197 ( 78) covalent geometry : bond 0.00338 (14645) covalent geometry : angle 0.58693 (19844) *********************** 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 57 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9287 (mmp) cc_final: 0.9007 (mmm) REVERT: A 504 MET cc_start: 0.7554 (tpt) cc_final: 0.7278 (tpt) REVERT: A 555 MET cc_start: 0.9509 (mmp) cc_final: 0.9165 (mmp) REVERT: B 11 MET cc_start: 0.8768 (ppp) cc_final: 0.8553 (ppp) REVERT: B 98 MET cc_start: 0.9177 (mmp) cc_final: 0.8860 (mmm) REVERT: B 110 MET cc_start: 0.9179 (mmp) cc_final: 0.8810 (mmm) REVERT: B 300 MET cc_start: 0.9240 (mmp) cc_final: 0.9033 (mmm) REVERT: E 15 LEU cc_start: 0.9697 (tp) cc_final: 0.9399 (tp) REVERT: F 6 LEU cc_start: 0.9612 (mm) cc_final: 0.9237 (pt) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.2185 time to fit residues: 21.5964 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 : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 138 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 25 optimal weight: 30.0000 chunk 51 optimal weight: 10.0000 chunk 14 optimal weight: 30.0000 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 overall best weight: 5.5788 ------------------------------------------------------------------------------- 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 406 GLN ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.028111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.018343 restraints weight = 244079.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.019046 restraints weight = 151811.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.019540 restraints weight = 109336.885| |-----------------------------------------------------------------------------| r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 14684 Z= 0.264 Angle : 0.703 10.579 19922 Z= 0.361 Chirality : 0.044 0.285 2153 Planarity : 0.005 0.135 2565 Dihedral : 5.457 27.173 1933 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 27.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.95 % Favored : 90.81 % Rotamer: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.21), residues: 1731 helix: -0.47 (0.32), residues: 242 sheet: -1.07 (0.26), residues: 354 loop : -0.92 (0.20), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 529 HIS 0.006 0.002 HIS A 386 PHE 0.020 0.002 PHE A 400 TYR 0.028 0.002 TYR B 847 ARG 0.010 0.001 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.04585 ( 365) hydrogen bonds : angle 7.57459 ( 1011) SS BOND : bond 0.00355 ( 39) SS BOND : angle 0.89836 ( 78) covalent geometry : bond 0.00547 (14645) covalent geometry : angle 0.70253 (19844) *********************** 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 49 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.930 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: 0.9331 (mmp) cc_final: 0.9059 (mmm) REVERT: A 504 MET cc_start: 0.7394 (tpt) cc_final: 0.7189 (tpt) REVERT: A 555 MET cc_start: 0.9515 (mmp) cc_final: 0.9148 (mmm) REVERT: B 11 MET cc_start: 0.8881 (ppp) cc_final: 0.8616 (ppp) REVERT: B 62 LEU cc_start: 0.9600 (tp) cc_final: 0.9378 (tp) REVERT: B 98 MET cc_start: 0.9280 (mmp) cc_final: 0.8854 (mmm) REVERT: E 15 LEU cc_start: 0.9671 (tp) cc_final: 0.9448 (tp) REVERT: F 6 LEU cc_start: 0.9615 (mm) cc_final: 0.9268 (pt) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.2766 time to fit residues: 21.8074 Evaluate side-chains 40 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 12 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 59 optimal weight: 0.0670 chunk 157 optimal weight: 30.0000 chunk 69 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 overall best weight: 4.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN ** 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 199 HIS ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2932 r_free = 0.2932 target = 0.028273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.018445 restraints weight = 237508.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.019160 restraints weight = 146489.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.019658 restraints weight = 105010.843| |-----------------------------------------------------------------------------| r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 14684 Z= 0.230 Angle : 0.654 10.626 19922 Z= 0.340 Chirality : 0.044 0.280 2153 Planarity : 0.005 0.137 2565 Dihedral : 5.456 28.810 1933 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 25.03 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.38 % Favored : 91.39 % Rotamer: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.21), residues: 1731 helix: -0.51 (0.32), residues: 243 sheet: -1.13 (0.26), residues: 350 loop : -1.00 (0.20), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 414 HIS 0.012 0.002 HIS A 199 PHE 0.015 0.002 PHE A 400 TYR 0.018 0.002 TYR E 16 ARG 0.012 0.001 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 365) hydrogen bonds : angle 7.46827 ( 1011) SS BOND : bond 0.00336 ( 39) SS BOND : angle 1.05610 ( 78) covalent geometry : bond 0.00479 (14645) covalent geometry : angle 0.65202 (19844) *********************** 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 50 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.9580 (mpp) cc_final: 0.9372 (mpp) REVERT: A 38 MET cc_start: 0.9387 (mmp) cc_final: 0.9093 (mmm) REVERT: A 555 MET cc_start: 0.9466 (mmp) cc_final: 0.9158 (mmm) REVERT: B 11 MET cc_start: 0.8890 (ppp) cc_final: 0.8652 (ppp) REVERT: B 98 MET cc_start: 0.9322 (mmp) cc_final: 0.8918 (mmm) REVERT: B 300 MET cc_start: 0.9256 (mmp) cc_final: 0.9010 (mmm) REVERT: E 15 LEU cc_start: 0.9673 (tp) cc_final: 0.9409 (tp) REVERT: F 6 LEU cc_start: 0.9622 (mm) cc_final: 0.9281 (pt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2618 time to fit residues: 21.3321 Evaluate side-chains 37 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 153 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 97 optimal weight: 40.0000 chunk 171 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS A 281 ASN A 337 ASN A 527 ASN ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 GLN ** A 860 HIS ** 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 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 GLN ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 835 GLN C 60 GLN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 10 HIS F 60 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.027473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.018043 restraints weight = 257485.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.018695 restraints weight = 160806.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.019133 restraints weight = 116457.873| |-----------------------------------------------------------------------------| r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 14684 Z= 0.381 Angle : 0.878 12.879 19922 Z= 0.447 Chirality : 0.048 0.282 2153 Planarity : 0.007 0.139 2565 Dihedral : 6.244 31.136 1933 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 38.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.57 % Favored : 89.25 % Rotamer: Outliers : 0.12 % Allowed : 5.70 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.20), residues: 1731 helix: -1.06 (0.30), residues: 242 sheet: -1.53 (0.26), residues: 339 loop : -1.33 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 529 HIS 0.015 0.002 HIS B 199 PHE 0.027 0.003 PHE B 381 TYR 0.029 0.003 TYR B 581 ARG 0.011 0.001 ARG A 759 Details of bonding type rmsd hydrogen bonds : bond 0.05282 ( 365) hydrogen bonds : angle 8.24649 ( 1011) SS BOND : bond 0.00596 ( 39) SS BOND : angle 1.40552 ( 78) covalent geometry : bond 0.00783 (14645) covalent geometry : angle 0.87496 (19844) *********************** 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 41 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9461 (mmp) cc_final: 0.9209 (mmm) REVERT: A 555 MET cc_start: 0.9431 (mmp) cc_final: 0.9211 (mmm) REVERT: B 38 MET cc_start: 0.9472 (mmp) cc_final: 0.9252 (mmm) REVERT: B 98 MET cc_start: 0.9362 (mmp) cc_final: 0.9061 (mmm) REVERT: B 300 MET cc_start: 0.9344 (mmp) cc_final: 0.9124 (mmm) REVERT: E 15 LEU cc_start: 0.9662 (tp) cc_final: 0.9446 (tp) REVERT: F 6 LEU cc_start: 0.9638 (mm) cc_final: 0.9284 (pt) outliers start: 2 outliers final: 0 residues processed: 41 average time/residue: 0.2184 time to fit residues: 16.1808 Evaluate side-chains 32 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 90 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN ** A 860 HIS ** 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 406 GLN ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 GLN ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2946 r_free = 0.2946 target = 0.028669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.018771 restraints weight = 238237.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.019536 restraints weight = 144630.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.020046 restraints weight = 102168.439| |-----------------------------------------------------------------------------| r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2308 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= 0.143 Angle : 0.625 11.088 19922 Z= 0.329 Chirality : 0.045 0.273 2153 Planarity : 0.005 0.140 2565 Dihedral : 5.665 28.795 1933 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.28 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.21), residues: 1731 helix: -0.67 (0.32), residues: 238 sheet: -1.22 (0.26), residues: 344 loop : -1.12 (0.20), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 493 HIS 0.006 0.001 HIS B 199 PHE 0.020 0.002 PHE A 703 TYR 0.019 0.002 TYR E 16 ARG 0.008 0.001 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 365) hydrogen bonds : angle 7.44555 ( 1011) SS BOND : bond 0.00320 ( 39) SS BOND : angle 1.07773 ( 78) covalent geometry : bond 0.00319 (14645) covalent geometry : angle 0.62281 (19844) *********************** 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 52 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9352 (mmp) cc_final: 0.9049 (mmm) REVERT: A 504 MET cc_start: 0.7789 (tpt) cc_final: 0.7399 (tpt) REVERT: B 11 MET cc_start: 0.9010 (ppp) cc_final: 0.8632 (ppp) REVERT: B 38 MET cc_start: 0.9303 (mmp) cc_final: 0.9047 (mmm) REVERT: B 62 LEU cc_start: 0.9678 (tp) cc_final: 0.9467 (tp) REVERT: B 98 MET cc_start: 0.9351 (mmp) cc_final: 0.8892 (mmm) REVERT: B 300 MET cc_start: 0.9272 (mmp) cc_final: 0.9033 (mmm) REVERT: E 15 LEU cc_start: 0.9690 (tp) cc_final: 0.9439 (tp) REVERT: F 6 LEU cc_start: 0.9664 (mm) cc_final: 0.9323 (pt) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2385 time to fit residues: 20.9210 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 : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 104 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 125 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 160 optimal weight: 0.0470 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 HIS A 860 HIS ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN ** B 470 ASN ** 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 = 0.2964 r_free = 0.2964 target = 0.028984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.018808 restraints weight = 222686.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.019607 restraints weight = 134647.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.020153 restraints weight = 95038.567| |-----------------------------------------------------------------------------| r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 14684 Z= 0.110 Angle : 0.585 11.188 19922 Z= 0.304 Chirality : 0.045 0.278 2153 Planarity : 0.004 0.141 2565 Dihedral : 5.107 25.160 1933 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.63 % Favored : 92.20 % Rotamer: Outliers : 0.06 % Allowed : 1.49 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.21), residues: 1731 helix: -0.38 (0.33), residues: 234 sheet: -0.89 (0.27), residues: 340 loop : -1.00 (0.20), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 529 HIS 0.004 0.001 HIS A 100 PHE 0.020 0.001 PHE A 703 TYR 0.013 0.001 TYR B 847 ARG 0.008 0.001 ARG A 498 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 365) hydrogen bonds : angle 6.74600 ( 1011) SS BOND : bond 0.00195 ( 39) SS BOND : angle 0.80344 ( 78) covalent geometry : bond 0.00257 (14645) covalent geometry : angle 0.58355 (19844) *********************** 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 61 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9334 (mmp) cc_final: 0.8989 (mmm) REVERT: A 504 MET cc_start: 0.7915 (tpt) cc_final: 0.7459 (tpt) REVERT: B 11 MET cc_start: 0.8834 (ppp) cc_final: 0.8451 (ppp) REVERT: B 38 MET cc_start: 0.9403 (mmp) cc_final: 0.9108 (mmm) REVERT: B 98 MET cc_start: 0.9317 (mmp) cc_final: 0.8833 (mmm) REVERT: B 300 MET cc_start: 0.9255 (mmp) cc_final: 0.9042 (mmm) REVERT: E 15 LEU cc_start: 0.9678 (tp) cc_final: 0.9377 (tp) REVERT: F 6 LEU cc_start: 0.9680 (mm) cc_final: 0.9294 (pt) outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.2285 time to fit residues: 23.0715 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 : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 82 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 139 optimal weight: 8.9990 chunk 38 optimal weight: 0.0470 chunk 86 optimal weight: 6.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 HIS ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.028923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.018772 restraints weight = 222503.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.019573 restraints weight = 135247.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.020114 restraints weight = 95426.198| |-----------------------------------------------------------------------------| r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 14684 Z= 0.106 Angle : 0.561 11.331 19922 Z= 0.291 Chirality : 0.044 0.279 2153 Planarity : 0.004 0.141 2565 Dihedral : 4.934 26.789 1933 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.70 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.21), residues: 1731 helix: -0.39 (0.33), residues: 239 sheet: -0.80 (0.27), residues: 351 loop : -0.94 (0.20), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 553 HIS 0.006 0.001 HIS D 10 PHE 0.016 0.001 PHE A 703 TYR 0.012 0.001 TYR E 16 ARG 0.004 0.000 ARG A 498 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 365) hydrogen bonds : angle 6.48418 ( 1011) SS BOND : bond 0.00192 ( 39) SS BOND : angle 0.69096 ( 78) covalent geometry : bond 0.00254 (14645) covalent geometry : angle 0.56015 (19844) *********************** 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 58 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9332 (mmp) cc_final: 0.8973 (mmm) REVERT: A 504 MET cc_start: 0.7782 (tpt) cc_final: 0.7377 (tpt) REVERT: A 555 MET cc_start: 0.9391 (mmp) cc_final: 0.9159 (mmm) REVERT: B 11 MET cc_start: 0.8662 (ppp) cc_final: 0.8293 (ppp) REVERT: B 38 MET cc_start: 0.9376 (mmp) cc_final: 0.9131 (mmm) REVERT: B 62 LEU cc_start: 0.9668 (tp) cc_final: 0.9456 (tp) REVERT: B 98 MET cc_start: 0.9193 (mmp) cc_final: 0.8839 (mmm) REVERT: B 300 MET cc_start: 0.9229 (mmp) cc_final: 0.9011 (mmm) REVERT: E 15 LEU cc_start: 0.9692 (tp) cc_final: 0.9399 (tp) REVERT: F 6 LEU cc_start: 0.9667 (mm) cc_final: 0.9265 (pt) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2301 time to fit residues: 22.5577 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 : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 125 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 161 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 470 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.028893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.018821 restraints weight = 227610.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.019626 restraints weight = 137555.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.020161 restraints weight = 97031.548| |-----------------------------------------------------------------------------| r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 14684 Z= 0.107 Angle : 0.558 11.323 19922 Z= 0.288 Chirality : 0.044 0.281 2153 Planarity : 0.004 0.142 2565 Dihedral : 4.841 28.721 1933 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.64 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.21), residues: 1731 helix: -0.25 (0.33), residues: 233 sheet: -0.69 (0.27), residues: 345 loop : -0.93 (0.20), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 414 HIS 0.003 0.001 HIS A 100 PHE 0.017 0.001 PHE A 703 TYR 0.012 0.001 TYR E 16 ARG 0.004 0.000 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.03155 ( 365) hydrogen bonds : angle 6.34406 ( 1011) SS BOND : bond 0.00176 ( 39) SS BOND : angle 0.71198 ( 78) covalent geometry : bond 0.00253 (14645) covalent geometry : angle 0.55710 (19844) *********************** 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 59 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9367 (mmp) cc_final: 0.9035 (mmm) REVERT: A 504 MET cc_start: 0.7755 (tpt) cc_final: 0.7327 (tpt) REVERT: A 555 MET cc_start: 0.9428 (mmp) cc_final: 0.9177 (mmm) REVERT: B 11 MET cc_start: 0.8550 (ppp) cc_final: 0.8225 (ppp) REVERT: B 38 MET cc_start: 0.9358 (mmp) cc_final: 0.9153 (mmm) REVERT: B 62 LEU cc_start: 0.9632 (tp) cc_final: 0.9415 (tp) REVERT: B 98 MET cc_start: 0.9070 (mmp) cc_final: 0.8777 (mmm) REVERT: E 15 LEU cc_start: 0.9705 (tp) cc_final: 0.9426 (tp) REVERT: F 6 LEU cc_start: 0.9681 (mm) cc_final: 0.9279 (pt) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2541 time to fit residues: 24.5392 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 : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 11 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 15 optimal weight: 30.0000 chunk 133 optimal weight: 7.9990 chunk 158 optimal weight: 0.0050 chunk 13 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 122 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 overall best weight: 3.5200 ------------------------------------------------------------------------------- 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 786 GLN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.028347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.018496 restraints weight = 233680.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.019249 restraints weight = 144777.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.019750 restraints weight = 103278.146| |-----------------------------------------------------------------------------| r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 14684 Z= 0.177 Angle : 0.605 11.300 19922 Z= 0.312 Chirality : 0.043 0.278 2153 Planarity : 0.005 0.142 2565 Dihedral : 5.053 29.554 1933 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.91 % Favored : 91.97 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.21), residues: 1731 helix: -0.37 (0.32), residues: 239 sheet: -0.79 (0.27), residues: 353 loop : -0.90 (0.20), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 251 HIS 0.005 0.001 HIS B 199 PHE 0.015 0.002 PHE A 400 TYR 0.015 0.001 TYR E 16 ARG 0.005 0.001 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 365) hydrogen bonds : angle 6.58303 ( 1011) SS BOND : bond 0.00238 ( 39) SS BOND : angle 0.81993 ( 78) covalent geometry : bond 0.00384 (14645) covalent geometry : angle 0.60434 (19844) ********************** 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 56 residues out of total 1613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9367 (mmp) cc_final: 0.9033 (mmm) REVERT: A 504 MET cc_start: 0.7592 (tpt) cc_final: 0.7228 (tpt) REVERT: A 555 MET cc_start: 0.9447 (mmp) cc_final: 0.9202 (mmm) REVERT: B 11 MET cc_start: 0.8669 (ppp) cc_final: 0.8347 (ppp) REVERT: B 62 LEU cc_start: 0.9623 (tp) cc_final: 0.9399 (tp) REVERT: B 98 MET cc_start: 0.9118 (mmp) cc_final: 0.8841 (mmm) REVERT: E 15 LEU cc_start: 0.9708 (tp) cc_final: 0.9464 (tp) REVERT: F 6 LEU cc_start: 0.9666 (mm) cc_final: 0.9281 (pt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2419 time to fit residues: 22.0401 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 : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 43 optimal weight: 4.9990 chunk 145 optimal weight: 20.0000 chunk 130 optimal weight: 0.0870 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 786 GLN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** 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 = 0.2959 r_free = 0.2959 target = 0.028842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.018730 restraints weight = 224428.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.019536 restraints weight = 136228.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.020078 restraints weight = 95931.661| |-----------------------------------------------------------------------------| r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 14684 Z= 0.111 Angle : 0.562 11.235 19922 Z= 0.290 Chirality : 0.044 0.277 2153 Planarity : 0.004 0.141 2565 Dihedral : 4.899 28.312 1933 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.82 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.21), residues: 1731 helix: -0.24 (0.33), residues: 233 sheet: -0.69 (0.27), residues: 341 loop : -0.90 (0.20), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 561 HIS 0.003 0.001 HIS B 199 PHE 0.015 0.001 PHE A 703 TYR 0.012 0.001 TYR E 16 ARG 0.004 0.000 ARG A 498 Details of bonding type rmsd hydrogen bonds : bond 0.03140 ( 365) hydrogen bonds : angle 6.39485 ( 1011) SS BOND : bond 0.00184 ( 39) SS BOND : angle 0.78638 ( 78) covalent geometry : bond 0.00259 (14645) covalent geometry : angle 0.56098 (19844) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4155.08 seconds wall clock time: 73 minutes 57.20 seconds (4437.20 seconds total)